BigScape

构建BGC序列相似性网络，将BGCs分组到基因簇家族中，探索与酶系统发育相关的基因簇多样性，探索大量基因组中生物合成基因簇（BGC）的多样性。

1.安装

1.1下载

wget https://github.com/medema-group/BiG-SCAPE/archive/refs/tags/v1.1.5.zip

1.2解压

unzip v1.1.5.zip

1.3模块补充

sudo apt-get update
sudo apt-get install build-essential
pip install biopython
conda install -n test scipy
conda install -n test scikit-learn

2.数据库

2.1pfam数据库

wget https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz && gunzip Pfam-A.hmm.gz

下载Pfam-A数据库，并处理。

hmmpress Pfam-A.hmm

 2.2mibig数据库

wget https://dl.secondarymetabolites.org/mibig/mibig_gbk_3.1.tar.gz

3.标准命令

python3 （具体地址）bigscape.py --version

help 

python3 /home/yaoxiaowen/anaconda3/envs/test/BiG-SCAPE-1.1.5/bigscape.py

-i /home/yaoxiaowen/geneome/gbk/

-o /home/yaoxiaowen/geneome/out/

-c 36 --mode auto

--cutoffs 0.5

--pfam_dir /home/yaoxiaowen/anaconda3/envs/test/Pfam

usage: BiG-SCAPE [-h] [-l LABEL] [-i INPUTDIR] -o OUTPUTDIR [--pfam_dir PFAM_DIR] [-c CORES]
                 [--include_gbk_str INCLUDE_GBK_STR [INCLUDE_GBK_STR ...]]
                 [--exclude_gbk_str EXCLUDE_GBK_STR [EXCLUDE_GBK_STR ...]] [-v] [--include_singletons]
                 [-d DOMAIN_OVERLAP_CUTOFF] [-m MIN_BGC_SIZE] [--mix] [--no_classify]
                 [--banned_classes {PKSI,PKSother,NRPS,RiPPs,Saccharides,Terpene,PKS-NRP_Hybrids,Others} [{PKSI,PKSother,NRPS,RiPPs,Saccharides,Terpene,PKS-NRP_Hybrids,Others} ...]]
                 [--cutoffs CUTOFFS [CUTOFFS ...]] [--clans-off] [--clan_cutoff CLAN_CUTOFF CLAN_CUTOFF] [--hybrids-off]
                 [--mode {global,glocal,auto}] [--anchorfile ANCHORFILE] [--force_hmmscan] [--skip_ma] [--mibig] [--mibig21]
                 [--mibig14] [--mibig13] [--query_bgc QUERY_BGC] [--domain_includelist] [--version]
BiG-SCAPE: error: the following arguments are required: -o/--outputdir