Mercurial > repos > pcingola > snpeff
view snpEff_2_1a/snpEff_2_1a/scripts/fastaSample.pl @ 3:c052639fa666 default tip
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author | pcingola |
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date | Fri, 20 Apr 2012 11:22:59 -0400 |
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#!/usr/bin/perl #--- # Initialize parameters #--- $sampleStart = $ARGV[0]; $sampleEnd = $ARGV[1]; if(( $ARGV[0] eq '' ) || ($ARGV[1] eq '')) { die "Usage: fastaSample sampleStart sampleEnd\n"; } $sampleStart--; $sampleEnd--; $sampleLen = $sampleEnd - $sampleStart + 1; #--- # Read fasta file #--- for($lineNum=0 ; $l = <STDIN> ; $lineNum++ ) { if( $l =~/^>/ ) { # Sample if not empty if( $seq ne "" ) { $s = substr( $seq, $sampleStart, $sampleLen); print "$s\n"; } # New sequence $seq = ""; } else { chomp($l); $seq .= $l; } } # Sample if not empty if( $seq ne "" ) { $s = substr( $seq, $sampleStart, $sampleLen); print "$s\n"; } $len = length($seq); print STDERR "Lines: $lineNum\n"; print STDERR "Sequence size: $len\n"; print STDERR "Sample size: $sampleLen\n";