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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 …