如何使用python获取带有条件的序列计数（在fasta中）？

Question

我有一个 fasta 文件（fasta 是一个文件，其中标题行以 > 开头，后跟与该标题对应的序列行）。我想在每个>TRINITY 序列之后获取与 TRINITY 匹配的序列和以>K 开头的总序列的计数。我能够获得>TRINITY 序列的计数，但不确定如何获得相应>TRINITY 序列组的>K 的计数。如何在 python 中完成这项工作？

myfasta.fasta：

>TRINITY_DN12824_c0_g1_i1
TGGTGACCTGAATGGTCACCACGTCCATACAGA
>K00363:119:HTJ23BBXX:1:1212:18730:9403 1:N:0:CGATGTAT
CACTATTACAATTCTGATGTTTTAATTACTGAGACAT
>K00363:119:HTJ23BBXX:1:2228:9678:46223_(reversed) 1:N:0:CGATGTAT
TAGATTTAAAATAGACGCTTCCATAGA
>TRINITY_DN12824_c0_g1_i1
TGGTGACCTGAATGGTCACCACGTCCATACAGA
>K00363:119:HTJ23BBXX:1:1212:18730:9403 1:N:0:CGATGTAT
CACTATTACAATTCTGATGTTTTAATTACTGAGACAT
>TRINITY_DN555_c0_g1_i1
>K00363:119:HTJ23BBXX:1:2228:9658:46188_(reversed) 1:N:0:CGATGTAT
CGATGCTAGATTTAAAATAGACG
>K00363:119:HTJ23BBXX:1:2106:15260:10387_(reversed) 1:N:0:CGATGTAT
TTAAAATAGACGCTTCCATAGAGA

我想要的结果：

reference   reference_counts    Corresponding_K_sequences
>TRINITY_DN12824_c0_g1_i1   2   3
>TRINITY_DN555_c0_g1_i1 1   2

这是我编写的代码，它仅考虑 >TRINITY 序列计数，但无法将其扩展到它也将计算相应 >K 序列的位，因此我们将不胜感激。 跑步： python code.py myfasta.fasta output.txt

import sys
import os
from Bio import SeqIO
from collections import defaultdict
filename = sys.argv[1]
outfile = sys.argv[2]
dedup_records = defaultdict(list)

for record in SeqIO.parse(filename, "fasta"):
    #print(record)
    #print(record.id)
    if record.id.startswith('TRINITY'):
        #print(record.id)
    # Use the sequence as the key and then have a list of id's as the value
        dedup_records[str(record.seq)].append(record.id)
        #print(dedup_records)
with open(outfile, 'w') as output:
#   # to get the counts of duplicated TRINITY ids (sorted order)
    for seq, ids in sorted(dedup_records.items(), key = lambda t: len(t[1]), reverse=True):
        #output.write("{}   {}\n".format(ids,len(ids)))
        print(ids, len(ids))

Answer 1

您的想法是正确的，但您需要跟踪以“TRINITY”开头的最后一个标题并稍微改变您的结构：

from Bio import SeqIO
from collections import defaultdict

TRIN, d = None, defaultdict(lambda: [0,0])

for r in SeqIO.parse('myfasta.fasta', 'fasta'):
    if r.id.startswith('TRINITY'):
        TRIN = r.id
        d[TRIN][0] += 1
    elif r.id.startswith('K'):
        if TRIN:
            d[TRIN][1] += 1

print('reference\treference_counts\tCorresponding_K_sequences')
for k,v in d.items():
    print('{}\t{}\t{}'.format(k,v[0],v[1])) 

输出：

reference   reference_counts    Corresponding_K_sequences
TRINITY_DN12824_c0_g1_i1    2   3
TRINITY_DN555_c0_g1_i1  1   2