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Old 02-11-2013, 08:40 AM   #1
Shishir
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Default Any script to parse HMMsearch results?

I have 146 resulting files of HMMsearch. I used 146 Hmm models to generate these files. Could someone share me any script to parse HmmSearch results?
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Old 02-11-2013, 09:21 AM   #2
suryasaha
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No script handy but you can code a bit and have BioPerl installed, try using this module
http://search.cpan.org/~cjfields/Bio...MER/Results.pm

See Synopsis for code snippets.
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Old 02-11-2013, 09:33 AM   #3
maubp
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And if you prefer Python to Perl, Biopython 1.61 includes a new experimental module SearchIO which includes support for HMMER output (v2 and v3):
http://news.open-bio.org/news/2013/0...1-61-released/
http://biopython.org/wiki/SearchIO

Also, if you ask HMMER for the table output you may not even need a complicated parser at all.
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