[Bioperl-l] bl2seq

[Paulo Almeida]

Hi Usha,

Perhaps something like this:

my @seqs;
open IN, "yourfile";
while (<IN>) {
chomp();  #get rid of newline character
my @line = split(/\s+/);
push @seqs, $line[3] if $line[3] =~ /^A-Z+$/;
}

foreach my $seq (@seqs) {
#Do whatever you are doing successfully for a single sequence
}

I'm not sure about the syntax. because I haven't been using Perl, but that's 
the general idea.

-Paulo

On Tuesday 23 August 2005 02:32, Usha Rani Reddi wrote:
> Hi,
> I am trying to compare two hundred thousand probes(each one of them) to
> another genome. Format of the file containing probes is like this
> SEQ_ID PROBE_ID POSITION PROBE_SEQUENCE
> NC_004116 1 1 AATTAACATTGTTGATTTTATTCTTCAACATC
> NC_004116 3 13 TGATTTTATTCTTCAACATCTGTGGAAAACTT
> NC_004116 5 25 TCAACATCTGTGGAAAACTTTATTTTTTTATG
> NC_004116 7 37 GAAAACTTTATTTTTTTATGGTACAATATAAC
> NC_004116 9 49 TTTTTATGGTACAATATAACAATAATTATCCA
> NC_004116 11 61 AATATAACAATAATTATCCACAAGACAATAAG
> NC_004116 13 73 ATTATCCACAAGACAATAAGGAAGAAGCTATG
> NC_004116 15 85 ACAATAAGGAAGAAGCTATGACGGAAAACGAA
> What I am trying to do is compare PROBE_SEQUENCE to fasta file of
> Streptococcus agalactiae. I am trying to loop through the probes but not
> sure how to proceed. My program is working fine for single sequence. One
> more thing is I am not interested in matches, I want to display only
> mismatches. I am new to Bioperl, some one please help me with this.
> Thanks
> Usha
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> Bioperl-l at portal.open-bio.org
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-- 
Paulo Almeida
Tel: +351 21 4464635, Fax: +351 21 4407970
Instituto Gulbenkian de Ciência
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