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src/b/i/biopython-1.63/Bio/SearchIO/HmmerIO/hmmer3_text.py   biopython(Download)
 
from Bio._py3k import _as_bytes, _bytes_to_string
from Bio._utils import read_forward
from Bio.Alphabet import generic_protein
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
    def __init__(self, handle):
        self.handle = handle
        self.line = read_forward(self.handle)
        self._meta = self._parse_preamble()
 
                return
            else:
                self.line = read_forward(self.handle)
 
    def _parse_preamble(self):
                    meta[regx.group(1)] = regx.group(2)
 
            self.line = read_forward(self.handle)
 
        return meta
            desc = '' # placeholder
            while not self.line.startswith('Scores for '):
                self.line = read_forward(self.handle)
 
                if self.line.startswith('Accession:'):

src/b/i/biopython-HEAD/Bio/SearchIO/HmmerIO/hmmer3_text.py   biopython(Download)
 
from Bio._py3k import _as_bytes, _bytes_to_string
from Bio._utils import read_forward
from Bio.Alphabet import generic_protein
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
    def __init__(self, handle):
        self.handle = handle
        self.line = read_forward(self.handle)
        self._meta = self._parse_preamble()
 
                return
            else:
                self.line = read_forward(self.handle)
 
    def _parse_preamble(self):
                    meta[regx.group(1)] = regx.group(2)
 
            self.line = read_forward(self.handle)
 
        return meta
            desc = '' # placeholder
            while not self.line.startswith('Scores for '):
                self.line = read_forward(self.handle)
 
                if self.line.startswith('Accession:'):

src/b/i/biopython-1.63/Bio/SearchIO/HmmerIO/hmmer2_text.py   biopython(Download)
 
from Bio._py3k import _as_bytes, _bytes_to_string
from Bio._utils import read_forward
from Bio.Alphabet import generic_protein
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
        # determine flag for hmmsearch
        is_hmmsearch = False
        line = read_forward(handle)
        if line.startswith(_as_bytes('hmmsearch')):
            is_hmmsearch = True
                break
 
            line = read_forward(handle)
 
# if not used as a module, run the doctest

src/b/i/biopython-HEAD/Bio/SearchIO/HmmerIO/hmmer2_text.py   biopython(Download)
 
from Bio._py3k import _as_bytes, _bytes_to_string
from Bio._utils import read_forward
from Bio.Alphabet import generic_protein
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
        # determine flag for hmmsearch
        is_hmmsearch = False
        line = read_forward(handle)
        if line.startswith(_as_bytes('hmmsearch')):
            is_hmmsearch = True
                break
 
            line = read_forward(handle)
 
# if not used as a module, run the doctest