Re: How to match the sequences with headers

while (<IFILE>) { ... elsif ($_ =~ /^(\w*)$/) { @sequence = $_; } ... foreach my $sequence(@sequence) { print OFILE1 "$headerseq\n$sequence\n"; } ... }
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I'm not familiar with processing FASTA sequence data, but a couple of things strike me in the code fragment originally posted by anonym:

The statement
@sequence = $_;
will only assign a single element to the @sequence array which, by the operation of the posted code alone, will never contain other than zero or one elements. Then
foreach my $sequence(@sequence) {
print OFILE1 "$headerseq\n$sequence\n";
}
loops over this zero or one element array to output to a file. This seems suspicious.
I'm assuming that other code sets up $/ to read multi-line FASTA records. The regex /^(\w*)$/ in the elsif condition statement above will only match records that have no whitespace (except that $ could match a newline at the very end of the string), but all the records in the sample input shown by anonym have embedded whitespace.

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Re^2: How to match the sequences with headers by anonym (Acolyte) on Oct 23, 2011 at 17:03 UTC
Thanks for your replies.I did get the two output files now ,one having the headers and associated protein sequences and the other with headers of Sec structures and associated structures. `if ($_ =~ /sequence/){ @headerseq = split('\n',$_); print OFILE1 "@headerseq\n"; } elsif ($_ =~ /^(\w*)$/){ @sequence = $_; print OFILE1 "@sequence\n"; } elsif ($_ =~ /secstr/) { @headersec = split('\n',$_); print OFILE2 "@headersec\n"; } else { @secseq = $_; print OFILE2 "@secseq\n"; }` [download]	[reply] [d/l]

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Re^2: How to match the sequences with headers
by anonym (Acolyte) on Oct 23, 2011 at 17:03 UTC

Thanks for your replies.I did get the two output files now ,one having the headers and associated protein sequences and the other with headers of Sec structures and associated structures.

       
if ($_ =~ /sequence/){
        @headerseq = split('\n',$_);
        print OFILE1 "@headerseq\n";
        }
        elsif ($_ =~ /^(\w*)$/){
        @sequence = $_;
        print OFILE1 "@sequence\n";
        }
        elsif ($_ =~ /secstr/) {
        @headersec = split('\n',$_);
        print OFILE2 "@headersec\n";
        }
        else {
        @secseq = $_;
        print OFILE2 "@secseq\n";
        }
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