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legumeinfo / bionorm

Normalize and check genomic data against Data Store standards
BSD 3-Clause "New" or "Revised" License
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index-gff does not seem to respect --compress option #59

Open adf-ncgr opened 3 years ago

adf-ncgr commented 3 years ago

bionorm index-gff --compress Aeschynomene_evenia/CIAT22838.gnm1.ann0.ZM3R/aesev.CIAT22838.gnm1.ann0.ZM3R.gene_models_main.gff3

File "/home/localhost/adf/.local/pipx/venvs/bionorm/lib/python3.8/site-packages/sh.py", line 865, in handle_command_exit_code raise exc sh.ErrorReturnCode_1:

RAN: /erdos/adf/bin/tabix -p gff Aeschynomene_evenia/CIAT22838.gnm1.ann0.ZM3R/aesev.CIAT22838.gnm1.ann0.ZM3R.gene_models_main.gff3

STDOUT:

STDERR: [tabix] the compression of 'Aeschynomene_evenia/CIAT22838.gnm1.ann0.ZM3R/aesev.CIAT22838.gnm1.ann0.ZM3R.gene_models_main.gff3' is not BGZF

adf-ncgr commented 3 years ago

or perhaps the option description is simply misleading?
--compress Compress with bgzip before indexing.

but if I run it on an uncompressed file it is perfectly happy whereas if I feed it a pre-compressed file I get 2021-01-10 15:34:05.542 | ERROR | bionorm.index:index_gff:84 - Uncompress Aeschynomene_evenia/CIAT22838.gnm1.ann0.ZM3R/aesev.CIAT22838.gnm1.ann0.ZM3R.gene_models_main.gff3.gz befor indexing.

the --help could probably be more --helpful

adf-ncgr commented 3 years ago

similarly with bionorm index-fasta it appears that if --compress argument is given it does not compress the given file, whereas if it is not given then it does compress it.