A convinient tool for item extracting with different format such as table, fasta, fastq
Description:
The design philosophy of brentcaodeng fisher.pl is of great importance in our daily work.
Say thanks to my best enlightened tutor and friend brentcaodeng.
I reimplemented this script based on my own logic.
--By CongfanBu
2019-10-30
[email protected]
Version:
1.3, In table mode, the fc and bc can be format customized
Usage:
% fishInWinter.pl [options] <bait_file> <fish_file>
--bformat set bait file format, fasta|table|fq
--fformat set fish file format, fasta|table|gff|fq|gff3|gtf|vcf
--bcolumn set bait file column, default=1, or it can be 1:3-4 customized
--fcolumn set fish file column, default=1, or it can be 1:3-4 customized
--except get things not in the bait file
--maxcount stop after NUM matches
--split separator when fisher, [table]or [space], default=table
--test output bc and fc contant to test
--nongreed only print minimum number of coincident line, which very adapt that query is uniq in subject
--version print version and change log
--note also print #
Notes:
Due to time constraints, --nonpreed and --maxcount are currently only implemented in Fasta and Table (version 1.2)
Use the Nongreed parameter with caution unless you are sure of the exact number in the pool
The --maxcount and --nongreed may be used together to maximize fishing speed
The except parameter does not support nongreed matching