均质化读取长度

Question

我有一个 fastq 文件中的双端读取数据集，长度范围为 300 到 414 bp（真菌 ITS2 序列）。我希望通过在较短读取的 3' 端用 Ns 填充，我所有的读取（几百万）都是 414 长。因此，如果读取长度为 400 bp，我希望通过在序列末尾添加 14 Ns 使其长度为 414。有人知道能够执行该任务的 python / perl 脚本吗？

Answer 1

$str .= 'N' x (414 - length($str));

Answer 2

使用BioPython。如果序列长于 414 bp，您可能想要更改 default_phred_score_for_N 值 and/or 添加行为。

from Bio import SeqIO
from Bio import Seq

path = r'C:\path\to\file.fastq'
default_phred_score_for_N = 60

def pad_sequence(record):
    sequence = str(record.seq)
    if len(sequence) < 414:
        #pad sequence
        padding_length = 414 - len(sequence)
        sequence += 'N' * padding_length

        # pad annotation
        annotation = record.letter_annotations['phred_quality']
        annotation  += [default_phred_score_for_N] * padding_length
        record.letter_annotations = {}

        record.seq = Seq.Seq(sequence)
        record.letter_annotations = {'phred_quality': annotation}
        return record
    return record


padded_sequences = (pad_sequence(record) for record in \
                    SeqIO.parse(path, 'fastq'))

SeqIO.write(padded_sequences, "padded.fastq", 'fastq')

均质化读取长度

Homogenize reads length

python

perl

bioinformatics

dna-sequence