如何继续追加到一个列表行中直到某个字符？

Question

I'm trying to make multiple lines before a '>' character append into one list so I can convert it to a value in a dictionary. For example, I'm trying to make:

> 1
AAA
CCC
> 2

become AAACCC.

The code is below:

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

You can create the dictionary as you go. Here is a method for doing that.

EDIT: removed defaultdict (so no modules)

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)

The sample file:

>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

Pretty print of the dictionary created is:

{'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*'}

EDIT: To work the solution following your try:

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)

You'll see I made some changes to get the correct output. I added an array total_seq to hold the sequences for each sequence header. (You didn't have this and was a problem in your solution). The joins in your code were not doing anything. The value was just a single string although you had the right idea. You'll see in the revised code the join was done to join the accumulated sequences for one header id into one string of fasta characters.

I tested for blank lines and did a continue if the line was blank, ( len(line) == 0 ).

There was a test if len(sequences) > 0 to see if any sequences had been seen yet. Which they wouldn't on the first record. It would see the ID before it had seen any sequences.

After the for loop completes, it is necessary to add the last sequence

total_seq.append(sequences)

since all other sequences except the last are added to the total_seq when a new ID is detected.

I hope this explanation is helpful as it more closely follows your code.