Python Question
executing python function on Linux
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")
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Answer Source
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")
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