List excluded SNPs instead of halting error

[frewmack]

At some point in the analysis, LocusFocus compares a user-provided list of SNPs to a list of valid IDs. If any of the IDs do not match, the analysis ends and an error is returned, requiring the user to remove that singular snip and try again. This process takes a long time, especially given that the number of invalid SNPs can be large (>100).

Instead of ending in error, each individual excluded snip should be provided back to the user, and the analysis should continue without the excluded SNPs. An error should be displayed in tandem, listing the excluded SNPs. This will save heaps of time for the user.

[frewmack]

LocusFocus/app.py

Lines 957 to 967 in f2e2513

	rsid_snps = [ x for x in snp_list if x.startswith('rs') ]
	b37_snps = [ x for x in snp_list if x.endswith('_b37') ]
	b38_snps = [ x for x in snp_list if x.endswith('_b38') ]
	if len(rsid_snps) > 0 and (len(b37_snps)>0 or len(b38_snps) > 0):
	raise InvalidUsage("There is a mix of rsid and other variant id formats; please use a consistent format")
	elif len(rsid_snps) > 0:
	rsids = True
	elif len(b37_snps) or len(b38_snps) > 0:
	rsids = False
	else:
	raise InvalidUsage('Variant naming format not supported; ensure all are rs ID\'s are formatted as chrom_pos_ref_alt_b37 eg. 1_205720483_G_A_b37')