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)。我想获得匹配TRINITY的序列和每个>K
序列后以>TRINITY
开头的总序列的计数。我能够获得>TRINITY
序列的计数,但不知道如何获得相应的>K
序列组的>TRINITY
计数。我怎么能在python中完成这个?
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
结果我想:
reference reference_counts Corresponding_K_sequences
>TRINITY_DN12824_c0_g1_i1 2 3
>TRINITY_DN555_c0_g1_i1 1 2
这里是我编写的代码,它只考虑>TRINITY
序列计数,但不能将它扩展到它也会计算相应的>K
序列的位,所以任何帮助都将受到赞赏。运行: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))
你有正确的想法,但你需要跟踪以“TRINITY”开头的最后一个标题并略微改变你的结构:
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