Bugfixes

[dampierch]

Intro

Thank you for sharing your code.
I am using it to analyze some of my own data.
In particular, I am using the qtl scripts.
I encountered a few bugs while running eqtl_prepare_expression.py and fixed them in a local branch.
I thought I should share them with you in case the fixes are helpful for others using your code.

Fixes

1. Added pyqtl to Dockerfile per Issue #61
2. Added some functions to make numeric indices in the sample_participant_lookup run smoothly.
3. Added an option to ignore ENSEMBL gene version numbers in the merging part of the BED preparation.

• One should never have different ENSEMBL gene version numbers if the gene model is the same in all processing steps. Unfortunately, sometimes the gene model used in a particular step is unknown due to insufficient documentation from a collaborator or commercial service.

[ActioTom]

Also, I believe the --convert-tpm option is broken because of a bug around line 100 in eqtl_prepare_expression.py:

    if args.convert_tpm:
        print('  * Converting to TPM', flush=True)
        tpm_df = tpm_df / tpm_df.sum(0) * 1e6

This fails because the first column of tpm_df is Name and contains the gene ids rather than numeric data.