[BiO BB] program for sequence length

[Martin Gollery]

One nice thing about this approach is that you could then sort them by
length, which might be very handy. You could find things like export all the
sequences of length >x but <y, for example.

Martin Gollery

On Fri, May 7, 2010 at 6:36 AM, Karger, Amir <akarger at cgr.harvard.edu>wrote:

> Check out the Scriptome (yes, this is an advertisement.) at
> http://sysbio.harvard.edu/csb/resources/computational/scriptome/ , which
> is a set of Perl one-liners you cut and paste onto your command line to do
> bio-y text-y thigns.
>
> Use the change_fasta_to_tab tool to change your fasta to a tab-delimited
> file with ID, description, sequence. Then use the calc_col_length tool on
> the result, which will add another column giving the length of the sequence
> column. You can throw that into excel and hide the sequence column (or use
> choose_cols_to_delete to make a file without the seqeuences themselves) and
> then read through it at your leisure.
>
> Feel free to contact me offline for details.
>
> -Amir Karger
>
> > -----Original Message-----
> > From: bbb-bounces at bioinformatics.org [mailto:bbb-
> > bounces at bioinformatics.org] On Behalf Of Pankaj Khurana
> > Sent: Wednesday, May 05, 2010 5:16 AM
> > To: bbb at bioinformatics.org
> > Subject: [BiO BB] program for sequence length
> >
> > 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
> > _______________________________________________
> > BBB mailing list
> > BBB at bioinformatics.org
> > http://www.bioinformatics.org/mailman/listinfo/bbb
>
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>



-- 
-- 
Martin Gollery
Senior Bioinformatics Scientist
Tahoe Informatics
www.bioinformaticist.biz
www.hiddenmarkovmodels.com