在Linux上执行python函数

Question

我是Python新手，但真的很想在Linux服务器命令行上执行以下功能。请帮忙找出当我执行下面的脚本（test.py）时为什么没有打印出来？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

你有一个问题，最后一个print语句的缩进。它应该在功能之外。

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 2

您没有调用该函数。

尝试

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

在你的文件的底部。

它应该是这样的：

##!/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")