Peter Rice wrote: > "JK (Jesper Agerbo Krogh)" <[EMAIL PROTECTED],<[EMAIL PROTECTED]>
I'm with Peter on this one. There are way too many possible formats for fasta comment lines for any software to support all of them. This command line reformatting is exactly the sort of task my 'extract' program was written to handle (having faced the same task myself more times than I can count). Example: % cat >foo.pfa <<EOD >IES3_YEAST Q12345 Ino eighty subunit 3. MKFEDLLATNKQVQFAHAATQHYKSVKTPDFLEKDPHHKKFHNADGLNQQGSSTPSTATD ANAASTASTHTNTTTFKRHIVAVDDISKMNYEMIKNSPGNVITNANQDEIDISTLKTRLY KDNLYAMNDNFLQAVNDQIVTLNAAEQDQETEDPDLSDDEKIDILTKIQENLLEEYQKLS QKERKWFILKELLLDANVELDLFSNRGRKASHPIAFGAVAIPTNVNANSLAFNRTKRRKI NKNGLLENIL EOD % cat foo.pfa | extract -if '>' -mt -cols 'UNIPROT:[2,]' UNIPROT:Q12345 Ino eighty subunit 3. MKFEDLLATNKQVQFAHAATQHYKSVKTPDFLEKDPHHKKFHNADGLNQQGSSTPSTATD ANAASTASTHTNTTTFKRHIVAVDDISKMNYEMIKNSPGNVITNANQDEIDISTLKTRLY KDNLYAMNDNFLQAVNDQIVTLNAAEQDQETEDPDLSDDEKIDILTKIQENLLEEYQKLS QKERKWFILKELLLDANVELDLFSNRGRKASHPIAFGAVAIPTNVNANSLAFNRTKRRKI NKNGLLENIL So you can process the whole thing in a pipe or in two stages through a temporary file. Your choice. Extract is part of drm_tools (these have nothing to do with "digital rights management", they were my initials long before drm took on its current common meaning) from here: ftp://saf.bio.caltech.edu/pub/software/linux_or_unix_tools/drm_tools.tar.gz The man page is here: http://saf.caltech.edu/saf_manuals/extract.html Regards, David Mathog [EMAIL PROTECTED] Manager, Sequence Analysis Facility, Biology Division, Caltech _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
