Question

我正在寻找 python 解决方案，根据与列表的匹配，将多个序列从FASTA文件提取到多个文件中标题ID在单独的文件中。

这是Extract sequences from a FASTA file based on entries in a separate file和https://www.biostars.org/p/2822/上发布的问题的稍微复杂版本，只为所有匹配输出单个文件。

我是python的新手，我正试图找到一种方法：

获取包含将在fasta标题中的字符串的文件
将所有与字符串匹配的记录写入单独的fasta文件

header_ID_strings文件如下所示：

CAP357_2030_09WPI，CAP357_2040_11WPI，CAP357_2050_13WPI等......

我的fasta文件示例如下：

＆GT; CAP357_2030_009wpi_v1v3_1_056_00002_000.4
GTAAAATTAACCCCACTCTGTGTCACTCTAAATTGTACAACTGCAAAGGG
＆GT; CAP357_2040_011wpi_v1v3_1_008_00006_001.1
GTAAAATTAACCCCACTCTGTGTCACTCTAAATTGTACAACTGCAAAGGGT
＆GT; CAP357_2040_011wpi_v1v3_1_030_00002_000.4
GTAAAATTAACCCCACTCTGTGTCACTCTAAATTGTACAACTGCAAAGGGT
＆GT; CAP357_2040_011wpi_v1v3_1_004_00001_000.2
GTAAAATTAACCCCACTCTGTGTCACTCTAAATTGTACAACTGCAAAGGGT
＆GT; CAP357_2050_013wpi_v1v3_1_047_00002_000.4
GTAAAATTAACCCCACTCTGTGTCACTCTAAATTGTACAACTGCAAAGGGT

预期产出

file1：CAP357_2030_009wpi_v1v3.fasta
＆GT; CAP357_2030_009wpi_v1v3_1_056_00002_000.4
GTAAAATTAACCCCACTCTGTGTCACTCTAAATTGTACAACTGCAAAGGG

file2：CAP357_2040_011wpi_v1v3.fasta
＆GT; CAP357_2040_011wpi_v1v3_1_008_00006_001.1
GTAAAATTAACCCCACTCTGTGTCACTCTAAATTGTACAACTGCAAAGGGT
＆GT; CAP357_2040_011wpi_v1v3_1_030_00002_000.4
GTAAAATTAACCCCACTCTGTGTCACTCTAAATTGTACAACTGCAAAGGGT
＆GT; CAP357_2040_011wpi_v1v3_1_004_00001_000.2
GTAAAATTAACCCCACTCTGTGTCACTCTAAATTGTACAACTGCAAAGGGT
等...

此代码来自上述链接，但我希望：
*匹配写入单独的outfiles
*我不必单独指定每个outfile，如果可能的话（我将有多达30个outfiles）

#!/usr/bin/env python

import sys
from Bio import SeqIO

input_file = sys.argv[1]
id_file = sys.argv[2]
output_file = sys.argv[3]

wanted = set(line.rstrip("\n").split(None,1)[0] for line in open(id_file))
print "Found %i unique identifiers in %s" % (len(wanted), id_file)

index = SeqIO.index(input_file, "fasta")
records = (index[r] for r in wanted)
count = SeqIO.write(records, output_file, "fasta")
assert count == len(wanted)

print "Saved %i records from %s to %s" % (count, input_file, output_file)

到目前为止，这是我提出的（下面的脚本），但不知道如何手动指定所有的outfiles和变量（我这里只包括三个）

from Bio import SeqIO
import pandas as pd
import sys

input_file = sys.argv[1]
id_file = sys.argv[2]
output_file2020 = sys.argv[3]
output_file2030 = sys.argv[4]
output_file2040 = sys.argv[5]

colnames = ["2020", "2030", "2040"]
headerlist = pd.read_csv(id_file, names = colnames, header = None)
infile = list(SeqIO.parse(input_file, "fasta"))
2020_seq = tuple(headerlist.2020)
2030_seq = tuple(headerlist.2030)
2040_seq = tuple(headerlist.2040)

count2020 = 0
count2030 = 0
count2040 = 0
for record in infile:
    if record.id in 2020_seq:
        SeqIO.write([record], output_file2020, "fasta")
        countSU += 1
    elif record.id in PI_seq:
        SeqIO.write([record], output_file2030, "fasta")
        countPI += 1
    elif record.id in REC_seq:
        SeqIO.write([record], output_file2040, "fasta")
        countREC += 1
    else:
        print("no matches found")

print("number of SU is", count2020)
print("number of PI is", count2030)
print("number of REC is", count2040)

Answer 1

一些简短的建议：

如果所有标题都遵循相同的模式，那么您可以提取唯一元素：

record.description.split("_")[1]

（从“CAP357_2040_011wpi_v1v3_1_008_00006_001.1”中收取“2040”）

如果你使用dict，你可以收集记录集合：

collected = {}
for record in records:
    descr = record.description.split("_")[1]
    try:
        collected[descr].append(record)
    except KeyError:
        collected[descr] = [record ,]

然后你可以把每个集合写成一个新文件：

file_name = "outfile%s" 
for (descr, records) in collected.items():   # iteritems in python2
    with open(os.path.join(file_path, file_name % descr), 'w') as f:
        SeqIO.write(records, f, 'fasta')

Answer 2

为了完整起见，这里是最后的＆＃39;脚本：

#!/usr/bin/env python
# a script to extract fasta records from a fasta file to multiple separate fasta files based on a particular ID (time point) in a particular field, for a given delimiter
# to run, navigate to file location with command prompt and enter: python split_fasta_by_collections.py infile.fasta
from Bio import SeqIO
import os
import sys

records = SeqIO.parse(sys.argv[1], "fasta")
collected = {}
for record in records:
    descr = record.description.split("_")[1] # "_" sets the delimeter, "1" sets the field where counting starts at 0 for the first field
    try:
    collected[descr].append(record)
    except KeyError:
    collected[descr] = [record ,]

file_name = "outfile%s.fasta" 
file_path = os.getcwd() #sets the output file path to your current working directory

for (descr, records) in collected.items():  
    with open(os.path.join(file_path, file_name % descr), 'w') as f:
    SeqIO.write(records, f, 'fasta')

将序列从FASTA文件提取到多个文件，文件基于另一个文件中的header_IDs

我是python的新手，我正试图找到一种方法：

header_ID_strings文件如下所示：

我的fasta文件示例如下：

预期产出

2 个答案: