连接多个.fasta文件

Question

我正在尝试将数百个.fasta文件连接成一个包含所有序列的单个大型fasta文件.我还没有找到在论坛中完成此任务的具体方法.我确实从http://zientzilaria.heroku.com/blog/2007/10/29/merging-single-or-multiple-sequence-fasta-files中找到了这个代码,我已经调整了一下.

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

以下是连接.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:

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？谢谢!

Answer 1

我认为用python这项工作是矫枉过正的.在命令行上,使用.fasta或.fa扩展连接单个/多个fasta文件的快速方法是:

cat *.fa* > newfile.txt