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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
 
                    hit_attr = hit_attrs.pop(0)
                    hit = Hit(hsp_list)
                    for attr, value in hit_attr.items():
                        setattr(hit, attr, value)

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 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_text.py   biopython(Download)
 
from Bio.Alphabet import generic_dna, generic_protein
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
 
import warnings
                    hsp_list.append(hsp)
 
                hit = Hit(hsp_list)
                hit.seq_len = aln.length
                hit.description = hdesc

src/b/i/biopython-HEAD/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
 
                    hit_attr = hit_attrs.pop(0)
                    hit = Hit(hsp_list)
                    for attr, value in hit_attr.items():
                        setattr(hit, attr, value)

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 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_text.py   biopython(Download)
 
from Bio.Alphabet import generic_dna, generic_protein
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
 
import warnings
                    hsp_list.append(hsp)
 
                hit = Hit(hsp_list)
                hit.seq_len = aln.length
                hit.description = hdesc

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
 
 
                if hit_state == state_HIT_NEW:
                    # create Hit and set its attributes
                    hit = Hit(hsp_list)
                    hit.seq_len = prev['tsize']
                    hit_list.append(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
 
 
                if hit_state == state_HIT_NEW:
                    # create Hit and set its attributes
                    hit = Hit(hsp_list)
                    hit.seq_len = prev['tsize']
                    hit_list.append(hit)

src/b/i/biopython-1.63/Bio/SearchIO/BlastIO/blast_xml.py   biopython(Download)
from Bio.Alphabet import generic_dna, generic_protein
from Bio.SearchIO._index import SearchIndexer
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
 
 
                        query_id, hit_id)]
 
            hit = Hit(hsps)
            hit.description = hit_desc
            # blast_hit_id is only set if the hit ID is Blast-generated

src/b/i/biopython-HEAD/Bio/SearchIO/BlastIO/blast_xml.py   biopython(Download)
from Bio.Alphabet import generic_dna, generic_protein
from Bio.SearchIO._index import SearchIndexer
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
 
 
                        query_id, hit_id)]
 
            hit = Hit(hsps)
            hit.description = hit_desc
            # blast_hit_id is only set if the hit ID is Blast-generated

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