我有多个fasta文件,有多个具有相同长度序列的个体。我想做的是沿着fasta文件创建一个物种序列的连接。在
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,我连接空白('-'),长度与其他序列相同。(请参见文件对齐)
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
您的concat应该是defaultdict,或者通过创建某种风格的iterable来处理缺少的键,可能是str,或者在本例中最好是一个list。然后可以使用新值扩展iterable:
但是基于字符串的方法效率非常低,因为每次连接都必须从头开始重建字符串。如果你需要一个字符串,你总是可以把它列为一个列表。一旦你完成构建,就加入它。在
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