How to extract the fasta sequence of a specified gene by perl
The editor will share with you how perl extracts the fasta sequence of a specified gene. I hope you will get something after reading this article. Let's discuss it together.
Easy to use perl script for sequence extraction
Here, introduce a very easy to use sequence extraction perl script, the use is very simple.
The usage is as follows:
Perl / share/work/huangls/piplines/01.script/get_fa_by_id.pl
For example:
Perl / share/work/huangls/piplines/01.script/get_fa_by_id.pl id.txt input.fasta out.fa
Where id.txt is the sequence to be extracted ID,input.fasta is the input sequence file and out.fa is the output sequence file.
The id.txt format is as follows:
TRINITY_DN116733_c6_g37TRINITY_DN116733_c6_g70TRINITY_DN95808_c0_g7TRINITY_DN104586_c1_g2TRINITY_DN108413_c2_g23TRINITY_DN37223_c0_g1TRINITY_DN107955_c0_g8TRINITY_DN117047_c0_g2TRINITY_DN78058_c0_g1
Here is the script code:
Die "perl $0" unless (@ ARGV==3); use Math::BigFloat;use Bio::SeqIO;use Bio::Seq;$in = Bio::SeqIO- > new (- file = > "$ARGV [1]",-format = > 'Fasta'); $out = Bio::SeqIO- > new (- file = > "> $ARGV [2]",-format = >' Fasta'); my%keep;open IN, "$ARGV [0]" or die "$!"; while () {chomp;next if / ^ # /; # next unless / > > / My@tmp=split (/\ tmp /); $keep {$tmp [0]} = 1;} close (IN); my$i=0;while (my$ seq = $in- > next_seq ()) {my ($id,$sequence,$desc) = ($seq- > id,$seq- > seq,$seq- > desc); if (exists $keep {$id}) {$out- > write_seq ($seq);} $in- > close (); $out- > close ()
The script uses the Bio::SeqIO module to process the sequence file, which is concise and efficient. First, it uses hash to store the sequence ID to be extracted, and then uses Bio::SeqIO to traverse the sequence file to determine whether each sequence is the sequence to be extracted. If so, output.
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