根据reads名称提取bam

软件： bbmap   filterbyname.sh

下载地址：https://sourceforge.net/projects/bbmap/

./filterbyname.sh -h

Written by Brian Bushnell
Last modified September 1, 2016

Description:  Filters reads by name.

Usage:  filterbyname.sh in=<file> in2=<file2> out=<outfile> out2=<outfile2> names=<string,string,string> include=<t/f>

in2 and out2 are for paired reads and are optional.
If input is paired and there is only one output file, it will be written interleaved.
Important!  Leading > and @ symbols are NOT part of sequence names;  they are part of
the fasta, fastq, and sam specifications.  Therefore, this is correct:
names=e.coli_K12
And these are incorrect:
names=>e.coli_K12
names=@e.coli_K12

Parameters:
include=f           Set to 'true' to include the filtered names rather than excluding them.
substring=f         Allow one name to be a substring of the other, rather than a full match.
                         f: No substring matching.
                         t: Bidirectional substring matching.
                         header: Allow input read headers to be substrings of names in list.
                         name: Allow names in list to be substrings of input read headers.
prefix=f            Allow names to match read header prefixes.
casesensitive=t     (case) Match case also.
ow=t                (overwrite) Overwrites files that already exist.
app=f               (append) Append to files that already exist.
zl=4                (ziplevel) Set compression level, 1 (low) to 9 (max).
int=f               (interleaved) Determines whether INPUT file is considered interleaved.
names=              A list of strings or files.  The files can have one name per line, or
                    be a standard read file (fasta, fastq, or sam).
minlen=0            Do not output reads shorter than this.
ths=f               (truncateheadersymbol) Ignore a leading @ or > symbol in the names file.
tws=f               (truncatewhitespace) Ignore leading or trailing whitespace in the names file.
truncate=f          Set both ths and tws at the same time.

Positional parameters:
These optionally allow you to output only a portion of a sequence.  Zero-based, inclusive.
Intended for a single sequence and include=t mode.
from=-1             Only print bases starting at this position.
to=-1               Only print bases up to this position.
range=              Set from and to with a single flag.


Java Parameters:
-Xmx                This will be passed to Java to set memory usage, overriding the program's automatic memory detection.
                    -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.  The max is typically 85% of physical memory.
-eoom               This flag will cause the process to exit if an out-of-memory exception occurs.  Requires Java 8u92+.
-da                 Disable assertions.

To read from stdin, set 'in=stdin'.  The format should be specified with an extension, like 'in=stdin.fq.gz'
To write to stdout, set 'out=stdout'.  The format should be specified with an extension, like 'out=stdout.fasta'

Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems

命令：~/bin/bbmap/filterbyname.sh in=proper.sam out=pick.sam  names=name.id2 include=t

输入：

 head proper.sam
A00184:770:HWV23DSXY:3:1101:10004:12618::umi:C7P242498724-GGTTGTA	147	7	142498724	60	36M	=	142498724	-36	GAGGACCTGAAAAACGTGTTCCCACCCGAGGTCGCT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:36	MC:Z:36M	AS:i:36XS:i:0
A00184:770:HWV23DSXY:3:1101:10004:12618::umi:C7P242498724-GGTTGTA	99	7	142498724	60	36M	=	142498724	36	GAGGACCTGAAAAACGTGTTCCCACCCGAGGTCGCT	FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:36	MC:Z:36M	AS:i:36XS:i:0


head name.id2 
A00184:770:HWV23DSXY:3:1171:27001:18161::umi:C9P233738047-TATAATG
A00184:770:HWV23DSXY:3:1309:19397:22216::umi:C10P143615217-TGTTCTT
A00184:770:HWV23DSXY:3:2364:29695:33849::umi:C11P169456137-GTTCTTT
A00184:770:HWV23DSXY:3:2321:8594:14998::umi:C16P102134348-CCACCTC

输出：

head pick.sam
A00184:770:HWV23DSXY:3:1101:13042:19257::umi:C4P155589827-ACTCTTT	147	4	55589827	60	59S91M	=	55589827	-91	GGAGTAACACTCTTTCCCTACACGACGCTCTCCGATCTACTCTTTAGCCGGTAGAGTATACAATAGATTGGTATTTTTGTCCAGGAACTGAGCAGAGGTGAGATGATTATTTTTGGCACTGCTTATAATGCAGAGGGGAAGGACTGCAAT	FFF:FFFFFFFFFFFFFFFFF,FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:91	MC:Z:91M	AS:i:91	XS:i:19
A00184:770:HWV23DSXY:3:1101:13042:19257::umi:C4P155589827-ACTCTTT	99	4	55589827	60	91M	=	55589827	91	ACAATAGATTGGTATTTTTGTCCAGGAACTGAGCAGAGGTGAGATGATTATTTTTGGCACTGCTTATAATGCAGAGGGGAAGGACTGCAAT	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:91	MC:Z:59S91M	AS:i:91	XS:i:19