basil at ovi.ac.za (Basil Allsopp) wrote:
>Does anyone know why MSF files formatted by readseq are not recognized by GCG
>Version 8.1? (I don't know whether they were recognized by earlier versions).
>>The file test.msf as written by readseq (through gde) is as follows:
>> gde842_9 MSF: 100 Type: N January 01, 1776 12:00 Check: 9397 ..
>> Name: test1 Len: 100 Check: 1581 Weight: 1.00
> Name: test2 Len: 100 Check: 6389 Weight: 1.00
> Name: test3 Len: 100 Check: 1427 Weight: 1.00
>>//
>> test1 AAACGATGCA CATATGTATT GTGCTCTAGA TACAGCATCA ---AGCTCTA
> test2 AAATGATGCA CACATGTACT GTGCTTTAGA TACAGCACAA CAGAGTGCTA
> test3 AAAAAGTGGT GCGGAATCTC TGGCAGCTAT TACCCGCGAC GCTAACATTA
>> test1 CTGCAGGAGC AACT------ ACATCTGTTA TGGTAAAAAA TGAAAATTTA
> test2 CTAATGGTGC AACATTAGCT TCATCTGTTA TGATAAAAAA TGAAAATTTA
> test3 CTGAG----- -------ACC AATTACTTCG TAGTCAAAAT TGAGAAATTA
>>>If I try to use "distances" on this file I get:
>> *** ERROR, bad sequence format in test.msf ! ***
> *** No files in test.msf ! ***
>>Thanks in advance to anyone who can help.
>>--
>---
>Basil Allsopp | E-mail basil at ovisun.ovi.ac.za>Onderstepoort Veterinary Institute | Phone +27 12 5299385
>Onderstepoort 0110, South Africa | Fax +27 12 5299431
This error looks suspiciously like the one you get in PRETTY if you
fail to specify *which* sequences in the MSF file you wish to use.
Try typing whatever.msf{*} as the input. The {*} means all sequences
included in the MSF.
Hope this helps...
Mike
mjcoyne at warren.med.harvard.edu
