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