Splitting a GenBank file into smaller files I have a genbank file that I have been trying to run in HMMER using the following command:
hmmscan --domtblout NC_000962.3.final.gbk.out -E 0.000001 prot_profile.hmm NC_000962.3.final.gbk

However, since the file is too big for HMMER, I get the following error:
Fatal exception (source file p7_pipeline.c, line 697): 
Target sequence length &gt; 100K, over comparison pipeline limit. 
(Did you mean to use nhmmer/nhmmscan?) 
Aborted (core dumped)

I need to split this file into smaller files for the HMMER run. The problem is, I would need the ORIGIN field (containing the nucleotide sequence) at the bottom of the file split into relevant chunks into the subfile as well. This is where I am getting stuck.
I have already looked at GenBank Parser and seqretsplit to no avail.
I would greatly appreciate some help with this. Thank you.
You can use NCBI EntrezDirect to download data in GenBank format for a specific region of the sequence as follows:
efetch -db nuccore -id NC_000962.3 -format gb -seq_start 1 -seq_stop 99000 &gt; seq.gb