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Fix bug #19

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Fix bug #19

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67ccd21
minPathogenicScore could be equal
icebert Apr 17, 2019
ed33c67
fix HGVSc override would result in wrong genomic ref and alt for minu…
icebert Apr 17, 2019
7e1e2b5
Merge branch 'master' into fix_bug
icebert Aug 16, 2019
133ab98
Fix coordinate in getMacClinVarTSV
icebert Aug 16, 2019
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33 changes: 25 additions & 8 deletions charger/charger.py
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Original file line number Diff line number Diff line change
Expand Up @@ -903,26 +903,43 @@ def getMacClinVarTSV( self , tsvfile ):
for line in macFile:
fields = ( line.rstrip( ) ).split( "\t" )
[ description , status ] = self.parseMacPathogenicity( header, fields ) # no need to specify which fields here anymore; parseMacPathogenicity now knows which specific columns to look for
pos = int(fields[header.index("pos")])
ref = fields[header.index("ref")]
alt = fields[header.index("alt")]
if len(ref) == 1 and len(alt) > 1: # insertion
ref = '-'
alt = alt[1:]
start = pos
stop = pos + 1
elif len(ref) > 1 and len(alt) == 1: # deletion
ref = ref[1:]
alt = '-'
start = pos + 1
stop = pos + len(ref)
else: # snv
start = pos
stop = pos
if len(header) > 27: # if yes, file is in the new format
var = clinvarvariant( chromosome = fields[header.index("chrom")] , \
start = fields[header.index("pos")] , \
reference = fields[header.index("ref")] , \
alternate = fields[header.index("alt")] , \
start = start , \
stop = stop , \
reference = ref , \
alternate = alt , \
uid = fields[header.index("variation_id")], \
gene = fields[header.index("symbol")] , \
clinical = { "description" : description , "review_status" : status } , \
trait = { fields[header.index("xrefs")] : fields[header.index("all_traits")] } )
else: # file in the old format
var = clinvarvariant( chromosome = fields[header.index("chrom")] , \
start = fields[header.index("pos")] , \
reference = fields[header.index("ref")] , \
alternate = fields[header.index("alt")] , \
start = start , \
stop = stop , \
reference = ref , \
alternate = alt , \
uid = fields[header.index("measureset_id")], \
gene = fields[header.index("symbol")] , \
clinical = { "description" : description , "review_status" : status } , \
trait = { fields[-1] : fields[header.index("all_traits")] } )
var.setStopFromReferenceAndAlternate( )
var.splitHGVSc( fields[header.index("hgvs_c")] , override = True )
var.splitHGVSc( fields[header.index("hgvs_c")] )
var.splitHGVSp( fields[header.index("hgvs_p")] )
#var.printVariant( "," )
#print( var.proteogenomicVar( ) )
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