genbank_get_genomes_by_taxon.py seems to ignore "--format" argument

[jvollme]

Summary & Description:

I am currently using pyani v.2.3 as installed via bioconda. genbank_get_genomes_by_taxon.py seems work generally for downloading contig-fastas.
However, when I try to download genbanks instead (which I need for some additional analyses), by setting the --format option to "gbk" (as stated in the help function), this argument seems to be ignored and i still just get the contig-fastas.

Reproducible Steps:

genbank_get_genomes_by_taxon.py -t 1107 -l chloroflexuslog --email myemail@wherever.com -o chloroflexus --format gbk -v

Current Output:

.fna & .fna.gz for each genome (BTW: I guess only the "*.fna.gz" files were actually meant to remain as final output here?)

Expected Output:

.gbk[.gz] for each genome

pyani Version:

v2.3

Python Version:

v3.5.2

Operating System:

Linux Ubuntu 14.04

Summary & Description:

I am currently using pyani v.2.3 as installed via bioconda. genbank_get_genomes_by_taxon.py seems work generally for downloading contig-fastas.
However, when I try to download genbanks instead, by setting the --format option to "gbk" (as stated in the help function), this argument seems to be ignored and I still just get the contig-fastas.

Reproducible Steps:

genbank_get_genomes_by_taxon.py -t 1107 -l chloroflexuslog --email myemail@wherever.com -o chloroflexus --format gbk -v

Current Output:

.fna & .fna.gz for each genome

Expected Output:

.gbk[.gz] for each genome

pyani Version:

v2.3 (installed via bioconda)

Python Version:

v3.5.2

Operating System:

Linux Ubuntu 14.04

[widdowquinn]

Thanks John - I'll get on it.

[widdowquinn]

Hi John,

Thanks for the bug report - the root cause of the problem was that when I changed the internals to cope with the NCBI restructure, I forgot to reimplement the choice of format. I didn't notice this in part because the test suite doesn't currently cover the scripts (this will be fixed in the next iteration of pyani).

I've reimplemented and tested the download format choice in the latest commit: 43ba088

The following command-line now works for me, as I would expect:

genbank_get_genomes_by_taxon.py -t 203804 -v -l C_blochmannia_dl.log  -o issue_89_dl --email my.email@my.domain --format=gbk -f

Re: the .fna vs .fna.gz files. At the FTP source site all files are gzipped. They're downloaded as .fna.gz and then uncompressed on the local disk.

Please let me know if this fix works for you (if so, I'll close the issue), or if you have any further comments/questions.

Cheers,

L.

[jvollme]

Hi, sorry for the late reply. It seems to work nicely now. Thanks!