Question

我有一个类似下面的小例子的文件。每4行与一个ID相关。每个ID的第二行以N开头。我想在thoses行的开头删除N，其他所有内容都保持不变。我想在python中做到这一点。你知道怎么做吗？

示例：

@SRR2163140.1 HISEQ:148:C670LANXX:3:1101:1302:1947 length=50
NGCGACCTCAGATCAGACGTGGCGACC
+SRR2163140.1 HISEQ:148:C670LANXX:3:1101:1302:1947 length=50
#<<ABGGGGGGGGGGGGGGGGGGGGGG
@SRR2163140.3 HISEQ:148:C670LANXX:3:1101:1381:1997 length=50
NGCCGACATCGAAGGATCAA
+SRR2163140.3 HISEQ:148:C670LANXX:3:1101:1381:1997 length=50
#<<ABFGGGGGGGGGGGGGG
@SRR2163140.4 HISEQ:148:C670LANXX:3:1101:1705:1940 length=50
NACAAACCCTTGTGTCGAGGGC
+SRR2163140.4 HISEQ:148:C670LANXX:3:1101:1705:1940 length=50
#=ABBGGGGGGGGGGGGGGGGG
@SRR2163140.7 HISEQ:148:C670LANXX:3:1101:1704:1965 length=50
NGGGACATGACAGCCTGGACCATCG
+SRR2163140.7 HISEQ:148:C670LANXX:3:1101:1704:1965 length=50
#=ABBGGGGGGGGGGGGGGGGGGGG

输出：

@SRR2163140.1 HISEQ:148:C670LANXX:3:1101:1302:1947 length=50
GCGACCTCAGATCAGACGTGGCGACC
+SRR2163140.1 HISEQ:148:C670LANXX:3:1101:1302:1947 length=50
#<<ABGGGGGGGGGGGGGGGGGGGGGG
@SRR2163140.3 HISEQ:148:C670LANXX:3:1101:1381:1997 length=50
GCCGACATCGAAGGATCAA
+SRR2163140.3 HISEQ:148:C670LANXX:3:1101:1381:1997 length=50
#<<ABFGGGGGGGGGGGGGG
@SRR2163140.4 HISEQ:148:C670LANXX:3:1101:1705:1940 length=50
ACAAACCCTTGTGTCGAGGGC
+SRR2163140.4 HISEQ:148:C670LANXX:3:1101:1705:1940 length=50
#=ABBGGGGGGGGGGGGGGGGG
@SRR2163140.7 HISEQ:148:C670LANXX:3:1101:1704:1965 length=50
GGGACATGACAGCCTGGACCATCG
+SRR2163140.7 HISEQ:148:C670LANXX:3:1101:1704:1965 length=50
#=ABBGGGGGGGGGGGGGGGGGGGG

Answer 1

如果我完全按照你的要求行事（从每个序列中移除起始N），那么FASTQ file将处于不一致的状态。

FASTQ文件的每四行保留前两行序列的质量值。因此，如果从序列中删除第一个字符，则还需要从具有质量值的行中删除第一个字符。

你可以在纯Python中做一些非常简单的事情，比如

with open("example.fastq") as f:
    for idx, line in enumerate(f.read().splitlines()):
        if idx % 2:
            print(line[1:])
        else:
            print(line)

但是如果您要定期处理生物数据，那么您真的应该开始使用像BioPython这样的生物信息学模块。如果你试图做一些会使文件形状不一致或没有意义的事情，它会警告你。

然后解决方案如下：

from Bio import SeqIO
from Bio import Seq

new_records = []
for record in SeqIO.parse("example.fastq", "fastq"):
    sequence = str(record.seq)
    letter_annotations = record.letter_annotations

    # You first need to empty the existing letter annotations
    record.letter_annotations = {}

    new_sequence = sequence[1:]
    record.seq = Seq.Seq(new_sequence)


    new_letter_annotations = {'phred_quality': letter_annotations['phred_quality'][1:]}
    record.letter_annotations = new_letter_annotations

    new_records.append(record)


with open('without_starting_N.fastq', 'w') as output_handle:
    SeqIO.write(new_records, output_handle, "fastq")

输出

@SRR2163140.1 HISEQ:148:C670LANXX:3:1101:1302:1947 length=50
GCGACCTCAGATCAGACGTGGCGACC
+
<<ABGGGGGGGGGGGGGGGGGGGGGG
@SRR2163140.3 HISEQ:148:C670LANXX:3:1101:1381:1997 length=50
GCCGACATCGAAGGATCAA
+
<<ABFGGGGGGGGGGGGGG
@SRR2163140.4 HISEQ:148:C670LANXX:3:1101:1705:1940 length=50
ACAAACCCTTGTGTCGAGGGC
+
=ABBGGGGGGGGGGGGGGGGG
@SRR2163140.7 HISEQ:148:C670LANXX:3:1101:1704:1965 length=50
GGGACATGACAGCCTGGACCATCG
+
=ABBGGGGGGGGGGGGGGGGGGGG

（每三行的'+'字符可选后跟两行中相同的序列标识符和描述）

如何在python

1 个答案: