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cambiotraining / bacterial-genomics

Course materials for "Working with Bacterial Genomes"
https://cambiotraining.github.io/bacterial-genomics/
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seqtk_parser.py error #6

Closed tavareshugo closed 10 months ago

tavareshugo commented 10 months ago

With the S_pneumoniae dataset, I got this error when running the pseudogenome_check script: 

TypeError: unsupported operand type(s) for /: 'str' and 'str'

I think it's coming from the seqkt_parser.py, most likely from this line: 

seqtk_df['mapped'] / seqtk_df['ref_length'] * 100

Might need to wrap in int():

int(seqtk_df['mapped']) / int(seqtk_df['ref_length']) * 100

But I haven't done enough troubleshooting yet to confirm this. Will get back to it eventually.

tavareshugo commented 10 months ago

nevermind, this was again because the script had failed half-way through and therefore other TSV files were being included in the analysis.

In the future, it might be nice if this is included in the bactmap workflow.