I’m trying to add several mult-HMM files together but I haven’t had much luck. First I tried to just
cat them, then I realized that it won’t work if there is an overlap of HMMs within the files. I then made a script that only concatenates unique ones but once I tried to use it, I get this
Error: bad file format in HMM file.
I suspect it’s because there are different fields for different files. For example, the first HMM in the first file has these fields:
HMMER3/f [3.1b2 | February 2015] NAME Adenylsucc_synt ACC PF00709.21 DESC Adenylosuccinate synthetase LENG 419 ALPH amino RF no MM no CONS yes CS yes MAP yes DATE Sat Aug 4 15:42:20 2018 NSEQ 755 EFFN 2.301197 CKSUM 4189663105 GA 20.40 20.40 TC 20.40 20.40 NC 20.20 20.30 STATS LOCAL MSV -11.3493 0.69897 STATS LOCAL VITERBI -12.6105 0.69897 STATS LOCAL FORWARD -5.7752 0.69897
The first HMM of the second file has this:
# Freely distributed under the GNU General Public License (GPLv3). HMMER3/f [3.1b1 | May 2013] NAME EPrGT00050000000570 LENG 553 ALPH amino RF no MM no CONS yes CS no MAP yes DATE Thu Oct 13 16:48:58 2016 NSEQ 33 EFFN 1.816772 CKSUM 2711521311 STATS LOCAL MSV -11.9038 0.69756 STATS LOCAL VITERBI -12.5276 0.69756 STATS LOCAL FORWARD -6.3393 0.69756
I’m thinking that I can just propogate the
NAME field for the
DESC fields if they don’t exist. However, I don’t know what to do with the cutoffs (i.e.
GA, TC, NC).
Does anyone know how I can merge these HMM files together?
Read more here: Source link