Question

我是Python的新手，但我真的想在Linux服务器命令行上执行以下功能。当我执行以下脚本（test.py）时，请帮助弄清楚为什么没有打印出来？要执行，我键入python test.py。谢谢。

##!/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

您没有调用此功能。

尝试

if __name__ == '__main__':
    print "the result is: ", get_minimal_representation( pos = 1001, ref = "CTCC", alt = "CCC,C,CCCC")

位于文件底部。

应该是这样的：

##!/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

if __name__ == '__main__':
    print "the result is: ", get_minimal_representation( pos = 1001, ref = "CTCC", alt = "CCC,C,CCCC")

Answer 2

您对上一个print语句的缩进有问题。它应该在函数之外。

v2.0.0

在Linux上执行python函数

2 个答案: