文件:
>1
ATTTTttttGGGG
ccCgCgGAgggGGT
gggggttttTTTTTTTTT
>2
ATcggGGGGGGA
>3
ATCGGGGGGATTT
gggggttAGTAttt
我正在构建一个读取具有这种格式的文件的函数。 该格式嵌入了多个文件,这些文件由“>”+名称分隔(例如“>1”、“>2”)
我正在尝试获取“>”行两侧的文本行,并将它们编译为每个部分的一个字符串
所以这看起来像
name_list = ['>1','>2','>3']
sequence_list = ['ATTTTttttGGGGccCgCgGAgggGGTgggggttttTTTTTTTTT','ATcggGGGGGGA','ATCGGGGGGATTTgggggttAGTAttt']
import os
import re
# Open File
in_file=open(FASTA,'r')
dir,file=os.path.split(FASTA)
temp = os.path.join(dir,output)
out_file=open(temp,'w')
# Generating lines
lines = []
name_list = []
seq_list = []
for line in in_file:
line = line.strip()
lines.append(line)
in_file.close()
indx = range(0,len(lines))
# Organizing the elements
for line in lines:
for i in line:
if i == '>':
name_list.append(line)
else:
break
我不知道如何处理 else: 语句 我尝试使用 range(0,len(lines)) 创建索引 所以也许我可以在找到“>”的地方做一些事情,并编译以下索引的所有行,直到找到下一个“>”并将它们添加到名为 seq_list 的列表中
任何帮助将不胜感激
最佳答案
您应该看看Biopython它有一个 FASTA 解析器,但这里有一个使用标准库的示例:
import re
with open('filename') as f:
print [i.replace('\n','') for i in re.split(r'\>\d+',f.read()) if i]
输出:
['ATTTTttttGGGGccCgCgGAgggGGTgggggttttTTTTTTTTT',
'ATcggGGGGGGA',
'ATCGGGGGGATTTgggggttAGTAttt']
<小时/>
使用Biopython
[sudo pip install biopython
]:
from Bio import SeqIO
with open("example.fasta", "rU") as handle:
print list(SeqIO.parse(handle, "fasta"))
输出:
[SeqRecord(seq=Seq('ATTTTttttGGGGccCgCgGAgggGGTgggggttttTTTTTTTTT', SingleLetterAlphabet()), id='1', name='1', description='1', dbxrefs=[]),
SeqRecord(seq=Seq('ATcggGGGGGGA', SingleLetterAlphabet()), id='2', name='2', description='2', dbxrefs=[]),
SeqRecord(seq=Seq('ATCGGGGGGATTTgggggttAGTAttt', SingleLetterAlphabet()), id='3', name='3', description='3', dbxrefs=[])]
关于python - 编译文件中由特定元素分隔的行。 Python,我们在Stack Overflow上找到一个类似的问题: https://stackoverflow.com/questions/14841428/