Python parse_into_seqrecs示例

示例#1

文件： seqio.py 项目： fangly/seq_crumbs

def _read_seqrecords(fhands, file_format=GUESS_FORMAT):
    'It returns an iterator of seqrecords'
    seq_iters = []
    for fhand in fhands:
        if file_format == GUESS_FORMAT or file_format is None:
            fmt = guess_format(fhand)
        else:
            fmt = file_format

        fmt = remove_multiline(fmt)

        if fmt in ('fasta', 'qual') or 'fastq' in fmt:
            title = title2ids
        if fmt == 'fasta':
            seq_iter = FastaIterator(fhand, title2ids=title)
        elif fmt == 'qual':
            seq_iter = QualPhredIterator(fhand, title2ids=title)
        elif fmt == 'fastq' or fmt == 'fastq-sanger':
            seq_iter = FastqPhredIterator(fhand, title2ids=title)
        elif fmt == 'fastq-solexa':
            seq_iter = FastqSolexaIterator(fhand, title2ids=title)
        elif fmt == 'fastq-illumina':
            seq_iter = FastqIlluminaIterator(fhand, title2ids=title)
        else:
            seq_iter = parse_into_seqrecs(fhand, fmt)
        seq_iters.append(seq_iter)
    return chain.from_iterable(seq_iters)

示例#2

文件： seqio.py 项目： terrycojones/seq_crumbs

def _read_seqrecords(fhands, file_format=GUESS_FORMAT):
    'It returns an iterator of seqrecords'
    seq_iters = []
    for fhand in fhands:
        if file_format == GUESS_FORMAT or file_format is None:
            fmt = guess_format(fhand)
        else:
            fmt = file_format

        fmt = remove_multiline(fmt)

        if fmt in ('fasta', 'qual') or 'fastq' in fmt:
            title = title2ids
        if fmt == 'fasta':
            seq_iter = FastaIterator(fhand, title2ids=title)
        elif fmt == 'qual':
            seq_iter = QualPhredIterator(fhand, title2ids=title)
        elif fmt == 'fastq' or fmt == 'fastq-sanger':
            seq_iter = FastqPhredIterator(fhand, title2ids=title)
        elif fmt == 'fastq-solexa':
            seq_iter = FastqSolexaIterator(fhand, title2ids=title)
        elif fmt == 'fastq-illumina':
            seq_iter = FastqIlluminaIterator(fhand, title2ids=title)
        else:
            seq_iter = parse_into_seqrecs(fhand, fmt)
        seq_iters.append(seq_iter)
    return chain.from_iterable(seq_iters)

示例#3

文件： seqio.py 项目： JoseBlanca/seq_crumbs

def _read_seqrecords(fhands):
    'It returns an iterator of seqrecords'
    seq_iters = []
    for fhand in fhands:
        fmt = get_format(fhand)

        if fmt in ('fasta', 'qual') or 'fastq' in fmt:
            title = title2ids
        if fmt == 'fasta':
            seq_iter = FastaIterator(fhand, title2ids=title)
        elif fmt == 'qual':
            seq_iter = QualPhredIterator(fhand, title2ids=title)
        elif fmt == 'fastq' or fmt == 'fastq-sanger':
            seq_iter = FastqPhredIterator(fhand, title2ids=title)
        elif fmt == 'fastq-solexa':
            seq_iter = FastqSolexaIterator(fhand, title2ids=title)
        elif fmt == 'fastq-illumina':
            seq_iter = FastqIlluminaIterator(fhand, title2ids=title)
        else:
            seq_iter = parse_into_seqrecs(fhand, fmt)
        seq_iters.append(seq_iter)
    return chain.from_iterable(seq_iters)

示例#4

def _read_seqrecords(fhands):
    'It returns an iterator of seqrecords'
    seq_iters = []
    for fhand in fhands:
        fmt = get_format(fhand)

        if fmt in ('fasta', 'qual') or 'fastq' in fmt:
            title = title2ids
        if fmt == 'fasta':
            seq_iter = FastaIterator(fhand, title2ids=title)
        elif fmt == 'qual':
            seq_iter = QualPhredIterator(fhand, title2ids=title)
        elif fmt == 'fastq' or fmt == 'fastq-sanger':
            seq_iter = FastqPhredIterator(fhand, title2ids=title)
        elif fmt == 'fastq-solexa':
            seq_iter = FastqSolexaIterator(fhand, title2ids=title)
        elif fmt == 'fastq-illumina':
            seq_iter = FastqIlluminaIterator(fhand, title2ids=title)
        else:
            seq_iter = parse_into_seqrecs(fhand, fmt)
        seq_iters.append(seq_iter)
    return chain.from_iterable(seq_iters)

示例#5

def _get_lengths(fhand):
    lengths = {}
    for seq in parse_into_seqrecs(fhand, 'fasta'):
        lengths[seq.id] = len(seq)
    return lengths

示例#6

文件： annotation.py 项目： fw1121/ngs_crumbs

def _get_lengths(fhand):
    lengths = {}
    for seq in parse_into_seqrecs(fhand, 'fasta'):
        lengths[seq.id] = len(seq)
    return lengths