Error using the function gethmmprof

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Arnold Hayer 2015-10-3

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https://ww2.mathworks.cn/matlabcentral/answers/246508-error-using-the-function-gethmmprof

编辑： per isakson 2015-10-5

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!

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Walter Roberson 2015-10-3

Please show the error messages.

gethmmprof appears to be part of the Bioinformatics Toolbox

per isakson 2015-10-3

编辑：per isakson 2015-10-5

在 MATLAB Online 中打开

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?

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Answer 1

Paola Favaretto 2015-10-5

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https://ww2.mathworks.cn/matlabcentral/answers/246508-error-using-the-function-gethmmprof#answer_194742

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