def genenum_to_geneabbr(num, virus):
'''
Attempt to lookup gene abbreviation from its position
>>> for i in range( 1, 9 ):
... genenum_to_geneabbr( i, 'H3N2' )
'PB2'
'PB1'
'PA'
'HA'
'NP'
'NA'
'MP'
'NS'
'''
num = int(num)
genes = GENES.get(virus, False)
if genes:
if len(genes) > num and num >= 0:
return genes[num]
else:
raise ValueError("%s is out of bounds" % num)
else:
raise ValueError("%s has no associated genes" % virus)
def genenum_to_geneabbr( num, virus ):
'''
Attempt to lookup gene abbreviation from its position
>>> for i in range( 1, 9 ):
... genenum_to_geneabbr( i, 'H3N2' )
'PB2'
'PB1'
'PA'
'HA'
'NP'
'NA'
'MP'
'NS'
'''
num = int( num )
genes = GENES.get( virus, False )
if genes:
if len( genes ) > num and num >= 0:
return genes[num]
else:
raise ValueError( "%s is out of bounds" % num )
else:
raise ValueError( "%s has no associated genes" % virus )
def geneabbr_to_genenum(abbr, virus):
'''
Attempt to lookup gene position number from gene abbreviation
>>> g = ['PB2', 'PB1', 'PA', 'HA', 'NP', 'NA', 'MP', 'NS']
>>> for gene in g:
... geneabbr_to_genenum( gene, 'H3N2' )
1
2
3
4
5
6
7
8
'''
genes = GENES.get(virus, False)
# Raise ValueError if virus not found or abbr not found
if genes:
return genes.index(abbr)
raise ValueError("%s has no associated genes" % virus)
def geneabbr_to_genenum( abbr, virus ):
'''
Attempt to lookup gene position number from gene abbreviation
>>> g = ['PB2', 'PB1', 'PA', 'HA', 'NP', 'NA', 'MP', 'NS']
>>> for gene in g:
... geneabbr_to_genenum( gene, 'H3N2' )
1
2
3
4
5
6
7
8
'''
genes = GENES.get( virus, False )
# Raise ValueError if virus not found or abbr not found
if genes:
return genes.index( abbr )
raise ValueError( "%s has no associated genes" % virus )
