循环连接fasta文件

Question

我有多个 fasta 文件，其中包含多个具有相同长度序列的个体。我想要做的是沿着 fasta 文件创建一个物种序列的串联。

在循环中：如果在下一个文件中找到一个物种，我连接它的序列，如果没有，我连接间隙（'-'），与其余序列的长度相同。（查看文件是否对齐）

species_list = []
files = [file for file in glob.glob('~/*.fa')]
for aln in files:
    with open (aln, 'rU') as multispecies:
        sequences = SeqIO.parse(multispecies, 'fasta')
        for species in sequences:
            species_list.append(species.id)

species_list=list(set(species_list))
#print(species_list)

concat = {}
for aln in files:
    #print(aln)
    dict = {}
    with open (aln, 'rU') as multispecies:
        sequences = SeqIO.parse(multispecies, 'fasta')
        names = []
        for fasta in sequences:
            names.append(fasta.id)
            dict[fasta.id] = fasta.seq
        count_species = 0
        for i in species_list:
            if i in names:
                count_species = count_species + 1
                print('>' + i + '\n' + dict[i])
                gap = int(len(dict[i]))
                concat[i] += dict[i]    #I cannot find a way to concatenate here
            else:
                print('>' + i + '\n' + '-'*gap)
                concat[i] += '-'*gap #I cannot find a way to concatenate here

Answer 1

您的 concat 应该是 defaultdict 或通过创建某种可迭代风格来处理丢失的键，在这种情况下可能是 str 或最好是列表。然后你可以用新值扩展迭代器：

# list-based
concat.setdefault(i, []).extend(dict[i]) # should work if you keep the data in a list
# string-based
concat[i] = concat.get(i, '') + dict[i]

虽然基于字符串的方法效率极低，因为您必须在每次连接时从头开始重建字符串。如果你需要一个字符串，你总是可以把它做成一个列表然后“”。一旦你完成构建它就加入它。

循环连接fasta文件

Concatenate fasta files in loop

python

biopython