蛋白酶MEROPS，脂肪酶Lipase注释步骤（含批量）

已于 2023-08-08 15:55:52 修改
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分类专栏： 基因组功能注释 文章标签： 数据库 ubuntu linux 服务器
于 2023-04-18 11:06:14 首次发布
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JoF | Free Full-Text | Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma SpeciesThe annotation of secreted proteases and lipases was performed by BLASTP search (E-value = 10−5) against MEROPS (MEROPS - the Peptidase Database, accessed on 16 January 2022) and Lipase Engineering Database (Lipase Engineering Database, accessed on 16 January 2022).

https://www.sciencedirect.com/science/article/pii/S1878614620300015?via%3Dihub

BLASTP was run using NCBI-BLAST-2.7.1+ (Camacho et al., 2009) against fungal sequences in the UniProt database, against the PHI database version 45 (Urban et al., 2017), and against the MEROPS release 12.0 database (Rawlings et al., 2018). 


Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum | Nature CommunicationsThey were classified into four functional categories: CAZymes, lipases, proteases and small-secreted proteins (SSP; proteins less than 300 amino-acids long with no CAZyme, protease or lipase domains). The secreted proteases were identified in the genome using the MEROPS peptide database (MEROPS - the Peptidase Database) and the secreted lipases using the Lipase engineering database (www.led.uni-stuttgart.de).Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum | Nature Communications

MEROPS蛋白酶

MEROPS - the Peptidase Database

下载界面具体内容如下

1. MEROPS Release 12.4
The large file "meropsweb124.tar.gz" is a compressed version of all the SQL statements required to build a MySQL instance of the current release of the MEROPS database. Some functions such as the Searches and BLAST server are not supported in this format, however.
2. Peptidase and Inhibitor Accession Numbers
The file "dnld_list.txt" contains a non-redundant list of accession numbers, and enables the user to create a library of peptidase and peptidase inhibitor amino acid sequences. Accession numbers are given for all the peptidases for which we have them, but some sequences that have not been deposited inevitably are not included. To retrieve all the sequences, use the GCG command "fetch@filename" (where "filename" is the name of the text file). Alternatively, use the file of accession numbers as a reduced data set for searching with FastA. When prompted for the database name enter "@filename" instead. Included in each line after the exclamation mark are identifiers for peptidase family and species of organism that allow filtering of the data. The organism identifier is that from the NCBI Taxonomy database shown on each organism card in MEROPS.
3. Peptidase Protein Sequences √
The file "pepunit.lib" is a non-redundant library of protein sequences in FastA format the peptidase units and inhibitor units of all the peptidases and peptidase inhibitors that are included in MEROPS. The library can be searched by use of FastA without further modification, but must be converted and indexed for BLAST searches. The restriction of the library to peptidase and inhibitor units should decrease the risk of false positive matches to other domains.
4. Peptidase Full-length Sequences
The file "protease.lib" is a non-redundant library of protein sequences in FastA format for all the peptidases and peptidase inhibitors included in MEROPS. The library can be searched by use of FastA without further modification, but must be converted and indexed for BLAST searches.
5. MEROPS Scan Sequences √
The file "merops_scan.lib" is a subset of pepunit.lib containing the sequences used for the MEROPS batch Blast. It contains a non-redundant library of protein sequences in FastA format of the peptidase units for all the family type examples and peptidase/inhibitor holotypes. The library can be searched by use of FastA without further modification, but must be converted and indexed for BLAST searches.
6. Family Protein Sequences
It is possible to download a FastA format file of peptidase/inhibitor unit amino acid sequences for each family in MEROPS. Select your family from the directory listing for the following location:
7. MEROPS References
The file "meropsrefs.txt" is a text version of all the SQL statements required to build a MySQL instance of the current release of the MEROPS reference database.

下载数据，使用ctrl+A（全选）和 ctrl+D（保存）

# 下载好的PHI数据库位置如下
/media/aa/DATA/SZQ2/MEROPS/*
dnld_list.fasta        meropsrefs.fasta  pepunit.lib.fasta
merops_scan.lib.fasta  meropsweb121/     readme.txt
# 在(pfam_scan)下
conda activate pfam_scan
# 新建文件夹
mkdir 15.MEROPS && cd 15.MEROPS

选用pepunit.lib.fasta

在进行序列比对前，首先需要构建数据库。

# 构建数据库
makeblastdb -in genome.fasta -dbtype prot -parse_seqids -out ./index
-in：构建数据库所用的序列文件。
-dbtype：数据库类型。构建的数据库是核苷酸数据库时，dbtype设置为nucl，数据库是氨基酸数据库时，dbtype设置为prot。
-out：数据库名称,输出文件的前缀。
-input_type 默认为fasta文件，其他支持文件asn1_bin,asn1_txt, blastdb
-parse_seqids 添加该参数，结果文件将多三个文件，不加默认为3个结果文件
执行上述代码后将生成后缀为nin,nhr,nsq,nsi,nsd,nog六个文件，至此，自定义搜索库文件生成完成
# 操作如下
makeblastdb -in /media/aa/DATA/SZQ2/MEROPS/pepunit.lib.fasta -dbtype prot -title pepunit.lib -parse_seqids -out pepunit.lib -logfile pepunit.lib.log
# 报错
Building a new DB, current time: 04/15/2023 20:43:15
New DB name:   /media/aa/DATA/SZQ2/MEROPS/pepunit.lib
New DB title:  pepunit.lib
Sequence type: Protein
Keep MBits: T
Maximum file size: 3000000000B
Error: (803.7) [makeblastdb] Blast-def-line-set.E.title
Bad char [0x96] in string at byte 76
- stanniocalcin-1 (Homo sapiens) [I100.001]#I100#{inhibitor unit: 34\96247}~source NP_003146~
Error: (803.7) [makeblastdb] Blast-def-line-set.E.title
Bad char [0x96] in string at byte 76
- stanniocalcin-1 (Homo sapiens) [I100.001]#I100#{inhibitor unit: 34\96247}~source NP_003146~
Adding sequences from FASTA; added 1227939 sequences in 46.0684 seconds.

makeblastdb error: Error: (803.7) [makeblastdb] Blast-def-line-set.E.seqid.E.local.str Bad char [0xC3] in string at byte 45科学网-基因家族聚类软件Orthofinder的报错与解决措施-2022.12.02-姚刚的博文makeblastdb error: Error: (803.7) [makeblastdb] Blast-def-line-set.E.seqid.E.local.str Bad char [0xC3] in string at byte 45

报错内容：nError: Error reading input stream at line 22022: Invalid character (.) in sequence\n'

解决措施：删除氨基酸序列中的点或把点替换为X（未知氨基酸），sed -i '/^>/!s/\./X/g' filename.fasta

# 解决
cat /media/aa/DATA/SZQ2/MEROPS/pepunit.lib.fasta | perl -ne 's/[^\x00-\x7F]+/ /g; print;' > pepunit.lib.tmp.fasta
# 把空格替换成X，否则会报错Invalid character ( ) in sequence
sed -i '/^>/!s/\ /X/g' /media/aa/DATA/SZQ2/MEROPS/pepunit.lib.tmp.fasta
# 重新运行
makeblastdb -in /media/aa/DATA/SZQ2/MEROPS/pepunit.lib.tmp.fasta -dbtype prot -title pepunit.lib.tmp -parse_seqids -out pepunit.lib.tmp -logfile pepunit.lib.tmp.log
# 成功
Building a new DB, current time: 04/16/2023 15:47:52
New DB name:   /media/aa/DATA/SZQ2/MEROPS/pepunit.lib.tmp
New DB title:  pepunit.lib.tmp
Sequence type: Protein
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 1227939 sequences in 46.6807 seconds.

根据下载好的MEROPS数据库，将需要查找的蛋白序列，与数据库进行BLASTP比对，命令如下：

新建文件夹

mkdir 15.MEROPS && cd 15.MEROPS

1） diamond blastp

 evalue为1e-5

diamond blastp --db /media/aa/DATA/SZQ2/MEROPS/pepunit.lib.tmp.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out $i.MEROPS10.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1

批量运行

# pep70
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/MEROPS/pepunit.lib.tmp.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out $i.MEROPS5.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.MEROPS.list
ParaFly -c command.MEROPS.list -CPU 48
# pepmy
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/MEROPS/pepunit.lib.tmp.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out $i.MEROPS5.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.MEROPS.list
ParaFly -c command.MEROPS.list -CPU 48

2）parsing_blast_result.pl

新建文件夹

mkdir MEROPS5.tab && cd MEROPS5.tab
# pep70
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../$i.MEROPS5.xml > $i.MEROPS5.tab"
done > command.MEROPS.list
ParaFly -c command.MEROPS.list -CPU 48
# pepmy
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../$i.MEROPS5.xml > $i.MEROPS5.tab"
done > command.MEROPS.list
ParaFly -c command.MEROPS.list -CPU 48

Blast分析后的注释结果中一条序列含有多种结果，后续的分析需要提取得到基因最可能的注释结果。

3）比对结果中筛选每个query的最佳subject

# 在(jcvi)下
conda activate jcvi

批量运行 

# pep70
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 $i.MEROPS5.tab"
done > command.jcvi.list
ParaFly -c command.jcvi.list -CPU 48
# pepmy
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 $i.MEROPS5.tab"
done > command.jcvi.list
ParaFly -c command.jcvi.list -CPU 48

4）移动并重命名

cd ..
# 新建文件夹
mkdir best && cd best
# 移动*.MEROPS5.tab.best
mv ../MEROPS5.tab/*.MEROPS5.tab.best ./

最后整理时，要结合*.MEROPS10.tab.best和*.MEROPS10.tab查看！

Lipase脂肪酶

Lipase Engineering Database

The Lipase Engineering Database

下载文件，readme！

##### 
##### Lipase Engineering Database - Content Download
#####
##### This Internet database integrates information on sequence and structure 
##### of lipases and related proteins sharing the same a/b hydrolase fold to facilitate protein engineering.
#####
##### This database is maintained by Jürgen Pleiss (juergen.pleiss@itb.uni-stuttgart.de)
#####
##### Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany 
##### 


##### Folder str ######
|
|-> all pdb structure files corresponding to LED
|
|-collection of superfamily structures
|	|-> strs[superfamily_id].tar
|
|-collection of homologous family structures
|	|-> strs[homologous_family_id].tar
 
##### Folder aln ######
|
|-> all clustalw and html multi sequence alignments
|
|-superfamily
|	|-> saln[superfamily_id].html / .aln
|
|-homologous family
|	|-> aln[homologous_family_id].html / .aln

##### Folder seq ###### √
|
|-> all LED sequence files
|
|-superfamily
|	|-> seqs[superfamily_id].txt √
|
|-homologous family
|	|-> seq[homologous_family_id].txt

##### Folder hmm ######
|
|-> all LED hmmer files
|
|-superfamily
|	|-> saln[superfamily_id].hmm
|
|-homologous family
|	|-> aln[homologous_family_id].hmm

##### Folder tree ######
|
|-> all LED tree files
|
|
|-homologous family
|	|-> tree[homologous_family_id].html / .gif

参考 Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits | Nature Communications

需要得到：Class|Superfamily

重命名文件夹，如下

新建文件夹

mkdir 16.Lipase && cd 16.Lipase

Class GGGX

Superfamilies
Homologous families
Proteins
Sequences
Structures 		4
11
52
160
282

seqs2_GGGX_abH01.fasta    seqs15_GGGX_abH03.fasta    seqs16_GGGX_abH04.fasta    seqs70_GGGX_abH06.fasta

# 新建文件夹
mkdir GGGX && cd GGGX

1） diamond blastp

 evalue为1e-5

diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs2_GGGX_abH01.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out $i.Lipase5.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1

批量运行

# pep70
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs2_GGGX_abH01.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GGGX_abH01.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GGGX_abH01.list
ParaFly -c command.GGGX_abH01.list -CPU 4
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs15_GGGX_abH03.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GGGX_abH03.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GGGX_abH03.list
ParaFly -c command.GGGX_abH03.list -CPU 4
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs16_GGGX_abH04.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GGGX_abH04.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GGGX_abH04.list
ParaFly -c command.GGGX_abH04.list -CPU 4
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs70_GGGX_abH06.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GGGX_abH06.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GGGX_abH06.list
ParaFly -c command.GGGX_abH06.list -CPU 4
# pepmy
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs2_GGGX_abH01.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GGGX_abH01.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GGGX_abH01.list
ParaFly -c command.GGGX_abH01.list -CPU 4
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs15_GGGX_abH03.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GGGX_abH03.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GGGX_abH03.list
ParaFly -c command.GGGX_abH03.list -CPU 4
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs16_GGGX_abH04.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GGGX_abH04.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GGGX_abH04.list
ParaFly -c command.GGGX_abH04.list -CPU 4
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs70_GGGX_abH06.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GGGX_abH06.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GGGX_abH06.list
ParaFly -c command.GGGX_abH06.list -CPU 4

2）parsing_blast_result.pl

新建文件夹

mkdir Lipase5.tab && cd Lipase5.tab

批量运行

# pep70
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GGGX_abH01.$i.xml > GGGX_abH01.$i.tab"
done > command.GGGX_abH01.list
ParaFly -c command.GGGX_abH01.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GGGX_abH03.$i.xml > GGGX_abH03.$i.tab"
done > command.GGGX_abH03.list
ParaFly -c command.GGGX_abH03.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GGGX_abH04.$i.xml > GGGX_abH04.$i.tab"
done > command.GGGX_abH04.list
ParaFly -c command.GGGX_abH04.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GGGX_abH06.$i.xml > GGGX_abH06.$i.tab"
done > command.GGGX_abH06.list
ParaFly -c command.GGGX_abH06.list -CPU 4

# pepmy
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GGGX_abH01.$i.xml > GGGX_abH01.$i.tab"
done > command.GGGX_abH01.list
ParaFly -c command.GGGX_abH01.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GGGX_abH03.$i.xml > GGGX_abH03.$i.tab"
done > command.GGGX_abH03.list
ParaFly -c command.GGGX_abH03.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GGGX_abH04.$i.xml > GGGX_abH04.$i.tab"
done > command.GGGX_abH04.list
ParaFly -c command.GGGX_abH04.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GGGX_abH06.$i.xml > GGGX_abH06.$i.tab"
done > command.GGGX_abH06.list
ParaFly -c command.GGGX_abH06.list -CPU 4

Blast分析后的注释结果中一条序列含有多种结果，后续的分析需要提取得到基因最可能的注释结果。

3）比对结果中筛选每个query的最佳subject

# 在(jcvi)下
conda activate jcvi

批量运行

# pep70
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GGGX_abH01.$i.tab"
done > command.GGGX_abH01jcvi.list
ParaFly -c command.GGGX_abH01jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GGGX_abH03.$i.tab"
done > command.GGGX_abH03jcvi.list
ParaFly -c command.GGGX_abH03jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GGGX_abH04.$i.tab"
done > command.GGGX_abH04jcvi.list
ParaFly -c command.GGGX_abH04jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GGGX_abH06.$i.tab"
done > command.GGGX_abH06jcvi.list
ParaFly -c command.GGGX_abH06jcvi.list -CPU 4

# pepmy
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GGGX_abH01.$i.tab"
done > command.GGGX_abH01jcvi.list
ParaFly -c command.GGGX_abH01jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GGGX_abH03.$i.tab"
done > command.GGGX_abH03jcvi.list
ParaFly -c command.GGGX_abH03jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GGGX_abH04.$i.tab"
done > command.GGGX_abH04jcvi.list
ParaFly -c command.GGGX_abH04jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GGGX_abH06.$i.tab"
done > command.GGGX_abH06jcvi.list
ParaFly -c command.GGGX_abH06jcvi.list -CPU 4

4）移动并重命名

cd ..
# 新建文件夹
mkdir best && cd best
# 移动*.Lipase5.tab.best
mv ../Lipase5.tab/*.tab.best ./

最后整理时，要结合*.Lipase5.tab.best和*.Lipase5.tab查看！

Class Y

Superfamilies
Homologous families
Proteins
Sequences
Structures 		4
4
15
71
225

seqs50_Y_abH30.fasta        seqs52_Y_abH28.fasta        seqs72_Y_abH38.fasta        seqs53_Y_abH27.fasta

cd ../..
# 新建文件夹
mkdir Y && cd Y

1） diamond blastp

 evalue为1e-5

批量运行

# pep70
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs50_Y_abH30.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out Y_abH30.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.Y_abH30.list
ParaFly -c command.Y_abH30.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs52_Y_abH28.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out Y_abH28.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.Y_abH28.list
ParaFly -c command.Y_abH28.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs72_Y_abH38.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out Y_abH38.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.Y_abH38.list
ParaFly -c command.Y_abH38.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs53_Y_abH27.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out Y_abH27.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.Y_abH27.list
ParaFly -c command.Y_abH27.list -CPU 4

# pepmy
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs50_Y_abH30.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out Y_abH30.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.Y_abH30.list
ParaFly -c command.Y_abH30.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs52_Y_abH28.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out Y_abH28.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.Y_abH28.list
ParaFly -c command.Y_abH28.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs72_Y_abH38.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out Y_abH38.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.Y_abH38.list
ParaFly -c command.Y_abH38.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs53_Y_abH27.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out Y_abH27.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.Y_abH27.list
ParaFly -c command.Y_abH27.list -CPU 4

2）parsing_blast_result.pl

新建文件夹

mkdir Lipase5.tab && cd Lipase5.tab

批量运行

# pep70
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../Y_abH27.$i.xml > Y_abH27.$i.tab"
done > command.Y_abH27.list
ParaFly -c command.Y_abH27.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../Y_abH28.$i.xml > Y_abH28.$i.tab"
done > command.Y_abH28.list
ParaFly -c command.Y_abH28.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../Y_abH30.$i.xml > Y_abH30.$i.tab"
done > command.Y_abH30.list
ParaFly -c command.Y_abH30.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../Y_abH38.$i.xml > Y_abH38.$i.tab"
done > command.Y_abH38.list
ParaFly -c command.Y_abH38.list -CPU 4

# pepmy
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../Y_abH27.$i.xml > Y_abH27.$i.tab"
done > command.Y_abH27.list
ParaFly -c command.Y_abH27.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../Y_abH28.$i.xml > Y_abH28.$i.tab"
done > command.Y_abH28.list
ParaFly -c command.Y_abH28.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../Y_abH30.$i.xml > Y_abH30.$i.tab"
done > command.Y_abH30.list
ParaFly -c command.Y_abH30.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../Y_abH38.$i.xml > Y_abH38.$i.tab"
done > command.Y_abH38.list
ParaFly -c command.Y_abH38.list -CPU 4

3）比对结果中筛选每个query的最佳subject

# 在(jcvi)下
conda activate jcvi

批量运行

# pep70
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 Y_abH27.$i.tab"
done > command.Y_abH27jcvi.list
ParaFly -c command.Y_abH27jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 Y_abH28.$i.tab"
done > command.Y_abH28jcvi.list
ParaFly -c command.Y_abH28jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 Y_abH30.$i.tab"
done > command.Y_abH30jcvi.list
ParaFly -c command.Y_abH30jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 Y_abH38.$i.tab"
done > command.Y_abH38jcvi.list
ParaFly -c command.Y_abH38jcvi.list -CPU 4

# pepmy
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 Y_abH27.$i.tab"
done > command.Y_abH27jcvi.list
ParaFly -c command.Y_abH27jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 Y_abH28.$i.tab"
done > command.Y_abH28jcvi.list
ParaFly -c command.Y_abH28jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 Y_abH30.$i.tab"
done > command.Y_abH30jcvi.list
ParaFly -c command.Y_abH30jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 Y_abH38.$i.tab"
done > command.Y_abH38jcvi.list
ParaFly -c command.Y_abH38jcvi.list -CPU 4

4）移动并重命名

cd ..
# 新建文件夹
mkdir best && cd best
# 移动*.Lipase5.tab.best
mv ../Lipase5.tab/*.tab.best ./

 最后整理时，要结合*.Lipase5.tab.best和*.Lipase5.tab查看！

Class GX

Superfamilies
Homologous families
Proteins
Sequences
Structures 		23
41
151
403
610

seqs10_GX_abH20.fasta        seqs30_GX_abH11.fasta        seqs5_GX_abH15.fasta
seqs11_GX_abH36.fasta        seqs3_GX_abH07.fasta        seqs60_GX_abH12.fasta
seqs14_GX_abH25.fasta        seqs47_GX_abH32.fasta        seqs61_GX_abH19.fasta
seqs49_GX_abH33.fasta        seqs65_GX_abH31.fasta        seqs4_GX_abH18.fasta   seqs6_GX_abH37.fasta        seqs19_GX_abH09.fasta        seqs1_GX_abH23.fasta  
seqs20_GX_abH08.fasta        seqs7_GX_abH24.fasta        seqs23_GX_abH35.fasta    seqs55_GX_abH34.fasta        seqs9_GX_abH14.fasta        seqs24_GX_abH22.fasta    seqs57_GX_abH26.fasta        seqs59_GX_abH13.fasta

cd ../..
# 新建文件夹
mkdir GX && cd GX

1） diamond blastp

 evalue为1e-5

批量运行

# pep70
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs10_GX_abH20.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH20.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH20.list
ParaFly -c command.GX_abH20.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs30_GX_abH11.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH11.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH11.list
ParaFly -c command.GX_abH11.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs5_GX_abH15.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH15.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH15.list
ParaFly -c command.GX_abH15.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs11_GX_abH36.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH36.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH36.list
ParaFly -c command.GX_abH36.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs3_GX_abH07.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH07.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH07.list
ParaFly -c command.GX_abH07.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs60_GX_abH12.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH12.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH12.list
ParaFly -c command.GX_abH12.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs14_GX_abH25.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH25.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH25.list
ParaFly -c command.GX_abH25.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs47_GX_abH32.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH32.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH32.list
ParaFly -c command.GX_abH32.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs61_GX_abH19.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH19.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH19.list
ParaFly -c command.GX_abH19.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs49_GX_abH33.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH33.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH33.list
ParaFly -c command.GX_abH33.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs65_GX_abH31.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH31.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH31.list
ParaFly -c command.GX_abH31.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs4_GX_abH18.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH18.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH18.list
ParaFly -c command.GX_abH18.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs6_GX_abH37.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH37.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH37.list
ParaFly -c command.GX_abH37.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs19_GX_abH09.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH09.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH09.list
ParaFly -c command.GX_abH09.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs1_GX_abH23.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH23.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH23.list
ParaFly -c command.GX_abH23.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs20_GX_abH08.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH08.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH08.list
ParaFly -c command.GX_abH08.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs7_GX_abH24.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH24.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH24.list
ParaFly -c command.GX_abH24.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs23_GX_abH35.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH35.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH35.list
ParaFly -c command.GX_abH35.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs55_GX_abH34.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH34.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH34.list
ParaFly -c command.GX_abH34.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs9_GX_abH14.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH14.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH14.list
ParaFly -c command.GX_abH14.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs24_GX_abH22.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH22.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH22.list
ParaFly -c command.GX_abH22.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs57_GX_abH26.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH26.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH26.list
ParaFly -c command.GX_abH26.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs59_GX_abH13.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pep70/$i.fasta --out GX_abH13.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH13.list
ParaFly -c command.GX_abH13.list -CPU 4

# pepmy
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs10_GX_abH20.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH20.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH20.list
ParaFly -c command.GX_abH20.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs30_GX_abH11.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH11.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH11.list
ParaFly -c command.GX_abH11.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs5_GX_abH15.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH15.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH15.list
ParaFly -c command.GX_abH15.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs11_GX_abH36.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH36.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH36.list
ParaFly -c command.GX_abH36.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs3_GX_abH07.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH07.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH07.list
ParaFly -c command.GX_abH07.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs60_GX_abH12.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH12.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH12.list
ParaFly -c command.GX_abH12.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs14_GX_abH25.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH25.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH25.list
ParaFly -c command.GX_abH25.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs47_GX_abH32.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH32.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH32.list
ParaFly -c command.GX_abH32.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs61_GX_abH19.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH19.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH19.list
ParaFly -c command.GX_abH19.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs49_GX_abH33.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH33.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH33.list
ParaFly -c command.GX_abH33.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs65_GX_abH31.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH31.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH31.list
ParaFly -c command.GX_abH31.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs4_GX_abH18.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH18.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH18.list
ParaFly -c command.GX_abH18.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs6_GX_abH37.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH37.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH37.list
ParaFly -c command.GX_abH37.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs19_GX_abH09.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH09.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH09.list
ParaFly -c command.GX_abH09.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs1_GX_abH23.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH23.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH23.list
ParaFly -c command.GX_abH23.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs20_GX_abH08.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH08.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH08.list
ParaFly -c command.GX_abH08.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs7_GX_abH24.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH24.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH24.list
ParaFly -c command.GX_abH24.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs23_GX_abH35.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH35.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH35.list
ParaFly -c command.GX_abH35.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs55_GX_abH34.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH34.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH34.list
ParaFly -c command.GX_abH34.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs9_GX_abH14.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH14.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH14.list
ParaFly -c command.GX_abH14.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs24_GX_abH22.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH22.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH22.list
ParaFly -c command.GX_abH22.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs57_GX_abH26.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH26.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH26.list
ParaFly -c command.GX_abH26.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "diamond blastp --db /media/aa/DATA/SZQ2/Lipase/runseqs/seqs59_GX_abH13.fasta --query /media/aa/DATA/SZQ2/bj/functional_annotation/pepmy/$i.fasta --out GX_abH13.$i.xml --outfmt 5 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 20 --tmpdir /dev/shm --index-chunks 1"
done > command.GX_abH13.list
ParaFly -c command.GX_abH13.list -CPU 4

2）parsing_blast_result.pl

新建文件夹

mkdir Lipase5.tab && cd Lipase5.tab

批量运行

# pep70
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH07.$i.xml > GX_abH07.$i.tab"
done > command.GX_abH07.list
ParaFly -c command.GX_abH07.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH08.$i.xml > GX_abH08.$i.tab"
done > command.GX_abH08.list
ParaFly -c command.GX_abH08.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH09.$i.xml > GX_abH09.$i.tab"
done > command.GX_abH09.list
ParaFly -c command.GX_abH09.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH11.$i.xml > GX_abH11.$i.tab"
done > command.GX_abH11.list
ParaFly -c command.GX_abH11.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH12.$i.xml > GX_abH12.$i.tab"
done > command.GX_abH12.list
ParaFly -c command.GX_abH12.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH13.$i.xml > GX_abH13.$i.tab"
done > command.GX_abH13.list
ParaFly -c command.GX_abH13.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH14.$i.xml > GX_abH14.$i.tab"
done > command.GX_abH14.list
ParaFly -c command.GX_abH14.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH15.$i.xml > GX_abH15.$i.tab"
done > command.GX_abH15.list
ParaFly -c command.GX_abH15.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH18.$i.xml > GX_abH18.$i.tab"
done > command.GX_abH18.list
ParaFly -c command.GX_abH18.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH19.$i.xml > GX_abH19.$i.tab"
done > command.GX_abH19.list
ParaFly -c command.GX_abH19.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH20.$i.xml > GX_abH20.$i.tab"
done > command.GX_abH20.list
ParaFly -c command.GX_abH20.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH22.$i.xml > GX_abH22.$i.tab"
done > command.GX_abH22.list
ParaFly -c command.GX_abH22.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH23.$i.xml > GX_abH23.$i.tab"
done > command.GX_abH23.list
ParaFly -c command.GX_abH23.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH24.$i.xml > GX_abH24.$i.tab"
done > command.GX_abH24.list
ParaFly -c command.GX_abH24.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH25.$i.xml > GX_abH25.$i.tab"
done > command.GX_abH25.list
ParaFly -c command.GX_abH25.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH26.$i.xml > GX_abH26.$i.tab"
done > command.GX_abH26.list
ParaFly -c command.GX_abH26.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH31.$i.xml > GX_abH31.$i.tab"
done > command.GX_abH31.list
ParaFly -c command.GX_abH31.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH32.$i.xml > GX_abH32.$i.tab"
done > command.GX_abH32.list
ParaFly -c command.GX_abH32.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH33.$i.xml > GX_abH33.$i.tab"
done > command.GX_abH33.list
ParaFly -c command.GX_abH33.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH34.$i.xml > GX_abH34.$i.tab"
done > command.GX_abH34.list
ParaFly -c command.GX_abH34.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH35.$i.xml > GX_abH35.$i.tab"
done > command.GX_abH35.list
ParaFly -c command.GX_abH35.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH36.$i.xml > GX_abH36.$i.tab"
done > command.GX_abH36.list
ParaFly -c command.GX_abH36.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH37.$i.xml > GX_abH37.$i.tab"
done > command.GX_abH37.list
ParaFly -c command.GX_abH37.list -CPU 4

# pepmy
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH07.$i.xml > GX_abH07.$i.tab"
done > command.GX_abH07.list
ParaFly -c command.GX_abH07.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH08.$i.xml > GX_abH08.$i.tab"
done > command.GX_abH08.list
ParaFly -c command.GX_abH08.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH09.$i.xml > GX_abH09.$i.tab"
done > command.GX_abH09.list
ParaFly -c command.GX_abH09.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH11.$i.xml > GX_abH11.$i.tab"
done > command.GX_abH11.list
ParaFly -c command.GX_abH11.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH12.$i.xml > GX_abH12.$i.tab"
done > command.GX_abH12.list
ParaFly -c command.GX_abH12.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH13.$i.xml > GX_abH13.$i.tab"
done > command.GX_abH13.list
ParaFly -c command.GX_abH13.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH14.$i.xml > GX_abH14.$i.tab"
done > command.GX_abH14.list
ParaFly -c command.GX_abH14.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH15.$i.xml > GX_abH15.$i.tab"
done > command.GX_abH15.list
ParaFly -c command.GX_abH15.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH18.$i.xml > GX_abH18.$i.tab"
done > command.GX_abH18.list
ParaFly -c command.GX_abH18.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH19.$i.xml > GX_abH19.$i.tab"
done > command.GX_abH19.list
ParaFly -c command.GX_abH19.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH20.$i.xml > GX_abH20.$i.tab"
done > command.GX_abH20.list
ParaFly -c command.GX_abH20.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH22.$i.xml > GX_abH22.$i.tab"
done > command.GX_abH22.list
ParaFly -c command.GX_abH22.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH23.$i.xml > GX_abH23.$i.tab"
done > command.GX_abH23.list
ParaFly -c command.GX_abH23.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH24.$i.xml > GX_abH24.$i.tab"
done > command.GX_abH24.list
ParaFly -c command.GX_abH24.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH25.$i.xml > GX_abH25.$i.tab"
done > command.GX_abH25.list
ParaFly -c command.GX_abH25.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH26.$i.xml > GX_abH26.$i.tab"
done > command.GX_abH26.list
ParaFly -c command.GX_abH26.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH31.$i.xml > GX_abH31.$i.tab"
done > command.GX_abH31.list
ParaFly -c command.GX_abH31.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH32.$i.xml > GX_abH32.$i.tab"
done > command.GX_abH32.list
ParaFly -c command.GX_abH32.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH33.$i.xml > GX_abH33.$i.tab"
done > command.GX_abH33.list
ParaFly -c command.GX_abH33.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH34.$i.xml > GX_abH34.$i.tab"
done > command.GX_abH34.list
ParaFly -c command.GX_abH34.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH35.$i.xml > GX_abH35.$i.tab"
done > command.GX_abH35.list
ParaFly -c command.GX_abH35.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH36.$i.xml > GX_abH36.$i.tab"
done > command.GX_abH36.list
ParaFly -c command.GX_abH36.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "/media/aa/DATA2/bin/parsing_blast_result.pl --evalue 1e-5 --HSP-num 1 --out-hit-confidence --suject-annotation ../GX_abH37.$i.xml > GX_abH37.$i.tab"
done > command.GX_abH37.list
ParaFly -c command.GX_abH37.list -CPU 4

3）比对结果中筛选每个query的最佳subject

# 在(jcvi)下
conda activate jcvi

批量运行

# pep70
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH07.$i.tab"
done > command.GX_abH07jcvi.list
ParaFly -c command.GX_abH07jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH08.$i.tab"
done > command.GX_abH08jcvi.list
ParaFly -c command.GX_abH08jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH09.$i.tab"
done > command.GX_abH09jcvi.list
ParaFly -c command.GX_abH09jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH11.$i.tab"
done > command.GX_abH11jcvi.list
ParaFly -c command.GX_abH11jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH12.$i.tab"
done > command.GX_abH12jcvi.list
ParaFly -c command.GX_abH12jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH13.$i.tab"
done > command.GX_abH13jcvi.list
ParaFly -c command.GX_abH13jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH14.$i.tab"
done > command.GX_abH14jcvi.list
ParaFly -c command.GX_abH14jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH15.$i.tab"
done > command.GX_abH15jcvi.list
ParaFly -c command.GX_abH15jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH18.$i.tab"
done > command.GX_abH18jcvi.list
ParaFly -c command.GX_abH18jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH19.$i.tab"
done > command.GX_abH19jcvi.list
ParaFly -c command.GX_abH19jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH20.$i.tab"
done > command.GX_abH20jcvi.list
ParaFly -c command.GX_abH20jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH22.$i.tab"
done > command.GX_abH22jcvi.list
ParaFly -c command.GX_abH22jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH23.$i.tab"
done > command.GX_abH23jcvi.list
ParaFly -c command.GX_abH23jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH24.$i.tab"
done > command.GX_abH24jcvi.list
ParaFly -c command.GX_abH24jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH25.$i.tab"
done > command.GX_abH25jcvi.list
ParaFly -c command.GX_abH25jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH26.$i.tab"
done > command.GX_abH26jcvi.list
ParaFly -c command.GX_abH26jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH31.$i.tab"
done > command.GX_abH31jcvi.list
ParaFly -c command.GX_abH31jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH32.$i.tab"
done > command.GX_abH32jcvi.list
ParaFly -c command.GX_abH32jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH33.$i.tab"
done > command.GX_abH33jcvi.list
ParaFly -c command.GX_abH33jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH34.$i.tab"
done > command.GX_abH34jcvi.list
ParaFly -c command.GX_abH34jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH35.$i.tab"
done > command.GX_abH35jcvi.list
ParaFly -c command.GX_abH35jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH36.$i.tab"
done > command.GX_abH36jcvi.list
ParaFly -c command.GX_abH36jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH37.$i.tab"
done > command.GX_abH37jcvi.list
ParaFly -c command.GX_abH37jcvi.list -CPU 4

# pepmy
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH07.$i.tab"
done > command.GX_abH07jcvi.list
ParaFly -c command.GX_abH07jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH08.$i.tab"
done > command.GX_abH08jcvi.list
ParaFly -c command.GX_abH08jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH09.$i.tab"
done > command.GX_abH09jcvi.list
ParaFly -c command.GX_abH09jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH11.$i.tab"
done > command.GX_abH11jcvi.list
ParaFly -c command.GX_abH11jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH12.$i.tab"
done > command.GX_abH12jcvi.list
ParaFly -c command.GX_abH12jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH13.$i.tab"
done > command.GX_abH13jcvi.list
ParaFly -c command.GX_abH13jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH14.$i.tab"
done > command.GX_abH14jcvi.list
ParaFly -c command.GX_abH14jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH15.$i.tab"
done > command.GX_abH15jcvi.list
ParaFly -c command.GX_abH15jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH18.$i.tab"
done > command.GX_abH18jcvi.list
ParaFly -c command.GX_abH18jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH19.$i.tab"
done > command.GX_abH19jcvi.list
ParaFly -c command.GX_abH19jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH20.$i.tab"
done > command.GX_abH20jcvi.list
ParaFly -c command.GX_abH20jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH22.$i.tab"
done > command.GX_abH22jcvi.list
ParaFly -c command.GX_abH22jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH23.$i.tab"
done > command.GX_abH23jcvi.list
ParaFly -c command.GX_abH23jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH24.$i.tab"
done > command.GX_abH24jcvi.list
ParaFly -c command.GX_abH24jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH25.$i.tab"
done > command.GX_abH25jcvi.list
ParaFly -c command.GX_abH25jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH26.$i.tab"
done > command.GX_abH26jcvi.list
ParaFly -c command.GX_abH26jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH31.$i.tab"
done > command.GX_abH31jcvi.list
ParaFly -c command.GX_abH31jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH32.$i.tab"
done > command.GX_abH32jcvi.list
ParaFly -c command.GX_abH32jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH33.$i.tab"
done > command.GX_abH33jcvi.list
ParaFly -c command.GX_abH33jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH34.$i.tab"
done > command.GX_abH34jcvi.list
ParaFly -c command.GX_abH34jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH35.$i.tab"
done > command.GX_abH35jcvi.list
ParaFly -c command.GX_abH35jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH36.$i.tab"
done > command.GX_abH36jcvi.list
ParaFly -c command.GX_abH36jcvi.list -CPU 4

for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
    echo "python -m jcvi.formats.blast best -n 1 GX_abH37.$i.tab"
done > command.GX_abH37jcvi.list
ParaFly -c command.GX_abH37jcvi.list -CPU 4

4）移动并重命名

cd ..
# 新建文件夹
mkdir best && cd best
# 移动*.Lipase5.tab.best
mv ../Lipase5.tab/*.tab.best ./

 最后整理时，要结合*.Lipase5.tab.best和*.Lipase5.tab查看！

Xsisikk
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专栏目录
diamond:加速的BLAST兼容的本地序列比对器
04-09
介绍 DIAMOND是用于蛋白质和翻译后的DNA搜索的序列比对器，旨在用于大序列数据的高性能分析。 主要功能是： BLAST以100x-10,000x的速度对蛋白质和翻译的DNA进行成对比对。 移码比对，用于长时间阅读分析。 资源需求低，适合在标准台式机或笔记本电脑上运行。 各种输出格式，包括成对的BLAST，表格和XML，以及分类标准。 文献资料 在线文档位于。 支持 Diamond是积极支持和开发的软件。 请使用来查找故障，并使用中的问题，评论，功能请求等。 关于 DIAMOND由本杰明·布赫芬克（Benjamin Buchfink）在德国图宾根马克斯·普朗克发育生物学研究所Drost实验室开发。 [ ] [ ] [ Google学术搜索] [ Drost实验室] [ MPI-EBIO ] 在已发表的研究中使用该工具时，请引用： Buchfink B，路透K，德罗斯
【天坑】BLAST比对序列时遭受的痛苦
sinat_21011081的博客
07-18 1794
初学者使用blast时可能遇到的各种问题。
php爬虫抓取商标数据库,异步爬虫抓取merops数据库底物谱
weixin_33392336的博客
04-14 312
异步的使用方法异步需要用到python的两个异步库asynoioaiohttp从python 更新至3.4版本后，新增了异步的语法糖(async 和 await)，使得异步操作用起来很容易为什么要在爬虫中使用异步呢？爬虫，顾名思义就是抓去网页内容，但是也要先去访问网站，但是访问网站是需要等待时间的，有时候网页访问卡顿会严重阻塞后续的网页抓取操作，因此，就有大把的时间浪费在了等待上，这也是使用异步的...
利用 DIAMOND、MCScanX、TBtools 分析物种基因组间的共线性区段与基因复制事件
浓香鸭腿面的博客
01-29 2万+
本文通过 4 个兰花的基因组注释，主要利用 MCScanX 软件分析 NB-ARC 基因家族在不同物种间的共线性区段以及基因复制事件。步骤参考文献 Genome- Wide Analysis of the Nucleotide Binding Site Leucine-Rich Repeat Genes of Four Orchids Revealed Extremely Low Numbers of Disease Resistance Genes，Front. Genet.，08 January 202
「JCVI」如何筛选得到最优blast比对结果？
陈有朴的博客
07-18 1846
JCVI格式处理模块的使用
分泌蛋白(SP)注释为CAZymes，蛋白酶MEROPS，脂肪酶Lipase
weixin_58269397的博客
04-18 251
由于分泌的CAZymes在木材降解过程中起着关键作用，因此我们研究了它们在该科的含量变化，不同进化枝具有独特的CAZyme含量。分泌蛋白(SP)被注释为 CAZymes，脂肪酶或蛋白酶。对于每个基因组，我们对于这些我们指定的活性在普通植物细胞壁基质。从真菌世界( Mycocosm.JGI.doe.gov )获得 JGI 基因组组装的统计数据(即 N50、基因和支架的数量以及基因组大小)。
转座子注释
weixin_58269397的博客
04-19 1079
也可使用在线网站# 进入conda环境sudo supassword# 运行# pepalldo。
PHI注释步骤（含批量）
weixin_58269397的博客
04-01 329
.将PHI数据库下载下来本地blast，需要先填资料，填完之后即可下载至本地，使用blast进行比对。
NC：上百个菌根真菌基因组
刘永鑫的博客——宏基因组公众号
05-26 452
要点菌根真菌是陆地生态系统中营养物质获取的共生体。菌根共生体在毛霉属、子囊菌纲和担子菌纲的多个谱系中反复出现。菌根真菌从土壤有机质中获取碳的能力存在很大差异。来自Nature Communications的一项研究综合分析了73个腐生,内生和致病真菌物种以及62个菌根物种(包括29个新的菌根基因组),共计135个真菌基因组。这项研究以生态优势真菌群落为样本,它们以前没有共...
diamond软件_BLAST本地比对太慢？不怕用diamond
weixin_36397372的博客
12-12 2562
在宏基因组学研究中，又或者你准备做大规模的系统进化的相关研究等等，需要分析了数百万个序列的reads，以确定来自环境的微生物样品的功能或分类学含量，找出对应reads同源的物种。这里重要的步骤是确定存在哪些基因，通常通过将翻译的DNA序列与蛋白质序列的参考数据库比对，例如NCBI非冗余(NCBI-nr)蛋白质数据库。长期以来，BLASTX因其高灵敏度而被认为是此标准的黄金标准工具。但是，...
makeblastdb
doudou8486的专栏
03-12 2550
<br />BLAST+中makeblastdb参数详解2010-04-29 16:21<br />以后打算工作中用到的相关BLAST操作全部用BLAST+来完成<br />与以前的Blast相以，我们还是从格式化数据库到比对开始<br />一般我们是有一个fasta文件用来格式化数据库，以前的命令是formatdb，现在是makeblastdb<br />一般用到的格式如下：<br />makeblastdb -in input_file -dbtype molecule_type -title data
makeblastdb注意事项
xxxxx
01-17 1万+
makeblastdb注意事项本地blast，需要自行构建数据库。那么就要用到makeblastdb。这个命令很简单。USAGE makeblastdb [-h] [-help] [-in input_file] [-input_type type] -dbtype molecule_type [-title database_title] [-parse_seqids] [-h
MeterSphere 数据库使用
WUXINOF的专栏
11-23 1万+
1. 环境配置 进入配置环境，选择“数据库配置”，配置好数据源名称（配置SQL选择环境的时候会用到），数据库鸡翅，数据库连接URL，用户名和密码等 2. 前置或者后置SQL 选择运行环境，如果运行环境配置了数据库配置，这里就可以看到，选择对应的数据库配置。 SQL脚本处，写对应的SQL脚本 3. 使用变量 ${cookie_1}，cookie为变量名，“_n”表示第几条数据 这样通过数据库读取的变量就算配置好了。 ...
Blast使用
huangliangbo的专栏
09-28 4197
简介 Blast，全称Basic Local Alignment Search Tool，即"基于局部比对算法的搜索工具"，由Altschul等人于1990年发布。Blast能够实现比较两段核酸或者蛋白序列之间的同源性的功能，它能够快速的找到两段序列之间的同源序列并对比对区域进行打分以确定同源性的高低。 Blast的运行方式是先用目标序列建数据库（这种数据库称为database，里面的每一条序
makeblastdb及blastn的使用
热门推荐
qq_35696312的博客
03-10 2万+
文章目录简介使用makeblastdb创建自定义搜索库blastn极短序列比对 简介 blast是常用的比对软件，在linux系统下安装完成blast套件后，可以使用blastn进行核酸序列的比对，基本的使用模式为确定搜索的库，然后使用blastn对指定的序列在库中进行比对，如果想要自定义搜索库，需要使用makeblastdb来创建，更多的细节可以参考blast 官方文档接下来我将介绍如何创建自定...
Blastdb
光尘的博客
04-25 2908
安装 在ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/中下载最新的BLAST可执行程序 wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.9.0+-x64-linux.tar.gz mv ncbi-blast-2.9....
blast 错误
常玉俊bioinfo
04-30 2445
在新环境中调用blastp出现错误blastp: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory 找不到libssl.so.1.0.0的正确位置，首先，利用 locate libssl.so.1.0.0 /home/pat...
Metabase 使用指南
FesonX的博客
06-26 5132
一. 为什么从 ELK 迁移到 Metabase + OLAP 1.1 ELK 的问题 扩展性不强：Kibana 只能应用在 ElasticSearch 上 管理不便：在阿里云等平台，一个 ElasticSearch 集群对应一个 Kibana，难以统一管理 开发成本：无法将图表嵌入到其他应用中，需要二次开发图形展示 性能一般：ElasticSearch 擅长全文搜索，在数据分...
Metabase的基本使用：10分钟快速入门
琦彦
11-18 9518
Metabase使用手册 初始配置 按提示一步步填写相关信息即可，注意第一个创建的账户默认即为管理员账户 数据分析 接下来就可以正式使用了，右上角各功能如下： 下面就以具体场景为例，分别解释各项功能，点击创建问题 --》简单查询，先从简单的开始，走一遍整体流程 简单查询 假设我要对一张名为train_task_info的实训考试成绩信息做多个维度的分析，表结构与测试记录如下： 字段说明 User Name:　用户姓名 Train Sim Type:　实训考试类型 Train Name:　实训考
MEROPS linux下载
最新发布
11-26
根据提供的引用内容，无法确定您需要下载MEROPS的具体内容。MEROPS是一个数据库，包含有关蛋白酶和蛋白酶抑制剂的信息。如果您需要下载MEROPS数据库，请按照以下步骤进行操作： 1.访问MEROPS官方网站（https://www.ebi.ac.uk/merops/）并注册账户。 2.登录后，单击“Download”选项卡，然后单击“Download MEROPS”按钮。 3.选择您需要的MEROPS版本并下载。 4.解压缩下载的文件并按照说明进行安装。 如果您需要下载MEROPS数据库中的特定数据，请提供更具体的信息，以便我能够更好地回答您的问题。

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