[BiO BB] program for sequence length

[Maximilian Haussler]

the ucsc source tools include faSize, pure C, very very fast. You
would need to compile though.

or use biopython:

from Bio import SeqIO
short_sequences = [] # Setup an empty list
for record in SeqIO.parse(open("cor6_6.fa", "rU"), "fasta") :
    print len(record.seq)

I remember that I spend several days on this problem many years ago by
programming everything myself in pure perl... like so many people that
start in bioinformatics...

cheers
Max



On Wed, May 5, 2010 at 2:16 AM, Pankaj Khurana <pkhurana08 at gmail.com> wrote:
> Hi all,
>
> I have a few 1000 fasta files. I would like to get the list showing the
> sequence name and their respective lengths.
> Is there a program for this?
> I can write one but why reinvent the wheel.
> Thanking all in advance
>
> Regards,
> Pankaj
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