Python get_descriptionの例

コード例 #1

ファイル: seq_utils.py プロジェクト: terrycojones/seq_crumbs

def append_to_description(seqrecord, text):
    'it appends the text to the seqrecord description'
    desc = get_description(seqrecord)
    if desc in (None, get_name(seqrecord), '<unknown description>'):
        desc = ''
    desc += text
    seqrecord.object.description = desc

コード例 #2

ファイル: seq_utils.py プロジェクト: bharatpatel/seq_crumbs

def append_to_description(seqrecord, text):
    'it appends the text to the seqrecord description'
    desc = get_description(seqrecord)
    if desc in (None, get_name(seqrecord), '<unknown description>'):
        desc = ''
    desc += text
    seqrecord.object.description = desc

コード例 #3

ファイル: annotation.py プロジェクト: fastq/seq_crumbs

def _read_estcan_result(fhand, result, file_type):
    'It reads a dna or pep ESTscan result file'
    for seq in read_seqs([fhand], file_format='fasta'):
        items = [i.strip() for i in get_description(seq).split(';')]
        strand = -1 if 'minus strand' in items else 1
        start, end = items[0].split(' ', 3)[1:3]
        # estscan changes the name, we have to fix it
        seqid = get_name(seq).strip(';')
        try:
            seq_orfs = result[seqid]
        except KeyError:
            seq_orfs = {}
            result[seqid] = seq_orfs
        orf_key = (int(start), int(end), strand)
        if orf_key in seq_orfs:
            orf = seq_orfs[orf_key]
        else:
            orf = {}
            seq_orfs[orf_key] = orf
        orf[file_type] = get_str_seq(seq)

コード例 #4

ファイル: annotation.py プロジェクト: terrycojones/seq_crumbs

def _read_estcan_result(fhand, result, file_type):
    'It reads a dna or pep ESTscan result file'
    for seq in read_seqs([fhand], file_format='fasta'):
        items = [i.strip() for i in get_description(seq).split(';')]
        strand = -1 if 'minus strand' in items else 1
        start, end = items[0].split(' ', 3)[1:3]
        # estscan changes the name, we have to fix it
        seqid = get_name(seq).strip(';')
        try:
            seq_orfs = result[seqid]
        except KeyError:
            seq_orfs = {}
            result[seqid] = seq_orfs
        orf_key = (int(start), int(end), strand)
        if orf_key in seq_orfs:
            orf = seq_orfs[orf_key]
        else:
            orf = {}
            seq_orfs[orf_key] = orf
        orf[file_type] = get_str_seq(seq)