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abyzovlab / CNVpytor

a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads
MIT License
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Location example_ref_genome_conf.py in anaconda #215

Closed RenscoHogers closed 6 months ago

RenscoHogers commented 6 months ago

Hi,

I am currently using CNVpytor using an anaconda container, however I cannot find example_ref_genome_conf.py which I need to use my reference genome.

Do you have any clue about where I can find this script in the container?

arpanda commented 6 months ago

Your query is not clear to me. Could you please elaborate a bit.

If you are taking about Configuring reference genome. The example_ref_genome_conf.py is for the user to create to load custom reference genome. We have only limited number of pre-configured reference genomes.

-Arijit

RenscoHogers commented 6 months ago

In your tutorial "AddReferenceGenome.md" you include the following line: To use CNVpytor with new reference genome us -conf option in each cnvpytor command, e.g. cnvpytor -conf REL_PATH/example_ref_genome_conf.py -root file.pytor -rd file.bam

I would like to know where I can find the "example_ref_genome_conf.py" script so I can link it. I am using the anaconda container (https://anaconda.org/bioconda/cnvpytor). Not sure if that makes any difference.

arpanda commented 6 months ago

There is no such file with cnvpytor package. The example_ref_genome_conf.py is for the user to create.