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EddyRivasLab / hmmer

HMMER: biological sequence analysis using profile HMMs
http://hmmer.org
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How to merge profiles in different format? #250

Closed xiekunwhy closed 2 years ago

xiekunwhy commented 3 years ago

Hi,

How to merge following two type of hmm profiles (hmmsearch does not work if I cat them directly):

type 1

HMMER3/f [3.3.2 | Nov 2020] NAME 1-cysPrx_C ACC PF10417.11 DESC C-terminal domain of 1-Cys peroxiredoxin LENG 40 ALPH amino RF no MM no CONS yes CS yes MAP yes DATE Wed Feb 24 18:37:46 2021 NSEQ 40 EFFN 17.426758 CKSUM 4086680297 GA 21.10 21.10 TC 21.10 21.10 NC 21.00 21.00 STATS LOCAL MSV -7.5463 0.71948 STATS LOCAL VITERBI -7.8624 0.71948 STATS LOCAL FORWARD -4.3303 0.71948

type 2

HMMER3/f [3.2.1 | June 2018] NAME K00001 LENG 400 ALPH amino RF no MM no CONS yes CS no MAP yes DATE Mon Jul 5 14:37:13 2021 NSEQ 1325 EFFN 13.285685 CKSUM 3713403561 STATS LOCAL MSV -11.0499 0.69925 STATS LOCAL VITERBI -13.2873 0.69925 STATS LOCAL FORWARD -5.0859 0.69925

Best, Kun

cryptogenomicon commented 3 years ago

Shouldn't be any problem with concatenating those two profile files. They are in the same format, 3/f. Can you provide example files that reproduce the problem?

You can use hmmconvert to change the format of profile files. The default is to upgrade an old file to current format, if possible.