Question

我使用biopython从我的核苷酸比对计算位置特异性评分矩阵（PSSM）。 http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc255 所以，我的script.py是：

from Bio import AlignIO
from Bio.Align import AlignInfo

alignment = AlignIO.read("alignment_1.fasta", "fasta")
summary_align = AlignInfo.SummaryInfo(alignment)
consensus = summary_align.dumb_consensus()
my_pssm = summary_align.pos_specific_score_matrix(consensus, chars_to_ignore = ['N', '-'])

我想知道是否可以将my_pssm对象写入脚本内的文件？我在文档中找不到任何解决方案。现在我只能这样做：

python script.py > text.txt

但它并不适合我（我想用它作为批处理脚本）。

Answer 1

您可以在脚本末尾添加print my_pssm然后按照您的意愿python script.py > text.txt

对于不同的序列，您可以这样做：

for fasta in files:
    alignment = AlignIO.read(fasta, "fasta")
    summary_align = AlignInfo.SummaryInfo(alignment)
    consensus = summary_align.dumb_consensus()
    my_pssm = summary_align.pos_specific_score_matrix(consensus, chars_to_ignore = ['N', '-'])
    file_pssm = fasta+"pssm"
    with open(file_pssm) as f:
         f.write(my_pssm)

如何将位置特定的分数矩阵biopython对象写入文件？

1 个答案: