[BiO BB] program for sequence length

[Larye D. Parkins]

On Thu, May 6, 2010 6:07 pm, Mike Marchywka wrote:
>
> ----------------------------------------
>> Date: Wed, 5 May 2010 14:46:28 +0530
>> From: pkhurana08 at gmail.com
>> 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?
>

infoseq, part of the EMBOSS suite should do what you want.

> You could probably write a perl or bash script to do it more quickly
> than you could find something and depending on your overall objective,
> assuming you want to do more, it may help to have something
> in source code that you understand. I was doing a lot of fasta
> manipulation
> and I ended up writing a c++ fasta command line utility since I needed
> speed  but I never documented it and keep forgetting how it works.
>
> Consider just using sed to put the name and sequence into a single line
> per entry
> and then just look at lengths using awk or something. For things
> I don't do very often the learning curve can be a nuisance and it is
> easier
> to "Reinvent the wheel" with a short script rather than relearn some
> special purpose utility.
> These generalpurpose text processing tools can be used anywhere.
>
>
>
>> I can write one but why reinvent the wheel.
>> Thanking all in advance
>>
>> Regards,
>> Pankaj
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