[BiO BB] program for sequence length

[Mike Marchywka]

----------------------------------------
> From: akarger at CGR.Harvard.edu
> To: bbb at bioinformatics.org
> Date: Fri, 7 May 2010 09:36:49 -0400
> Subject: Re: [BiO BB] program for sequence length
>
> 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.

I hadn't thought of this before but it is a good idea if you can search it easily, I often use google for
sed/awk one liners for stuff like this and its a great way to learn the tools and get your work done.
You seem to have a bit more than flat lists of one-liners but off hand I'd think this would be
a generally good idea. Now to argue," you should have done that in {perl,awk,sed,java,c++} instead of {perl, awk, sed, java, c++}"
LOL


>
> 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
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>
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