Question

我有一个这样的文件（+10000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

带有＆＃39;＆gt;＆＃39;的所有行是ID。以下行是关于ID的序列。

我还有一个文件，其中包含我想要的序列的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

我想编写一个匹配id的脚本并复制这些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

我不知道写些什么来获得“＆＃39; n＆＃39; ID之后的行，因为有时它是2行，其他序列有更多，如我在我的例子中所见。

问题是，我试图在不使用Biopython的情况下做到这一点，这会更容易。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

Answer 2

这对你有用。如果字符串中有一些特殊字符，例如\ r \ n，则if line == record[1:]:语句将不起作用。您有兴趣仅查找匹配的ID。以下代码适合您。

代码示例

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

for line in ids:
    for record in seqs:
        if line in  record :
            print record

输出

>DILT_0000000001-mRNA-1

>DILT_0000000101-mRNA-1

Python - 匹配模式，打印模式和后面的n行

2 个答案: