我正在尝试将数百个 .fasta 文件连接成一个包含所有序列的大型 fasta 文件。我还没有在论坛中找到实现此目的的特定方法。我确实从http://zientzilaria.heroku.com/blog/2007/10/29/merging-single-or-multiple-sequence-fasta-files中看到了这段代码,我对它做了一些调整。
Fasta.py 包含以下代码:
class fasta:
def __init__(self, name, sequence):
self.name = name
self.sequence = sequence
def read_fasta(file):
items = []
index = 0
for line in file:
if line.startswith(">"):
if index >= 1:
items.append(aninstance)
index+=1
name = line[:-1]
seq = ''
aninstance = fasta(name, seq)
else:
seq += line[:-1]
aninstance = fasta(name, seq)
items.append(aninstance)
return items
这是连接 .fasta 文件的改编脚本:
import sys
import glob
import fasta
#obtain directory containing single fasta files for query
filepattern = input('Filename pattern to match: ')
#obtain output directory
outfile = input('Filename of output file: ')
#create new output file
output = open(outfile, 'w')
#initialize lists
names = []
seqs = []
#glob.glob returns a list of files that match the pattern
for file in glob.glob(filepattern):
print ("file: " + file)
#we read the contents and an instance of the class is returned
contents = fasta.read_fasta(open(file).readlines())
#a file can contain more than one sequence so we read them in a loop
for item in contents:
names.append(item.name)
seqs.append(item.sequence)
#we print the output
for i in range(len(names)):
output.write(names[i] + '\n' + seqs[i] + '\n\n')
output.close()
print("done")
它能够读取 fasta 文件,但新创建的输出文件不包含序列。我收到的错误是由于 fasta.py,这超出了我的能力范围:
Traceback (most recent call last):
File "C:\Python32\myfiles\test\3\Fasta_Concatenate.py", line 28, in <module>
contents = fasta.read_fasta(open(file).readlines())
File "C:\Python32\lib\fasta.py", line 18, in read_fasta
seq += line[:-1]
UnboundLocalError: local variable 'seq' referenced before assignment
有什么建议么?谢谢!