Question

我试图从列表中的不同序列中获取结果，因此我的代码是：

from Bio.Blast import NCBIXML

from Bio.Blast import NCBIWWW

lst=['TGCCCCGAAAATGAACTCAGTAAAGAATGACAGTTTCGCAAGACCCGTTGCTTTTTCAGTGCTAGCTAGCTGACTGATCGTAGCTGACGTAGTCTAGCTAGC','ATCGATCGTACTACGTAGCTGATCGTAGCTAGCTAGCTGATCGTAGCTATCGTACGTAGCTGATCGATCGTAGCTGACTGACGTACGTAGCTGATCGTAGCTAGCTAGCTAGCTGATCGATC']

eq="Homo sapiens[Organism]"


for i in range(0,2):

    rslt  = NCBIWWW.qblast("blastn", "nr", lst[i],entrez_query=eq)
    rcrds = NCBIXML.parse(rslt)
    br = rcrds.next()
    for alignment in br.alignments:
        for hsp in alignment.hsps:
            if hsp.expect < 2:

                print "***** RECORD ****"+str(i)
                print "sequence:", alignment.title
                print "E-value:", hsp.expect

输出仅为lsts第二项和str（i）= 0

提供爆炸记录

***** RECORD ****0
sequence: gi|27436767|gb|AF274855.3| Homo sapiens chromosome X clone RP11-366F6 map q28, complete sequence

E-value: 0.197898

任何帮助将不胜感激。

Answer 1

嗯....你的代码是正确的！...但是你正在搜索不存在的数据...... 问题是，如果br.alignments为空，则没有输出...（这就是secont lst条目的情况）

>>> br.alignments
[]

看看这个剪片：

from Bio.Blast import NCBIXML
from Bio.Blast import NCBIWWW

lst=['TGCCCCGAAAATGAACTCAGTAAAGAATGACAGTTTCGCAAGACCCGTTGCTTTTTCAGTGCTAGCTAGCTGACTGATCGTAGCTGACGTAGTCTAGCTAGC','ATCGATCGTACTACGTAGCTGATCGTAGCTAGCTAGCTGATCGTAGCTATCGTACGTAGCTGATCGATCGTAGCTGACTGACGTACGTAGCTGATCGTAGCTAGCTAGCTAGCTGATCGATC']
eq="Homo sapiens[Organism]"
# download with lst[1]
print "download start"
rslt  = NCBIWWW.qblast("blastn", "nr", lst[1],entrez_query=eq)
print "download end"
print "parsing start"
rcrds = NCBIXML.parse(rslt)
print "parsing end"
br = rcrds.next()
print "br.alignments"
print br.alignments

你可以为lst [0]尝试相同的剪辑，结果将是以下输出：

>>> br.alignments
[<Bio.Blast.Record.Alignment object at 0x02ACCF90>, <Bio.Blast.Record.Alignment object at 0x02ACCE50>, <Bio.Blast.Record.Alignment object at 0x02ACCCF0>, <Bio.Blast.Record.Alignment object at 0x02ACCE10>, <Bio.Blast.Record.Alignment object at 0x02ACCCD0>, <Bio.Blast.Record.Alignment object at 0x02ACCBF0>, <Bio.Blast.Record.Alignment object at 0x02ACCD70>, <Bio.Blast.Record.Alignment object at 0x02ACC930>, <Bio.Blast.Record.Alignment object at 0x02ACC9B0>, <Bio.Blast.Record.Alignment object at 0x02ACCA90>, <Bio.Blast.Record.Alignment object at 0x02ACCAD0>, <Bio.Blast.Record.Alignment object at 0x02ACCB90>, <Bio.Blast.Record.Alignment object at 0x02ACC850>, <Bio.Blast.Record.Alignment object at 0x02ACC970>]

所以简短的版本是：输出仅提供str（i）= 0的blast记录，因为对于i = 1，没有DATA！如果你想查看i = 0的所有条目，你必须删除“hsp.expect＆lt; 2”行;

我希望有帮助

使用for循环从blast中下载结果

1 个答案: