Gnomad files expected to be in a specific folder structure

[IsmailM]

phenogenon/lib/gnomad_utils.py

Lines 60 to 63 in 9b0f832

	if mode == 'exome':
	file = os.path.join(path_to_gnomad,'vcf','exomes','gnomad.exomes.r2.0.1.sites.vcf.gz')
	elif mode == 'genome':
	file = os.path.join(path_to_gnomad,'vcf','genomes','gnomad.genomes.r2.0.1.sites.'+chrom+'.vcf.gz')

Better to allow users to provide an set (i.e. an array) of full paths to VCF files (as they might have downloaded the Chr vcfs separately).

[IsmailM]

Further to #5

Add support for remote gnomad search: i.e. something like:

tabix https://storage.googleapis.com/gnomad-public/release/2.1/vcf/exomes/gnomad.exomes.r2.1.sites.chrX.vcf.bgz  X

In theory - that would simply be setting the default value of the array of files to an array of URLs and it should "just work" 🤞

[logust79]

This sounds a legit option. Shall we add an option to allow users to choose whether to do it locally, or cloudly?

[IsmailM]

• maybe make the remote option as the default? (and allow people to provide local files instead)
• btw, I tried the remote URL with pysam (which is what you currently use) and it works perfectly - it downloads a small tbi file into the PWD, but that should be fine.

tbx = pysam.TabixFile('https://storage.googleapis.com/gnomad-public/release/2.1/vcf/exomes/gnomad.exomes.r2.1.sites.chrX.vcf.bgz')
for row in tbx.fetch("X"):
      print (str(row))