Question

I am trying to extract the first complete number on each line from a text file like this:

8 gcaggcaaactgcgataataaaaggctgtttcaacagcggagtggattgt 1.5307684822361e-176
11 tttacccagtgagtttgaagcaaggatcttttagtttaccgaaaaatgag 3.22210306380202e-293
14 agcaatagcgcgaacagacaacctcatcagtctaccgcgcaccctttccc 1.32107737963584e-52
20 agtgacagggaaaggcgatcgcggctttacgatcagagatcggtgtcggt 0.942504155078175
30 tccggagactttcgattgcatgcaattcaccatcataccctcttgccctc 0
45 actgagcccctgacgctggccagtgtagcgctgtgaagtcccctctcagg 9.49147409471272e-307
53 gaaccgagcgatcgctgctgccattgtctcgccttctgccgaggaatgcc 2.15850303270505e-28

using the regex in the following code:

my $id = undef;
while (my $line = <INFILE>){
  chomp $line;
  if ($line =~ /\A([0-9]+)/){
      $id = $1;
  }
print OUTFILE "$id\n";
$line = <INFILE>;
chomp $line;
}

The output I’m getting only includes every other line:

8
14
30
53

I’ve tried printing out every line without doing the match, and everything is there. Once I add the regex, it skips every other line. Any ideas why it’s doing this?

Answer 1

You’re reading from the INFILE handle twice, once in the while condition, and once at the end of the loop.

Remove, the final read:

my $id = undef;
while (my $line = <INFILE>){
  chomp $line;
  if ($line =~ /\A([0-9]+)/){
      $id = $1;
  }
  print OUTFILE "$id\n";
}