32 lines
640 B
Perl
32 lines
640 B
Perl
#!/usr/bin/env perl
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use strict;
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use warnings;
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use FindBin;
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use lib ("$FindBin::RealBin/../../PerlLib");
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use Fasta_reader;
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my $usage = "usage: $0 file.fa [kmer_length=25]\n\n";
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my $fa_file = $ARGV[0] or die $usage;
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my $kmer_length = $ARGV[1] || 25;
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main: {
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my $fasta_reader = new Fasta_reader($fa_file);
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while (my $seq_obj = $fasta_reader->next()) {
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my $sequence = $seq_obj->get_sequence();
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for (my $i = 0; $i < length($sequence) - $kmer_length + 1; $i++) {
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my $kmer = substr($sequence, $i, $kmer_length);
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print "$kmer\n";
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}
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}
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exit(0);
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}
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