Did I find the right examples for you? yes no      Crawl my project      Python Jobs

All Samples(60)  |  Call(36)  |  Derive(0)  |  Import(24)

src/b/i/biopython-1.63/Bio/SearchIO/ExonerateIO/_base.py   biopython(Download)
 
from Bio.SearchIO._index import SearchIndexer
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
from Bio.SeqUtils import seq1
 
 
                if qres_state == state_QRES_NEW or file_state == state_EOF:
                    qresult = QueryResult(id=prev_qid)
                    for hit in hit_list:
                        # not using append since Exonerate may separate the

src/b/i/biopython-HEAD/Bio/SearchIO/ExonerateIO/_base.py   biopython(Download)
 
from Bio.SearchIO._index import SearchIndexer
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
from Bio.SeqUtils import seq1
 
 
                if qres_state == state_QRES_NEW or file_state == state_EOF:
                    qresult = QueryResult(id=prev_qid)
                    for hit in hit_list:
                        # not using append since Exonerate may separate the

src/b/i/biopython-1.63/Bio/SearchIO/BlatIO.py   biopython(Download)
from Bio.Alphabet import generic_dna
from Bio.SearchIO._index import SearchIndexer
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
 
 
                # create qresult and yield if we're at a new qresult or at EOF
                if qres_state == state_QRES_NEW or file_state == state_EOF:
                    qresult = QueryResult(id=prev_qid)
                    for hit in hit_list:
                        qresult.absorb(hit)

src/b/i/biopython-HEAD/Bio/SearchIO/BlatIO.py   biopython(Download)
from Bio.Alphabet import generic_dna
from Bio.SearchIO._index import SearchIndexer
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
 
 
                # create qresult and yield if we're at a new qresult or at EOF
                if qres_state == state_QRES_NEW or file_state == state_EOF:
                    qresult = QueryResult(id=prev_qid)
                    for hit in hit_list:
                        qresult.absorb(hit)

src/b/i/biopython-1.63/Bio/SearchIO/HmmerIO/hmmer3_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
            # not initializing hit_list directly to handle empty hits
            # (i.e. need to set its query description manually)
            qresult = QueryResult(id=qid)
            for hit in hit_list:
                if not hit:

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
                raise StopIteration()
            _, id_ = self.parse_key_value()
            self.qresult = QueryResult(id=id_)
 
            description = None

src/b/i/biopython-1.63/Bio/SearchIO/BlastIO/blast_text.py   biopython(Download)
 
from Bio.Alphabet import generic_dna, generic_protein
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
 
import warnings
            qdesc = qdesc.replace('\n', '').replace('\r', '')
 
            qresult = QueryResult(id=qid)
            qresult.program = rec.application.lower()
            qresult.target = rec.database

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 qresult and yield if we're at a new qresult or at EOF
                if qres_state == state_QRES_NEW or file_state == state_EOF:
                    qresult = QueryResult(hit_list, prev_qid)
                    for attr, value in prev['qresult'].items():
                        setattr(qresult, 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
                # create qresult and yield if we're at a new qresult or EOF
                if qres_state == state_QRES_NEW or file_state == state_EOF:
                    qresult = QueryResult(hit_list, prev_qid)
                    for attr, value in prev['qresult'].items():
                        setattr(qresult, attr, value)

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
 
 
                    seq_len = regx.group(3)
                    desc = regx.group(2)
                    qresult = QueryResult(id=query_id)
                    qresult.seq_len = int(seq_len)
                    # get target from the next line

  1 | 2 | 3  Next