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如何在python中从多行文本的匹配行中获取内部文本?

python

MAPK · 技术社区 · 7 年前

我有一个文本文件叫做 test.txt . 从…起 ,我想抓住以 >lcl 然后提取后的值 locus 标记并在紧括号内 ] . 我想对以后的值做同样的事情 location . 我想要的结果如下所示。如何在python中实现这一点?

SS1G_08319  <504653..>506706
SS1G_12233  complement(<502136..>503461)
SS1G_02099  <2692251..>2693298
SS1G_05227  complement(<1032740..>1033620)

test.txt

>lcl|NW_001820825.1_gene_208 [locus_tag=SS1G_08319] [db_xref=GeneID:5486863] [partial=5',3'] [location=<504653..>506706] [gbkey=Gene]
ATGGGCAAAGCTTCTAGGAATAAGACGAAGCATCGCGCTGATCCTACCGCAAAAACTGTTAAGCCACCCA
CTGACCCAGAGCTTGCAGCAATTCGAGTTAACAAAATTCTGCCAATTCTCCAAGATTTACAAAGTGCAGA
CCAGTCAAAGAGATCAACTGCTGCAACTGCCATTGCGAACCTCGTTGACGATACAAAATGTCGAAAGTTA
TTCTTGAGAGAGCAAATTGTTCGTATTCTACTCGAACAAACCCTTACAGACTCAAGCATGGAAACTAGAA
>lcl|NW_001820817.1_gene_205 [locus_tag=SS1G_12233] [db_xref=GeneID:5483157] [partial=5',3'] [location=complement(<502136..>503461)] [gbkey=Gene]
ATGATCTGTAATACGCTCGGTGTTCCACCCTGCAACAGAATTCTTAAGAAATTCTCCGTTGGCGAGAGTC
GTCTCGAAATTCAAGACTCAGTACGAGGCAAAGATGTCTACATCATTCAATCGGGTGGAGGAAAGGCCAA
TGATCACTTCGTGGATCTTTGCATTATGATCTCCGCATGCAAAACTGGCTCTGCCAAGCGCGTCACTGTC
GTCCTTCCTTTGTTTCCTTATTCACGACAACCTGATCTGCCATACAACAAGATTGGCGCACCACTTGCCA
>lcl|NW_001820834.1_gene_1034 [locus_tag=SS1G_02099] [db_xref=GeneID:5493612] [partial=5',3'] [location=<2692251..>2693298] [gbkey=Gene]
ATGGCTTCTGTTTACAAGTCATTATCAAAGACCTCTGGTCATAAAGAAGAAACCCCGACTGGTGTCAAGA
AAAACAAGCAAAGAGTTTTGATCTTGTCTTCAAGAGGAATAACTTACAGGTATATAAATTTGTACCGATG
CGATGCAAAAAATCGCAGGAAAATGCTAACTCTACAACTTAGACATCGACATCTCCTCAATGACCTTGCG
TCCCTACTTCCCCACGGTAGGAAAGATGCGAAACTCGATACCAAGTCAAAGCTTTATCAATTGAATGAAT
>lcl|NW_001820830.1_gene_400 [locus_tag=SS1G_05227] [db_xref=GeneID:5489764] [partial=5',3'] [location=complement(<1032740..>1033620)] [gbkey=Gene]
ATGGCGGACGGATGTAAGTTAATTGATGTTCCTACTATTCCAGACTAATATTTGTTCTCGTCCCTACAAT
GCATTCGGAACGGATGGTACTCAGTTAACTTTGTAACTAATACAACGTCTAGTAAATGACCAAAGAACTG

我是python新手,因此我尝试提出如下内容:

results = []
f = open("test.txt", 'r')

while True:
    line = f.readline()
    if not line:
        break
    file_name = line.split("locus_tag")[-1].strip()
    f.readline()  # skip line 
    data_seq1 = f.readline().strip()
    f.readline()  
    data_seq2 = f.readline().strip()
    results.append((file_name, data_seq1))

2 回复 | 直到 7 年前

Chiheb Nexus 7 年前

我认为,解决你的问题最简单的方法就是使用 regex

import re

results = []
# Open the file in the 'read' mode
# with statement will take care to close the file
with open('YOUR_FILE_PATH', 'r') as f_file:
    # Read the entire file as a one string
    data = f_file.read()
    # Here we search for the string that begins with '>lcl'
    # and in which we find the [locus_tag=...] and [localtion=...]
    results = re.findall(r'>lcl.*\[locus_tag=(.*?)\].*\[location=(.*?)\]', data)

for locus, location in results:
    print(locus, location)

SS1G_08319 <504653..>506706
SS1G_12233 complement(<502136..>503461)
SS1G_02099 <2692251..>2693298
SS1G_05227 complement(<1032740..>1033620)

另一个变体使用 dict 因此,通过拆分行:

import re

results = {}
with open('fichier1', 'r') as f_file:
    # Here we split the file's lines into a list
    data = f_file.readlines()
    for line in data:
        # Here we search for the lines that begins by '>lcl'
        # and same as the first attempt
        results.update(re.findall(r'^>lcl.*\[locus_tag=(.*?)\].*\[location=(.*?)\]', line))

for locus, location in results.items():
    print(locus, location)

编辑:创建一个 DataFrame 并将其导出到 csv 文件:

import re
from pandas import DataFrame as df

results = {}
with open('fichier1', 'r') as f_file:
    data = f_file.readlines()
    for line in data:
        results.update(re.findall(
            r'^>lcl.*\[locus_tag=(.*?)\].*\[location=(.*?)\]',
            line
        ))

df_ = df(
    list(results.items()),
    index=range(1, len(results) + 1),
    columns=['locus', 'location']
)
print(df_)
df_.to_csv('results.csv', sep=',')

它将打印并创建一个名为 results.csv :

        locus                        location
1  SS1G_12233    complement(<502136..>503461)
2  SS1G_08319                <504653..>506706
3  SS1G_05227  complement(<1032740..>1033620)
4  SS1G_02099              <2692251..>2693298

Mad Physicist 7 年前

我想提出两种备选解决办法。一个是使用正则表达式提取行中的任何一组命名标记,另一个是完全滑稽的,但展示了一种不使用正则表达式的方法。

import re

def get_tags(filename, tags, prefix='>lcl'):
    tags = set(tags)
    pattern = re.compile(r'\[(.+?)=(.+?)\]')

    def parse_line(line):
        return {m.group(1): m.group(2) for m in pattern.finditer(line) if m.group(1) in tags}

    with open(filename) as f:
        return [parse_line(line) for line in f if prefix is None or line.startswith(prefix)]

此函数返回由您感兴趣的标记键入的字典列表。您可以这样使用它:

tags = ['locus_tag', 'location']
result = get_tags('test.txt', tags)

for line in get_tags('test.txt', tags):
    print(*(line[tag] for tag in tags))

这样做的好处是,您可以在以后选择时使用结果,并配置提取的标记。

无正则表达式解决方案

这个版本只是我写的东西,以表明这是可能的。请不要模拟它,因为代码是一个毫无意义的维护负担。

def get_tags2(filename, tags, prefix='>lcl'):
    tags = set(tags)

    def parse_line(line):
        items = [tag.split(']')[0].split('=') for tag in line.split('[')[1:]]
        return dict(tag for tag in items if tag[0] in tags)

    with open(filename) as f:
        return [parse_line(line) for line in data if prefix is None or line.startswith(prefix)]

此函数的行为与第一个函数类似,但相比之下,解析函数是一团乱麻。它的健壮性也要差得多,例如,因为它假设所有的方括号或多或少都是匹配的。

下面是一个IDEOne链接,展示了这两种方法: https://ideone.com/X2LKqL