On Thu, May 6, 2010 6:07 pm, Mike Marchywka wrote: > > ---------------------------------------- >> Date: Wed, 5 May 2010 14:46:28 +0530 >> From: [email protected] >> To: [email protected] >> 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 >> _______________________________________________ >> BBB mailing list >> [email protected] >> http://www.bioinformatics.org/mailman/listinfo/bbb > > _________________________________________________________________ > Hotmail has tools for the New Busy. Search, chat and e-mail from your > inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > > > -- Larye D. Parkins Information Engineering Services 600 Turner Ave. Shelton, WA 98584 Office: 360 426 1718 Mobile: 360 350 9645 http://www.info-engineering-svc.com "Making IT work since 1965." Member of ACM, IEEE Computer Society, USENIX, SAGE, and LOPSA _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
