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DRL / blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
GNU General Public License v3.0
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GC content is 0 #110

Open ginac opened 3 years ago

ginac commented 3 years ago

Hi, I'm using blobtools version 1.1.1 and running this command on the example: blobtools create -i example/assembly.fna -b example/mapping_1.sorted.bam -t example/blast.out -o example/test --nodes taxdump/nodes.dmp --names taxdump/names.dmp blobtools view -i test.blobDB.json -o junk

and the output file "junk.test.blobDB.table.txt" has a GC content of 0

1.1.1

assembly : ~/blobtools/example/assembly.fna

coverage bam0 - ~/blobtools/example/mapping_1.sorted.bam

taxonomy tax0 - ~/blobtools/example/blast.out

nodesDB : None

taxrule : bestsum

min_score : 0.0

min_diff : 0.0

tax_collision_random : False

name length GC N bam0 phylum.t.6%s phylum.s.7%s phylum.c.8

contig_1 756 0.0 0 120.8277 Actinobacteria 200.0 0 contig_2 1060 0.0 0 197.1055 Actinobacteria 2300.0 0 contig_3 602 0.0 0 77.3078 Actinobacteria 10000.0 0 contig_4 951 0.0 0 545.5981 Actinobacteria 1000.0 0 contig_5 614 0.0 0 183.8478 Nematoda 2000.0 0

Any idea why?

Thanks, Gina

DRL commented 3 years ago

Hi Gina,

that is weird. Are you sure you are running python3?

cheers,

dom

ginac commented 3 years ago

Thank you. This was the problem. Python2 was the culprit. Cheers!

smoretti commented 3 years ago

The setup.py file still contains 'Programming Language :: Python :: 2.7'