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Old 03-19-2012, 03:55 AM   #1
Pedro
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Location: Portugal

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Default batch rename multiple fasta

Hi,
I've a fairly high amount of hybrid assembly tests and the headers of the multiple-fasta files have different strings which I would like to normalize. Could you suggest how can I do a (customized) batch header renaming in multiple fasta files. I.e. [input multiple fasta file] [custom string in the headers, only differentiated by numbering of the contig] [output prefix]? If possible to add qualifiers even better.

Thanx
P
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Old 03-19-2012, 05:29 AM   #2
maasha
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You could have a look at Biopieces.

Especially read_fasta, write_fasta, add_ident and merge_vals.
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Old 03-19-2012, 06:47 AM   #3
maubp
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Learning a scripting language would be a good idea for working in bioinformatics. This would be easy with Perl and BioPerl, Python and Biopython, or Ruby and BioRuby etc.
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Old 03-19-2012, 01:35 PM   #4
Pedro
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Quote:
Originally Posted by maasha View Post
You could have a look at Biopieces.

Especially read_fasta, write_fasta, add_ident and merge_vals.
Thank you, it solved the question

cheers
P

P.S.-maubp, thank you for the hint...
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