Dear Monks ,following code works changing headers for some

files but for some files 

use strict;
use warnings;

#my $count = 1;
#my $file;

my @files = <xxxx/*>;


 foreach my $file(@files){ 
 open (FILE,"$file") or die "$!";
 my $outfile = $file."out";
 open (OFILE,'>',"$outfile") or die "$!"; 
 my $count = 1; 
 while (<FILE>) {
   chomp;
  if( s/^>\S+/>contig_$count/)
   {
     $count++;
   }
  if( /^(\S+)$/)
   {print OFILE"$1\n\n"}
   
}
}

[download]

input file

>ATCC33693_scaffold0

AAAAAAGAGAGAAACACTAGCTTCTCTCTTGTTATGAGCTTGGCAAATCCATACTCTCCC AGGCCGCTTCCAGCCAAGTACCATCAGCGTATATGGGCTTAACTTCTAGGTTCGGAATGT AACTAGGTGTACCCCCATAGCTATACTCACCAAGCATATATATTGTATCACATAAAGTTA

>ATCC33693_scaffold1

AAAAAAGAGAGAAACACTAGCTTCTCTCTTGTTATGAGCTTGGCAAATCCATACTCTCCC AGGCCGCTTCCAGCCAAGTACCATCAGCGTATATGGGCTTAACTTCTAGGTTCGGAATGT GTTATGAGCTTGGCAAATCCATACTCTCCCAGGCCGCTTCCAGCCAAGTA

output file

>contig_1

AAAAAAGAGAGAAACACTAGCTTCTCTCTTGTTATGAGCTTGGCAAATCCATACTCTCCC AGGCCGCTTCCAGCCAAGTACCATCAGCGTATATGGGCTTAACTTCTAGGTTCGGAATGT AACTAGGTGTACCCCCATAGCTATACTCACCAAGCATATATATTGTATCACATAAAGTTA

>contig_2

AAAAAAGAGAGAAACACTAGCTTCTCTCTTGTTATGAGCTTGGCAAATCCATACTCTCCC AGGCCGCTTCCAGCCAAGTACCATCAGCGTATATGGGCTTAACTTCTAGGTTCGGAATGT GTTATGAGCTTGGCAAATCCATACTCTCCCAGGCCGCTTCCAGCCAAGTA

i need to change for large number of files but some files fails and the output is empty file please help me where am going wrong

Thanks

In reply to Renaming headers works for some files but fails for some files by MVRS

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.