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Patch from Peter Cock (bug534) for cut tool to ignore commented lines.

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This commit is contained in:
Anton Nekrutenko
2011-06-08 17:17:11 -04:00
parent a2804a7b7e
commit d2d6956108
1 changed files with 31 additions and 12 deletions
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tools/filters/cutWrapper.pl
+31 -12
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@@ -39,19 +39,38 @@ $del = $column_delimiters_href->{$ARGV[2]};
open (OUT, ">$ARGV[3]") or die "Cannot create $ARGV[2]:$!\n";
open (IN, "<$ARGV[0]") or die "Cannot open $ARGV[0]:$!\n";
while (<IN>) {
chop;
@in = split /$del/;
foreach $field (@columns) {
if (defined($in[$field-1])) {
push(@out, $in[$field-1]);
} else {
push(@out, ".");
}
}
print OUT join("\t",@out), "\n";
@out = ();
while (my $line=<IN>) {
if ($line =~ /^#/) {
#Ignore comment lines
} else {
chop($line);
@in = split(/$del/, $line);
foreach $field (@columns) {
if (defined($in[$field-1])) {
push(@out, $in[$field-1]);
} else {
push(@out, ".");
}
}
print OUT join("\t",@out), "\n";
@out = ();
}
}
#while (<IN>) {
# chop;
# @in = split /$del/;
# foreach $field (@columns) {
# if (defined($in[$field-1])) {
# push(@out, $in[$field-1]);
# } else {
# push(@out, ".");
# }
# }
# print OUT join("\t",@out), "\n";
# @out = ();
#}
close IN;
close OUT;