error when converting hmmer table to off table

Question

[v.berriosfarias]

Hello, I performed an alignment using hmmer hmmsearch tool using metagenomic contigs as a query and a hydrocarbon database (hydrocarbon.hmm file).

I n first instance I first retrieved all ORFs from the contigs and translated them with esl-translate program as following:

esl-translate -c 11 input_contigs.fa > translated_orfs.fa

After getting the translated ORFs under the translated_orfs.fa file, I run the alignment with hmmsearch

hmmsearch --domtblout dom_results.txt --cpu 10 hydrocarbon.hmm translated_orfs.fa > logfile.

Once I get the dom_results.txt file I proceed to use the hmmer2gff program as the following:

hmmer2gff -d -o gffs/sample1.gff tanslated_orfs.fa $i dom_Results.txt

But I'm getting the following error:

Traceback (most recent call last):   File "/Users/valentin-ignacio/opt/miniconda3/envs/mgkit/bin/hmmer2gff", line 11, in <module>
    sys.exit(main())   File "/Users/valentin-ignacio/opt/miniconda3/envs/mgkit/lib/python3.7/site-packages/mgkit/workflow/hmmer2gff.py", line 212, in main
    options   File "/Users/valentin-ignacio/opt/miniconda3/envs/mgkit/lib/python3.7/site-packages/mgkit/workflow/hmmer2gff.py", line 153, in parse_domain_table_contigs
    aa_seqs = get_aa_data(options.aa_file)   File "/Users/valentin-ignacio/opt/miniconda3/envs/mgkit/lib/python3.7/site-packages/mgkit/workflow/hmmer2gff.py", line 143, in get_aa_data
    for name, seq in fasta.load_fasta(f_handle)   File "/Users/valentin-ignacio/opt/miniconda3/envs/mgkit/lib/python3.7/site-packages/mgkit/workflow/hmmer2gff.py", line 142, in <genexpr>
    (name.split(' ')[0], seq)   File "/Users/valentin-ignacio/opt/miniconda3/envs/mgkit/lib/python3.7/site-packages/mgkit/io/fasta.py", line 41, in load_fasta
    line = line.decode('ascii') AttributeError: 'str' object has no attribute 'decode'

What can be happening here ?

This is the header of the aminoacidic fasta file:

>orf4 source=k141_332722 coords=96..221 length=42 frame=3 desc=flag=0 multi=8.4159 len=1747
PPQAIEQDFKYGIKAASLTTPSPTSEFIFNLFKLSQLQIKHS

Thanks for your time :)

Valentín.

Answer 1

[Juke34]

Hmmr2gff code needs python2 apparently and you use python3