Python - 匹配模式，打印模式及其后面的n行

Question

我有一个这样的文件(包含+10000个序列，+98000行):

>DILT_0000000001-mRNA-1
MKVVKICSKLRKFIESRKDAVLPEQEEVLADLWAFEGISEFQMERFAKAAQCFQHQYELA
IKANLTEHASRSLENLGRARARLYDYQGALDAWTKRLDYEIKGIDKAWLHHEIGRAYLEL
NQYEEAIDHAATARDVADREADMEWDLNATVLIAQAHFYAGNLEEAKVYFEAAQNAAFRK
GFFKAESVLAEAIAEVDSEIRREEAKQERVYTKHSVLFNEFSQRAVWSEEYSEELHLFPF
AVVMLRCVLARQCTVHLQFRSCYNL
>DILT_0000000101-mRNA-1
MSCRRLSMNPGEALIKESSAPSRENLLKPYFDEDRCKFRHLTAEQFSDIWSHFDLDGVNE
LRFILRVPASQQAGTGLRFFGYISTEVYVHKTVKVSYIGFRKKNNSRALRRWNVNKKCSN
AVQMCGTSQLLAIVGPHTQPLTNKLCHTDYLPLSANFA
>DILT_0001999301-mRNA-1
LEHGIQPDGQMPSDKTIGGGDDSFQTFFSETGAGKHVPRAVMVDLEPTVIGEYLCVLLTS
FILFRLISTNLGPNSQLASRTLLFAADKTTLFRLLGLLPWSLLKIAVQ
>DILT_0001999401-mRNA-1
MAENGEDANMPEEGKEGNTQDQGEHQQDVQSDEPNEADSGYSSAASSDVNSQTIPITVIL
PNREAVNLSFDPNISVSELQERLNGPGITRLNENLFFTYSGKQLDPNKTLLDYKVQKSST
LYVHETPTALPKSAPNAKEEGVVPSNCLIHSGSRMDENRCLKEYQLTQNSVIFVHRPTAN
TAVQNREEKTSSLEVTVTIRETGNQLHLPINPHXXXXTVEMHVAPGVTVGDLNRKIAIKQ

所有带“>”的行都是 ID。以下几行是有关 ID 的序列。

我还有一个文件，其中包含我想要的序列 ID，例如:

DILT_0000000001-mRNA-1
DILT_0000000101-mRNA-1
DILT_0000000201-mRNA-1
DILT_0000000301-mRNA-1
DILT_0000000401-mRNA-1
DILT_0000000501-mRNA-1
DILT_0000000601-mRNA-1
DILT_0000000701-mRNA-1
DILT_0000000801-mRNA-1
DILT_0000000901-mRNA-1

我想编写一个脚本来匹配 ID 并复制该 ID 的序列，但我只是获取 ID，而没有序列。

seqs = open('WBPS10.protein.fa').readlines()
ids = open('ids.txt').readlines()

for line in ids:
    for record in seqs:
        if line == record[1:]:
            print record

我不知道要写什么来获取 ID 后的“n”行，因为有时它是 2 行，其他序列有更多，正如您在我的示例中看到的那样。

问题是，我试图在不使用 Biopython 的情况下做到这一点，这会容易得多。我只是想学习其他方法。

Answer 1

seqs_by_ids = {}
with open('WBPS10.protein.fa', 'r') as read_file:
    for line in read_file.readlines():
        if line.startswith('>'):
            current_key = line[1:].strip()
            seqs_by_ids[current_key] = ''
        else:
            seqs_by_ids[current_key] += line.strip()

ids = set([line.strip() for line in open('ids.txt').readlines()])

for id in ids:
    if id in seqs_by_ids:
        print(id)
        print('\t{}'.format(seqs_by_ids[id]))

输出:

DILT_0000000001-mRNA-1
    MKVVKICSKLRKFIESRKDAVLPEQEEVLADLWAFEGISEFQMERFAKAAQCFQHQYELAIKANLTEHASRSLENLGRARARLYDYQGALDAWTKRLDYEIKGIDKAWLHHEIGRAYLELNQYEEAIDHAATARDVADREADMEWDLNATVLIAQAHFYAGNLEEAKVYFEAAQNAAFRKGFFKAESVLAEAIAEVDSEIRREEAKQERVYTKHSVLFNEFSQRAVWSEEYSEELHLFPFAVVMLRCVLARQCTVHLQFRSCYNL
DILT_0000000101-mRNA-1
    MSCRRLSMNPGEALIKESSAPSRENLLKPYFDEDRCKFRHLTAEQFSDIWSHFDLDGVNELRFILRVPASQQAGTGLRFFGYISTEVYVHKTVKVSYIGFRKKNNSRALRRWNVNKKCSNAVQMCGTSQLLAIVGPHTQPLTNKLCHTDYLPLSANFA