To save yourself some grief, I would simply look for > and then replace the line, regardless of what else is there (which is what you are doing anyway). You can also use print $variable and sleep(3); in parts of the code to help see what is present in certain places, particularly if you don't get a match. We don't have the input files, so we can't tell if there are spaces or tabs in the FASTA headers.
use strict;
use warnings;
my @files = glob("*.fa");
for my $file ( @files ) {
# open the input file
open my $in, "<", "$file" or die "Cannot open "$file": $!\n";
# open the output file
open my $out, ">", "$file.out" or die "Cannot open "$file.out": $!\
+n";
# reset contig number
my $contig_number = 1;
while ( <$in> ) {
chomp;
if ( $_ ~= m/^>/ ) {
# it's a header
print $out ">config_$contig_number\n\n";
$contig_number++;
}
else {
# it's sequence
print $out "$_\n\n";
}
close $in;
close $out;
}
}
my $file_count = @files;
print "Successfully processed $file_count files!\n";
exit;
-
Are you posting in the right place? Check out Where do I post X? to know for sure.
-
Posts may use any of the Perl Monks Approved HTML tags. Currently these include the following:
<code> <a> <b> <big>
<blockquote> <br /> <dd>
<dl> <dt> <em> <font>
<h1> <h2> <h3> <h4>
<h5> <h6> <hr /> <i>
<li> <nbsp> <ol> <p>
<small> <strike> <strong>
<sub> <sup> <table>
<td> <th> <tr> <tt>
<u> <ul>
-
Snippets of code should be wrapped in
<code> tags not
<pre> tags. In fact, <pre>
tags should generally be avoided. If they must
be used, extreme care should be
taken to ensure that their contents do not
have long lines (<70 chars), in order to prevent
horizontal scrolling (and possible janitor
intervention).
-
Want more info? How to link
or How to display code and escape characters
are good places to start.
|