54 lines
1.0 KiB
Perl
54 lines
1.0 KiB
Perl
#!/usr/bin/env perl
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use strict;
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use warnings;
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my $usage = "\n\n\tusage: $0 acc_list_file.txt target_db.fasta\n\n";
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my $acc_list_file = $ARGV[0] or die $usage;
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my $target_db = $ARGV[1] or die $usage;
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main: {
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my $samtools = `sh -c "command -v samtools"`;
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unless ($samtools =~ /\w/) {
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die "Error, need samtools in your PATH setting.";
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}
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chomp $samtools;
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my @accs = `cat $acc_list_file`;
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chomp @accs;
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if (! -s "$target_db.fasta.fai") {
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my $cmd = "$samtools faidx $target_db";
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my $ret = system $cmd;
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if ($ret) {
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die "Error, cmd: $cmd died with ret $ret";
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}
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}
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my $ret = 0;
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foreach my $acc (@accs) {
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$acc =~ s/\s//g;
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unless ($acc =~ /\w/) { next; }
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my $cmd = "$samtools faidx $target_db \"$acc\"";
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my $result = `$cmd`;
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if ($result) {
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print $result;
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}
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else {
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print STDERR "No entry retrieved for acc: $acc\n";
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$ret = 1;
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}
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}
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exit($ret);
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}
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