executing python function on Linux

Question

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

. Thank you.

##!/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")

Answer 1

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")

executing python function on Linux

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