I'm new to Python but would really like to execute the following function on Linux server command line. Please help to figure out why nothing is being printed when I execute the following script (test.py)? To execute I typed
python test.py
##!/usr/bin/python
def get_minimal_representation(pos, ref, alt):
"""
Get the minimal representation of a variant, based on the ref + alt alleles in a VCF
This is used to make sure that multiallelic variants in different datasets,
with different combinations of alternate alleles, can always be matched directly.
Note that chromosome is ignored here - in xbrowse, we'll probably be dealing with 1D coordinates
Args:
pos (int): genomic position in a chromosome (1-based)
ref (str): ref allele string
alt (str): alt allele string
Returns:
tuple: (pos, ref, alt) of remapped coordinate
"""
pos = int(pos)
# If it's a simple SNV, don't remap anything
if len(ref) == 1 and len(alt) == 1:
return pos, ref, alt
else:
# strip off identical suffixes
while(alt[-1] == ref[-1] and min(len(alt),len(ref)) > 1):
alt = alt[:-1]
ref = ref[:-1]
# strip off identical prefixes and increment position
while(alt[0] == ref[0] and min(len(alt),len(ref)) > 1):
alt = alt[1:]
print "Alt: ", alt
ref = ref[1:]
print "Ref: ", ref
pos += 1
print "Pos: ", pos
return pos, ref, alt
print "the result is: ", get_minimal_representation( pos = 1001, ref = "CTCC", alt = "CCC,C,CCCC")
You had a problem with the indentation of the last print statement. It should be outside the function.
def get_minimal_representation(pos, ref, alt):
"""
Get the minimal representation of a variant, based on the ref + alt alleles in a VCF
This is used to make sure that multiallelic variants in different datasets,
with different combinations of alternate alleles, can always be matched directly.
Note that chromosome is ignored here - in xbrowse, we'll probably be dealing with 1D coordinates
Args:
pos (int): genomic position in a chromosome (1-based)
ref (str): ref allele string
alt (str): alt allele string
Returns:
tuple: (pos, ref, alt) of remapped coordinate
"""
pos = int(pos)
# If it's a simple SNV, don't remap anything
if len(ref) == 1 and len(alt) == 1:
return pos, ref, alt
else:
# strip off identical suffixes
while(alt[-1] == ref[-1] and min(len(alt),len(ref)) > 1):
alt = alt[:-1]
ref = ref[:-1]
# strip off identical prefixes and increment position
while(alt[0] == ref[0] and min(len(alt),len(ref)) > 1):
alt = alt[1:]
print "Alt: ", alt
ref = ref[1:]
print "Ref: ", ref
pos += 1
print "Pos: ", pos
return pos, ref, alt
print "the result is: ", get_minimal_representation( pos = 1001, ref = "CTCC", alt = "CCC,C,CCCC")