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src/b/i/biopython-1.63/Bio/SearchIO/HmmerIO/hmmer2_text.py   biopython(Download)
from Bio._utils import read_forward
from Bio.Alphabet import generic_protein
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
 
from ._base import _BaseHmmerTextIndexer
    def createHit(self, hsp_list):
        hit = Hit(hsp_list)
        hit.id_ = self.id_
        hit.evalue = self.evalue
        hit.bitscore = self.bitscore

src/b/i/biopython-HEAD/Bio/SearchIO/HmmerIO/hmmer2_text.py   biopython(Download)
from Bio._utils import read_forward
from Bio.Alphabet import generic_protein
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
 
from ._base import _BaseHmmerTextIndexer
    def createHit(self, hsp_list):
        hit = Hit(hsp_list)
        hit.id_ = self.id_
        hit.evalue = self.evalue
        hit.bitscore = self.bitscore

src/b/i/biopython-1.63/Bio/SearchIO/FastaIO.py   biopython(Download)
from Bio.File import UndoHandle
from Bio.SearchIO._index import SearchIndexer
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
 
 
            frag = HSPFragment(hit_id, qresult.id)
            hsp = HSP([frag])
            hit = Hit([hsp])
            qresult.append(hit)
 
                # process HSP alignment and coordinates
                _set_hsp_seqs(hsp, parsed_hsp, self._preamble['program'])
                hit = Hit(hsp_list)
                hit.description = hit_desc
                hit.seq_len = seq_len
                if hsp_list:
                    _set_hsp_seqs(hsp, parsed_hsp, self._preamble['program'])
                    hit = Hit(hsp_list)
                    hit.description = hit_desc
                    hit.seq_len = seq_len

src/b/i/biopython-HEAD/Bio/SearchIO/FastaIO.py   biopython(Download)
from Bio.File import UndoHandle
from Bio.SearchIO._index import SearchIndexer
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
 
 
            frag = HSPFragment(hit_id, qresult.id)
            hsp = HSP([frag])
            hit = Hit([hsp])
            qresult.append(hit)
 
                # process HSP alignment and coordinates
                _set_hsp_seqs(hsp, parsed_hsp, self._preamble['program'])
                hit = Hit(hsp_list)
                hit.description = hit_desc
                hit.seq_len = seq_len
                if hsp_list:
                    _set_hsp_seqs(hsp, parsed_hsp, self._preamble['program'])
                    hit = Hit(hsp_list)
                    hit.description = hit_desc
                    hit.seq_len = seq_len

src/b/i/biopython-1.63/Bio/SearchIO/HmmerIO/hmmer3_tab.py   biopython(Download)
from Bio.Alphabet import generic_protein
from Bio.SearchIO._index import SearchIndexer
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
 
 
 
                # create Hit and set its attributes
                hit = Hit([hsp])
                for attr, value in prev['hit'].items():
                    setattr(hit, attr, value)

src/b/i/biopython-1.63/Bio/SearchIO/HmmerIO/hmmer3_domtab.py   biopython(Download)
 
from Bio.Alphabet import generic_protein
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
 
from .hmmer3_tab import Hmmer3TabParser, Hmmer3TabIndexer
                # i.e. when hit state is state_HIT_NEW
                if hit_state == state_HIT_NEW:
                    hit = Hit(hsp_list)
                    for attr, value in prev['hit'].items():
                        setattr(hit, attr, value)

src/b/i/biopython-HEAD/Bio/SearchIO/HmmerIO/hmmer3_tab.py   biopython(Download)
from Bio.Alphabet import generic_protein
from Bio.SearchIO._index import SearchIndexer
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
 
 
 
                # create Hit and set its attributes
                hit = Hit([hsp])
                for attr, value in prev['hit'].items():
                    setattr(hit, attr, value)

src/b/i/biopython-HEAD/Bio/SearchIO/HmmerIO/hmmer3_domtab.py   biopython(Download)
 
from Bio.Alphabet import generic_protein
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
 
from .hmmer3_tab import Hmmer3TabParser, Hmmer3TabIndexer
                # i.e. when hit state is state_HIT_NEW
                if hit_state == state_HIT_NEW:
                    hit = Hit(hsp_list)
                    for attr, value in prev['hit'].items():
                        setattr(hit, attr, value)

src/b/i/biopython-1.63/Bio/SearchIO/BlastIO/blast_tab.py   biopython(Download)
 
from Bio.SearchIO._index import SearchIndexer
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
 
 
                # says we're not at the same hit or at a new query
                if hit_state == state_HIT_NEW:
                    hit = Hit(hsp_list)
                    for attr, value in prev['hit'].items():
                        setattr(hit, attr, value)

src/b/i/biopython-HEAD/Bio/SearchIO/BlastIO/blast_tab.py   biopython(Download)
 
from Bio.SearchIO._index import SearchIndexer
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
 
 
                # says we're not at the same hit or at a new query
                if hit_state == state_HIT_NEW:
                    hit = Hit(hsp_list)
                    for attr, value in prev['hit'].items():
                        setattr(hit, attr, value)

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