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#!/usr/bin/perl |
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use strict; |
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|
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my ($fastafile,$isofile,$outbase, $count)=@ARGV; |
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|
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#my ($fastafile,$isofile,$outfile)=@ARGV; |
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|
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open(F,$fastafile); |
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my $line=<F>; |
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chomp($line); |
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my ($header,$offset)=split(/\s+/,$line); |
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if ($offset) { |
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die ("Invalid fasta defline for this script: a numeric offset is expected after seqID\n") |
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unless $offset=~m/^\d+$/; |
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} |
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my $seq=''; |
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while (<F>) { |
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chomp; |
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last if m/^>/; |
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$seq.=$_; |
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} |
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close(F); |
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|
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open(F,$isofile); |
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while(<F>) { |
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next if m/^\s*#/; |
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chomp; |
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my @a=split(/\t/); |
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my $beg=$a[3]; |
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my ($len)=($a[8]=~m/len=(\d+)/); |
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my $outfile=$outbase.'.'.$count; |
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open(FO,">$outfile") || die ("Error creating $outfile!\n"); |
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$count++; |
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my $subseq=substr($seq,$beg-1,$len); |
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print FO "$header ".($offset+$beg-1)."\n"; |
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&printfa($subseq); |
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close(FO); |
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|
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|
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} |
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#select(STDOUT); |
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close(F); |
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|
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sub printfa { |
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my $seqlen=length($_[0]); |
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my $pos=0; |
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while ($pos<$seqlen) { |
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print FO substr($_[0],$pos,60)."\n"; |
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$pos+=60; |
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} |
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} |
