Question

我有一个FASTA文件，这是一个巨大的文件，我想采取那些拥有智人的序列。我们可以使用字典和列表等方法来获得结果。但由于巨大的尺寸，我们无法使用记忆。我们必须将结果写入文件。我的示例FASTA文件如下

GI | 489223532 | REF | WP_003131952.1 | 30S核糖体蛋白S18 [乳酸乳球菌] MAQQRRGGFKRRKKVDFIAANKIEVVDYKDTELLKRFISERGKILPRRVTGTSAKNQRKVVNAIKRARVMALLPFVAEDLTRYYDG

GI | 66816243 | REF | XP_642131.1 |假定蛋白DDB_G0277827 [智人] MASTQNIVEEVQKMLDTYDTNKDGEITKAEAVEYFKGKKAFNPERSAIYLFQVYDKDNDGKITIKELAGDIDFDKALKEYKEKQAKSKQQEAEVEEDIEAFILRHNKDDNTDITKDELIQGFKETGAKDPEKSANFILTEMDTNKDGTITVKELRVYYQKVQKLLNPDQ

GI | 66818355 | REF | XP_642837.1 |假定蛋白DDB_G0276911 [粘菌AX4] MKTKSSNNIKKIYYISSILVGIYLCWQIIIQIIFLMDNSIAILEAIGMVVFISVYSLAVAINGWILVGRMKKSSKKAQYEDFYKKMILKSKILLSTIIIVIIVVVVQDIVINFILPQNPQPYVYMIISNFIVGIADSFQMIMVIFVMGELSFKNYFKFKRIEKQKNHIVIGGSSLNSLPVSLPTVKSNESNESNTISINSENNNSKVSTDDTINNVM

GI | 446106212 | REF | WP_000184067.1 | MULTISPECIES：抗生素转运蛋白[Homo sapiens] MTNPFENDNYTYKVLKNEEGQYSLWPAFLDVPIGWNVVHKEASRNDCLQYVENNWEDLNPKSNQVGKKILVGKR

GI | 494110381 | REF | WP_007051162.1 |多物种：精氨基琥珀酸裂解酶[双歧杆菌属] MTENNEHLALWGGRFTSGPSPELARLSKSTQFDWRLADDDIAGSRAHARALGRAGLLTADELQRMEDALDTLQRHVDDGSFAPIEDDEDEATALERGLIDIAGDELGGKLRAGRSRNDQIACLIRMWLRRHSRVIAGLLLDLVNALIEQSEKAGRTVMPGRTHMQHAQPVLLAHQLMAHAWPLIRDVQRLIDWDKRINASPYGSGALAGNTLGLDPEAVARELGFIDGAD

预期输出

GI | 66816243 | REF | XP_642131.1 |假定蛋白DDB_G0277827 [智人] MASTQNIVEEVQKMLDTYDTNKDGEITKAEAVEYFKGKKAFNPERSAIYLFQVYDKDNDGKITIKELAGDIDFDKALKEYKEKQAKSKQQEAEVEEDIEAFILRHNKDDNTDITKDELIQGFKETGAKDPEKSANFILTEMDTNKDGTITVKELRVYYQKVQKLLNPDQ

GI | 446106212 | REF | WP_000184067.1 | MULTISPECIES：抗生素转运蛋白[Homo sapiens] MTNPFENDNYTYKVLKNEEGQYSLWPAFLDVPIGWNVVHKEASRNDCLQYVENNWEDLNPKSNQVGKKILVGKR

Answer 1

你应该在你的问题上表现出努力，因为你显然没有尝试过。我只是回答，因为它是3行。

for line in f:
    if('Homo sapiens' in line):
        print line+'\n'

修改

如果标题信息后面有一个新行，那么你需要一段更笨重的代码，但它会很快通过文件。

f = open('/Users/nfirth/Downloads/file.fasta') swapLine = False for line in f: if(swapLine): line = line2 swapLine = False if('Homo sapien' in line): print line, line2 = f.next() while('>' not in line2): print line2, line2 = f.next() swapLine = True f.close()

Answer 2

from Bio import SeqIO

my_data = []
with open("test.fasta", "r") as handle:
     for record in SeqIO.parse(handle, 'fasta'):
          if 'Homo sapiens' in record.name:
               my_data.append(str(record.seq))

with open("output.fasta", "w") as out:
     for item in my_data:
          out.write("{0}\n===End===\n".format(item))

解析庞大的FASTA文件

2 个答案: