Cgivar2vcf updates

[abeconnelly]

Some (hopefully) trivial changes and cleanup:

• cgivar_to_vcf.py wouldn't run unless I included 'twobit' from get_reference.py (instead of 'import .twobit')
• Added some simple input checking for parameters passed to cgvar_to_vcf.py from the command line.
• Updated the option parser.

[madprime]

Thanks! I'm going to reject change for importing "twobit", although I know this method for imports makes the code a little less convenient to use independently on the command line.

To run this code on the command line, it should be run with the "-m" flag, for example: python -m file_process.utils.cgivar_to_vcf -i var-file.tsv.bz2 -r external_data_files/hg19.2bit

[abeconnelly]

OK, sorry about that. This is my ignorance of how to use Python properly.

On Tue, Nov 18, 2014 at 9:18 AM, Madeleine Price Ball < notifications@github.com> wrote:

Thanks! I'm going to reject change for importing "twobit", although I know this method for imports makes the code a little less convenient to use independently on the command line.

To run this code on the command line, it should be run with the "-m" flag, for example: python -m file_process.utils.cgivar_to_vcf -i var-file.tsv.bz2 -r external_data_files/hg19.2bit

— Reply to this email directly or view it on GitHub https://github.com/madprime/Genevieve/pull/11#issuecomment-63476870.

[madprime]

No, it's fine! It's an advanced issue for code reusability that most people don't need to worry about when running simple scripts.

Can you update the PR by adding a commit that undoes this, and maybe add a comment somewhere in that file about running it with the -m flag.

I haven't tested it yet but, assuming it works, I'll go ahead and pull once that's fixed. :) On Nov 18, 2014 1:07 PM, "Abram Connelly" notifications@github.com wrote:

OK, sorry about that. This is my ignorance of how to use Python properly.

On Tue, Nov 18, 2014 at 9:18 AM, Madeleine Price Ball < notifications@github.com> wrote:

Thanks! I'm going to reject change for importing "twobit", although I know this method for imports makes the code a little less convenient to use independently on the command line.

To run this code on the command line, it should be run with the "-m" flag, for example: python -m file_process.utils.cgivar_to_vcf -i var-file.tsv.bz2 -r external_data_files/hg19.2bit

— Reply to this email directly or view it on GitHub https://github.com/madprime/Genevieve/pull/11#issuecomment-63476870.

— Reply to this email directly or view it on GitHub https://github.com/madprime/Genevieve/pull/11#issuecomment-63516457.