如何继续追加到一个列表行，直到某个字符？

Question

我尝试在一个'>‘字符之前添加多个行到一个列表中，这样我就可以将它转换为字典中的值。例如，我试图使：

> 1
AAA
CCC
> 2

成为AAACCC。

代码如下：

def parse_fasta(path):
    with open(path) as thefile:
        label = []
        sequences = []
        for k, line in enumerate(thefile):
            if line.startswith('>'):
                labeler = line.strip('>').strip('\n')
                label.append(labeler)
            else:
                seqfix = ''.join(line.strip('\n'))
                sequences.append(seqfix)
    dict_version = {k: v for k, v in zip(label, sequences)}
    return dict_version
parse_fasta('small.fasta')

Answer 1

你可以边走边创建字典。这里有一个方法可以做到这一点。

编辑:删除了defaultdict (没有模块)

from pprint import pprint

dict_version = {}

with open('fasta_sample.txt', 'r') as f:
    for line in f:
        line = line.rstrip()

        if line.startswith('>'):
            key = line[1:]
        else:
            if key in dict_version:
                dict_version[key] += line
            else:
                dict_version[key] = line

pprint(dict_version)

示例文件：

>1FN3:A|PDBID|CHAIN|SEQUENCE
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNAL
SALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR

>5OKT:A|PDBID|CHAIN|SEQUENCE
MGSSHHHHHHSSGLVPRGSHMELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQ
GGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGK
KGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAAT
KRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLK*

>2PAB:A|PDBID|CHAIN|SEQUENCE
GPTGTGESKCPLMVKVLDAVRGSPAINVAVHVFRKAADDTWEPFASGKTSESGELHGLTTEEQFVEGIYKVEIDTKSYWK
ALGISPFHEHAEVVFTANDSGPRRYTIAALLSPYSYSTTAVVTNPKE*

>3IDP:B|PDBID|CHAIN|SEQUENCE
HHHHHHDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRK
TRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHED
LTVKIGDFGLATEKSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIF
MVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPKIHRS

>4QUD:A|PDBID|CHAIN|SEQUENCE
MENTENSVDSKSIKNLEPKIIHGSESMDSGISLDNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRN
LKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKIFNFFRGDRCRSLTGKPKLFII
QACRGTELDCGIETDSGVDDDMACHKIPVEADFLYAYSTAPGYYSWRNSKDGSWFIQSLCAMLKQYADKLEFMHILTRVN
RKVATEFESFSFDATFHAKKQIPCIVSMLTKELYFYH

创建的字典的精美印刷体是：

{'1FN3:A|PDBID|CHAIN|SEQUENCE': 'VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR',
 '2PAB:A|PDBID|CHAIN|SEQUENCE': 'GPTGTGESKCPLMVKVLDAVRGSPAINVAVHVFRKAADDTWEPFASGKTSESGELHGLTTEEQFVEGIYKVEIDTKSYWKALGISPFHEHAEVVFTANDSGPRRYTIAALLSPYSYSTTAVVTNPKE*',
 '3IDP:B|PDBID|CHAIN|SEQUENCE': 'HHHHHHDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATEKSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPKIHRS',
 '4QUD:A|PDBID|CHAIN|SEQUENCE': 'MENTENSVDSKSIKNLEPKIIHGSESMDSGISLDNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKIFNFFRGDRCRSLTGKPKLFIIQACRGTELDCGIETDSGVDDDMACHKIPVEADFLYAYSTAPGYYSWRNSKDGSWFIQSLCAMLKQYADKLEFMHILTRVNRKVATEFESFSFDATFHAKKQIPCIVSMLTKELYFYH',
 '5OKT:A|PDBID|CHAIN|SEQUENCE': 'MGSSHHHHHHSSGLVPRGSHMELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLK*'}

编辑:在您尝试之后执行解决方案：

from pprint import pprint

def parse_fasta(path):
    with open(path) as thefile:
        label = []
        sequences = ''
        total_seq = []

        for line in thefile:
            line = line.strip()
            if len(line) == 0:
                continue
            if line.startswith('>'):
                line = line.strip('>')
                label.append(line)
                if len(sequences) > 0:
                    total_seq.append(sequences)
                    sequences = ''
            else:
                sequences += line

        total_seq.append(sequences)

    dict_version = {k: v for k, v in zip(label, total_seq)}
    return dict_version

d = parse_fasta('fasta_sample.txt')

pprint(d)

您将看到我做了一些更改以获得正确的输出。我添加了一个数组total_seq来保存每个序列标头的序列。(您没有这个，并且在您的解决方案中是一个问题)。代码中的joins没有做任何事情。虽然您的想法是正确的，但值只是一个字符串。在修改后的代码中，您将看到join用于将一个头id的累积序列连接到一个fasta字符串中。

我测试了空行，如果该行是空的，则执行continue (len(line) == 0)。

有一个测试if len(sequences) > 0，看看是否已经看到了任何序列。在第一张唱片里他们不会这么做的。它会在看到任何序列之前看到ID。

for循环完成后，需要添加最后一个序列

total_seq.append(sequences)

因为当检测到新的ID时，除了最后的序列之外的所有其它序列都被添加到total_seq。

我希望这个解释是有帮助的，因为它更紧跟您的代码。