Error using the function gethmmprof
1 vue (au cours des 30 derniers jours)
Afficher commentaires plus anciens
Arnold Hayer
le 3 Oct 2015
Modifié(e) : per isakson
le 5 Oct 2015
I am trying to use the "gethmmprof" function. Using the example given in the documentation, hmm_7tm = gethmmprof(2), I only get a series of error messages. Is the function up to date with the current database format? Thanks!
2 commentaires
Walter Roberson
le 3 Oct 2015
Please show the error messages.
gethmmprof appears to be part of the Bioinformatics Toolbox
per isakson
le 3 Oct 2015
Modifié(e) : per isakson
le 5 Oct 2015
With R2013a
Error using pfamhmmread (line 85)
Record 1 in the inputfile is not a valid PFAM file. PFAMHMMREAD supports HMMMER2.0 and
HMMER3/b formatted files.
Error in getsangerdata (line 175)
out = pfamhmmread(s);
Error in gethmmprof (line 79)
model = getsangerdata(accessnum,'database','hmm',varargin{:});
and the two first lines of the downloaded string are
HMMER3/f [3.1b1 | May 2013]
NAME 7tm_2
Thus, with R2013a it seems to be a problem with the file format.
Which Matlab release?
Réponse acceptée
Paola Favaretto
le 5 Oct 2015
The Bioinformatics Toolbox version you are running (R2013a) supports only HMMER2.0 and HMMER3/b. The format of the current database is HMMER3/f. The difference in the content is not significant, but the format is not recognized and therefore the function throws an error. If you contact Mathworks customer support they will send you a patch.
-Paola
0 commentaires
Plus de réponses (0)
Voir également
Catégories
En savoir plus sur Genomics and Next Generation Sequencing dans Help Center et File Exchange
Produits
Community Treasure Hunt
Find the treasures in MATLAB Central and discover how the community can help you!
Start Hunting!