Python 使用for循环从blast下载结果

我试图从列表中的不同序列中获得结果，因此下面是我的代码：

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

---

任何帮助都将不胜感激。

嗯……您的代码是正确的！。。。但您正在搜索不存在的数据。。。 问题是，如果br.alignments为空，则可能没有输出…（secont lst条目就是这种情况）

看看这个剪下来的：

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

您可以尝试对lst[0]进行相同的剪切，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>]

>>br.对齐
[, , , , , , , ]

因此短版本是： 输出仅提供str（i）=0的爆炸记录，因为i=1没有数据！ 如果要查看i=0的所有条目，必须删除行“hsp.expect<2”

---

我希望这能有所帮助

我以前单独做过，但结果是我没有按照相同的顺序做。我现在可以自杀，因为这个小小的错误花费了我的时间，让我崩溃，因为我确信我的代码是正确的：）非常感谢你的时间：）总是有这些小事情。。。。这花费了永恒的时间：）哈哈：）不客气请将问题标记为“已回答”

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

>>> 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>]