使用for循环从blast下载结果

Question

我试图从列表中的不同序列中获得结果，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

输出只提供lsts的第二项和str(i)=0的blast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

任何帮助都将不胜感激。

Answer 1

well....your代码是正确的！...but，你在搜索不存在的数据.问题是，如果br.alignments是空的，就不可能有输出.(第一个条目的情况就是这样)

>>> br.alignments
[]

看看这段片段：

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

对于lst，您可以尝试相同的代码片段，其结果将是以下输出：

>>> 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>]

因此，的简短版本是:输出只为str(i)=0提供blast记录，因为对于i=1，没有数据！如果要查看i=0的所有条目，则必须删除"hsp.expect < 2";一行

我希望这能帮上忙