Question

我有一个包含3列的excel数据文件。我将数据复制到文本板上以使用.txt（制表符分隔）代替.xls以便于数据解析。我想根据数字区间的第一个数字和＆＃34;补码＆＃34;对所有行进行排序。如果它们出现在数字间隔之前。我的数据如下（一些行有空的第3列行1,2,3,5,7,8,9,15）：

81228..81500    Gene 22 
81500..81856    Gene 17 
complement(82256..84292)    Gene 75 
84307..85275    Gene 23  2.7.4.8
complement(97435..98067)    Gene 91 
complement(85325..86527)    Gene 34 3.5.1.32
86756..87025    Gene 36 
complement(92373..93341)    Gene 45 
88076..90292    Gene 34 
complement(90289..92415)    Gene 89  3.6.1.-
93492..94931    Gene 92  2.2.1.1
complement(97087..97347)    Gene 12  2.7.7.6
complement(94928..97060)    Gene 58  2.5.6.3, 3.1.8.2
79951..81162    Gene 3   1.7.1.2
complement(87022..87837)    Gene 77
10..1008    Gene 500    
100059..100178  Gene 501    
100470..104660  Gene 502     6.3.5.5
100715..100861  Gene 503    
101721..103604  Gene 504    
101782..103698  Gene 505     1.1.1.49
1018..1137  Gene 506    
10230..11636    Gene 507     6.3.1.2
102328..104049  Gene 508    
10321..12651    Gene 509     2.3.1.16, 2.3.1.9
103256..104290  Gene 510    
103607..104647  Gene 511    
103658..104662  Gene 512     4.1.3.16, 4.1.2.14
103732..106095  Gene 513    
104045..106027  Gene 514    
104057..104305  Gene 515    
10416..14087    Gene 516    
104237..105262  Gene 517     3.1.11.2

我的预期输出：

79951..81162    Gene 3   1.7.1.2
81228..81500    Gene 22 
81500..81856    Gene 17 
84307..85275    Gene 23  2.7.4.8
86756..87025    Gene 36 
88076..90292    Gene 34 
93492..94931    Gene 92  2.2.1.1
complement(82256..84292)    Gene 75 
complement(85325..86527)    Gene 34 3.5.1.32
complement(87022..87837)    Gene 77 
complement(90289..92415)    Gene 89  3.6.1.-
complement(92373..93341)    Gene 45 
complement(94928..97060)    Gene 58  2.5.6.3, 3.1.8.2
complement(97087..97347)    Gene 12  2.7.7.6
complement(97435..98067)    Gene 91

我尝试使用python如下：

import re
import sys
#import csv


pattern = '^complement\(\d+\.{2}\d+\)$'

#pattern = '^complement'

regexp = re.compile(pattern)

input_file = open('infile.txt', 'r')

output_file = open('outfile.txt','w')

for line in input_file:
    item = line[0]
    match = regexp.search(item)
    if match:
              output_file.writerow([line[0],\t,line1[1],\t, line[2]])
      #output_file.writerow(line[0])

#del line[0], line[1], line[2], item

del output_file

我不确定如何从这里开始。有人可以帮忙！

Answer 1

这应该可以正常工作，无需创建txt文件。只需导入csv：

In [23]: reader = csv.reader(open('tets.xls','rb'),delimiter='\t')

In [24]: f = list(reader)

In [25]: f #original file
Out[25]: 
[['81228..81500', 'Gene', '22 '],
 ['81500..81856', 'Gene', '17 '],
 ['complement(82256..84292)', 'Gene', '75 '],
 ['84307..85275', 'Genne', '23', '2.7.4.8'],
 ['complement(97435..98067)', 'Gene', '91 '],
 ['complement(85325..86527)', 'Gene', '34', '3.5.1.32'],
 ['86756..87025', 'Gene', '36 '],
 ['complement(92373..93341)', 'Gene', '45 '],
 ['88076..90292', 'Gene', '34 '],
 ['complement(90289..92415)', 'Gene 89', '3.6.1.-'],
 ['93492..94931', 'Genne', '92', '2.2.1.1'],
 ['complement(97087..97347)', 'Gene', '12', '2.7.7.6'],
 ['complement(94928..97060)', 'Gene', '58', '2.5.6.3, 3.1.8.2'],
 ['79951..81162', 'Gene', '3', '1.7.1.2'],
 ['complement(87022..87837)', 'Gene', '77 ']]

In [26]: f.sort(key=lambda x: x[0])

In [27]: f #after sorting
Out[27]: 
[['79951..81162', 'Gene', '3', '1.7.1.2'],
 ['81228..81500', 'Gene', '22 '],
 ['81500..81856', 'Gene', '17 '],
 ['84307..85275', 'Genne', '23', '2.7.4.8'],
 ['86756..87025', 'Gene', '36 '],
 ['88076..90292', 'Gene', '34 '],
 ['93492..94931', 'Genne', '92', '2.2.1.1'],
 ['complement(82256..84292)', 'Gene', '75 '],
 ['complement(85325..86527)', 'Gene', '34', '3.5.1.32'],
 ['complement(87022..87837)', 'Gene', '77 '],
 ['complement(90289..92415)', 'Gene 89', '3.6.1.-'],
 ['complement(92373..93341)', 'Gene', '45 '],
 ['complement(94928..97060)', 'Gene', '58', '2.5.6.3, 3.1.8.2'],
 ['complement(97087..97347)', 'Gene', '12', '2.7.7.

Answer 2

这样的工作：

txt='''\
81228..81500    Gene 22 
81500..81856    Gene 17 
complement(82256..84292)    Gene 75 
84307..85275    Gene 23  2.7.4.8
complement(97435..98067)    Gene 91 
complement(85325..86527)    Gene 34 3.5.1.32
86756..87025    Gene 36 
complement(92373..93341)    Gene 45 
88076..90292    Gene 34 
complement(90289..92415)    Gene 89  3.6.1.-
93492..94931    Gene 92  2.2.1.1
complement(97087..97347)    Gene 12  2.7.7.6
complement(94928..97060)    Gene 58  2.5.6.3, 3.1.8.2
79951..81162    Gene 3   1.7.1.2
complement(87022..87837)    Gene 77 '''

import re

lines=txt.splitlines()

print('\n'.join(sorted(lines, key=lambda s: re.search(r'^((?:\d+)|(?:complement\(\d+))', s).group(1))))

或者，如果它真的是分隔符，你可以松开正则表达式并执行：

txt='''\
81228..81500\tGene 22 
81500..81856\tGene 17 
complement(82256..84292)\tGene 75 
84307..85275\tGene 23\t2.7.4.8
complement(97435..98067)\tGene 91 
complement(85325..86527)\tGene 34\t3.5.1.32
86756..87025\tGene 36 
complement(92373..93341)\tGene 45 
88076..90292\tGene 34 
complement(90289..92415)\tGene 89\t3.6.1.-
93492..94931\tGene 92\t2.2.1.1
complement(97087..97347)\tGene 12\t2.7.7.6
complement(94928..97060)\tGene 58\t2.5.6.3, 3.1.8.2
79951..81162\tGene 3\t1.7.1.2
complement(87022..87837)\tGene 77 '''

lines=txt.splitlines()
print('\n'.join(sorted(lines, key=lambda s: s.split('\t',1)[0])))

但是因为你要对第一个元素进行排序，所以根本不需要拆分它：

print('\n'.join(sorted(lines)))

以上任何情况，打印：

79951..81162    Gene 3   1.7.1.2
81228..81500    Gene 22 
81500..81856    Gene 17 
84307..85275    Gene 23  2.7.4.8
86756..87025    Gene 36 
88076..90292    Gene 34 
93492..94931    Gene 92  2.2.1.1
complement(82256..84292)    Gene 75 
complement(85325..86527)    Gene 34 3.5.1.32
complement(87022..87837)    Gene 77 
complement(90289..92415)    Gene 89  3.6.1.-
complement(92373..93341)    Gene 45 
complement(94928..97060)    Gene 58  2.5.6.3, 3.1.8.2
complement(97087..97347)    Gene 12  2.7.7.6
complement(97435..98067)    Gene 91

您的一条评论指出，您希望计算数字的大小，而不仅仅是字典顺序。

您可以使用natural sort order来实现此目标：

import re

data='''\
81728..81500    Gene 22 
81500..81856    Gene 17 
complement(82256..84292)    Gene 75 
812..815    Gene 3 num
complement(822..842)    Gene compliment 3 num75  
811..815    Gene 3 num
'''

def alpha_num_sort(li): 
    def convert(s):
        return int(s) if s.isdigit() else s

    def key_func(key):
        return tuple(convert(c) for c in re.split('([0-9]+)', key))

    return sorted(li, key = key_func)

print '\n'.join(alpha_num_sort(data.splitlines()))

打印：

811..815    Gene 3 num
812..815    Gene 3 num
81500..81856    Gene 17 
81728..81500    Gene 22 
complement(822..842)    Gene compliment 3 num75  
complement(82256..84292)    Gene 75

Answer 3

我的两分钱：

import csv
# get a list of lines in the file
with open('in.txt') as in_file:
    reader = csv.reader(in_file, delimiter = '\t')
    lines = [line for line in reader]

lines.sort()
# generator to produce the desired output
lines = ('\n'.join(('\t'.join(line) for line in lines)))

with open('out.txt', 'w') as out_file:
    out_file.write(lines)

使用键功能提取相关的排序参数 - 将上面的lines.sort()替换为：

def key_func(line):
    '''extract sorting parameters

    line --> list
    returns tuple
    '''
    key = line[0]
    complement = 'complement' in key
    # extract the interval
    key = key[key.find('(') + 1 : key.find(')')]
    # turn the interval into a 2 integer list
    key = map(int, key.split('..'))
    # return a tuple to sort on
    return complement, key


lines.sort(key = key_func)

key_func应返回您希望数据排序的值元组（按重要性排序）。如果您的实际数据与您发布的数据完全匹配，则会根据您的要求进行排序如果您的实际数据与发布的数据不完全匹配，则需要修改key_func。

根据行的内容排序所有行

3 个答案: