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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
 
 
        if hit_id not in qresult:
            frag = HSPFragment(hit_id, qresult.id)
            hsp = HSP([frag])
            hit = Hit([hsp])
            qresult.append(hit)
                # create the HSP object for Hit
                frag = HSPFragment(hit_id, query_id)
                hsp = HSP([frag])
                hsp_list.append(hsp)
                # set or reset the state to none
                # and create a new one
                frag = HSPFragment(hit_id, query_id)
                hsp = HSP([frag])
                hsp_list.append(hsp)
                # set the state ~ none yet

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
 
 
        if hit_id not in qresult:
            frag = HSPFragment(hit_id, qresult.id)
            hsp = HSP([frag])
            hit = Hit([hsp])
            qresult.append(hit)
                # create the HSP object for Hit
                frag = HSPFragment(hit_id, query_id)
                hsp = HSP([frag])
                hsp_list.append(hsp)
                # set or reset the state to none
                # and create a new one
                frag = HSPFragment(hit_id, query_id)
                hsp = HSP([frag])
                hsp_list.append(hsp)
                # set the state ~ none yet

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
 
 
                for attr, value in prev['frag'].items():
                    setattr(frag, attr, value)
                hsp = HSP([frag])
                for attr, value in prev['hsp'].items():
                    setattr(hsp, 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
                for attr, value in prev['frag'].items():
                    setattr(frag, attr, value)
                hsp = HSP([frag])
                for attr, value in prev['hsp'].items():
                    setattr(hsp, 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
 
 
                for attr, value in prev['frag'].items():
                    setattr(frag, attr, value)
                hsp = HSP([frag])
                for attr, value in prev['hsp'].items():
                    setattr(hsp, 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
                for attr, value in prev['frag'].items():
                    setattr(frag, attr, value)
                hsp = HSP([frag])
                for attr, value in prev['hsp'].items():
                    setattr(hsp, 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
 
 
                    setattr(frag, '%s_strand' % seq_type, strand)
 
                hsp = HSP([frag])
                for attr, value in prev['hsp'].items():
                    setattr(hsp, 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
 
 
                    setattr(frag, '%s_strand' % seq_type, strand)
 
                hsp = HSP([frag])
                for attr, value in prev['hsp'].items():
                    setattr(hsp, attr, value)

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
                frag.hit_end = int(seq_t)
 
            hsp = HSP([frag])
            hsp.evalue = float(evalue)
            hsp.bitscore = float(score)

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
 
                    # create HSP object with the fragment
                    hsp = HSP([frag])
                    hsp.evalue = bhsp.expect
                    hsp.bitscore = bhsp.bits

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