[Bioperl-l] Question: How to manipulate files

Brian Osborne osborne1 at optonline.net
Wed Mar 29 21:16:45 EST 2006


Michael,

Operations like these are easy using SeqIO - see the Beginners HOWTO or the
SeqIO HOWTO:

http://www.bioperl.org/wiki/HOWTOs

The script could look something like:

use Bio::SeqIO;

my $count = 0;
my $in = Bio::SeqIO->new(-file => "file.fa",-format => "fasta");
my $out = Bio::SeqIO->new(-file => ">newfile.fa",-format => "fasta");

while (my $seq = $in->next_seq) {
    $count++;
    next if $count < 8;
    $out->write_seq($seq);
}    

Then you can delete the old and rename the new...

Brian O.


On 3/29/06 5:41 PM, "Michael Craige" <mcraige at genetics.emory.edu> wrote:

> I am attempting to develop a script to open a DNA file contain 15 FASTA
> sequences and then delete the first 7 sequences and close the file leaving
> the remainder 8 sequences intact.
> 
> Can someone help me with a Perl script or point me to some doc that can
> help? Here is a sample, the first sequence in the file header is show below.
> All the header is the same except for the number "001 to 015"
> 
> 
>> 10kb_NN_Analysis.txt.nmrc_001
> NTNTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNNNNNNNN
> AANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
> NNNNNNNNNNNNNNNNNNNNNNNN
> 
> I trying to get the script to find the first sequences ".nmrc_001" and then
> delete files content to the end of file ".nmrc_007" without affect the
> header with ".nmrc_008"
> 
> Is there something already exist to do this?
> 
> 
> Michael Craige
> Emory University
> 
> 
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