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Dear monks, My question is related to file parsing within while loops. I have a large file containing many individual files all in the same format.

I want to extract certain features from each file which mainly is easy. My problem is when I need to extract everything between two markers in the file. I am struggling to get all the nice info between ORIGIN and // in each file.

This is how the file looks: How can I extract all the info between ORIGIN and // for each record??

# extract of file: #=============== FEATURES Location/Qualifiers /note="blah blah" COUNT 200 ORIGIN 1 lots of nice info 61 lots of nice info 121 lots of nice info //
This is my code so far:
open (FILE, $ARGV[0]) or die "unable to open FILE\n"; + my ($note, $info, $features,$count); my ($c,$d); my @seq; my $in_seq = 0; my $seq = ''; + while (<FILE>) { my $line = $_; if ($line =~ /(FEATURES)\s+(\w+)/) { $features = $2; } if ($line =~ /(COUNT)\s+(\d+)/) { $count = $2; } if ($line =~ /^ORIGIN/) { # print "$line\n"; push @seq, "$line\n"; } until ($line =~ /\/\/) {}; } + print "@seq\n";

Retitled by davido.

In reply to Genbank file parsing by Anonymous Monk

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