生物Python:从 Blast 输出文件中提取序列 ID
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18-09-2019 - |
题
我有一个 XML 格式的 BLAST 输出文件。它有 22 个查询序列,每个序列报告 50 个命中。我想提取所有 50x22 的点击。这是我当前拥有的代码,但它只从第一个查询中提取 50 个命中。
from Bio.Blast import NCBIXM
blast_records = NCBIXML.parse(result_handle)
blast_record = blast_records.next()
save_file = open("/Users/jonbra/Desktop/my_fasta_seq.fasta", 'w')
for alignment in blast_record.alignments:
for hsp in alignment.hsps:
save_file.write('>%s\n' % (alignment.title,))
save_file.close()
有人对提取所有点击有什么建议吗?我想我必须使用比对齐以外的东西。希望这一点是清楚的。谢谢!
乔恩
解决方案
这应该得到所有记录。与原作相比,新颖之处在于
for blast_record in blast_records
这是一个Python习惯用法,用于迭代“类似列表”对象中的项目,例如blast_records(检查 CBIXML 模块文档 表明 parse() 确实返回一个迭代器)
from Bio.Blast import NCBIXM
blast_records = NCBIXML.parse(result_handle)
save_file = open("/Users/jonbra/Desktop/my_fasta_seq.fasta", 'w')
for blast_record in blast_records:
for alignment in blast_record.alignments:
for hsp in alignment.hsps:
save_file.write('>%s\n' % (alignment.title,))
#here possibly to output something to file, between each blast_record
save_file.close()
其他提示
我使用此代码为提取所有结果
from Bio.Blast import NCBIXML
for record in NCBIXML.parse(open("rpoD.xml")) :
print "QUERY: %s" % record.query
for align in record.alignments :
print " MATCH: %s..." % align.title[:60]
for hsp in align.hsps :
print " HSP, e=%f, from position %i to %i" \
% (hsp.expect, hsp.query_start, hsp.query_end)
if hsp.align_length < 60 :
print " Query: %s" % hsp.query
print " Match: %s" % hsp.match
print " Sbjct: %s" % hsp.sbjct
else :
print " Query: %s..." % hsp.query[:57]
print " Match: %s..." % hsp.match[:57]
print " Sbjct: %s..." % hsp.sbjct[:57]
print "Done"
或更少的细节
from Bio.Blast import NCBIXML
for record in NCBIXML.parse(open("NC_003197.xml")) :
#We want to ignore any queries with no search results:
if record.alignments :
print "QUERY: %s..." % record.query[:60]
for align in record.alignments :
for hsp in align.hsps :
print " %s HSP, e=%f, from position %i to %i" \
% (align.hit_id, hsp.expect, hsp.query_start, hsp.query_end)
print "Done"
我用这个网站
HTTP://www2.warwick。 ac.uk/fac/sci/moac/currentstudents/peter_cock/python/rpsblast/
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