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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
 
 
        qseqlist = psl.get('qseqs')
        qseq = '' if not qseqlist else qseqlist[idx]
        frag = HSPFragment(hid, qid, hit=hseq, query=qseq)
        # set alphabet
        frag.alphabet = generic_dna

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
 
 
        qseqlist = psl.get('qseqs')
        qseq = '' if not qseqlist else qseqlist[idx]
        frag = HSPFragment(hid, qid, hit=hseq, query=qseq)
        # set alphabet
        frag.alphabet = generic_dna

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
 
        qseqlist = hspd.get('query')
        qseq = '' if qseqlist is None else qseqlist[idx]
        frag = HSPFragment(hid, qid, hit=hseq, query=qseq)
        # coordinates
        frag.query_start = qcoords[0]

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
 
        qseqlist = hspd.get('query')
        qseq = '' if qseqlist is None else qseqlist[idx]
        frag = HSPFragment(hid, qid, hit=hseq, query=qseq)
        # coordinates
        frag.query_start = qcoords[0]

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
 
 
        # The current method only looks at the Hit ID, none of the things above
        if hit_id not in qresult:
            frag = HSPFragment(hit_id, qresult.id)
            hsp = HSP([frag])
            hit = Hit([hsp])
                    hit_desc = ''
                # create the HSP object for Hit
                frag = HSPFragment(hit_id, query_id)
                hsp = HSP([frag])
                hsp_list.append(hsp)
                _set_hsp_seqs(hsp, parsed_hsp, self._preamble['program'])
                # and create a new one
                frag = HSPFragment(hit_id, query_id)
                hsp = HSP([frag])
                hsp_list.append(hsp)

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
 
 
        # The current method only looks at the Hit ID, none of the things above
        if hit_id not in qresult:
            frag = HSPFragment(hit_id, qresult.id)
            hsp = HSP([frag])
            hit = Hit([hsp])
                    hit_desc = ''
                # create the HSP object for Hit
                frag = HSPFragment(hit_id, query_id)
                hsp = HSP([frag])
                hsp_list.append(hsp)
                _set_hsp_seqs(hsp, parsed_hsp, self._preamble['program'])
                # and create a new one
                frag = HSPFragment(hit_id, query_id)
                hsp = HSP([frag])
                hsp_list.append(hsp)

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 fragment and HSP and set their attributes
                frag = HSPFragment(prev_hid, prev_qid)
                for attr, value in prev['frag'].items():
                    setattr(frag, 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
            if prev is not None:
                # each line is basically an HSP with one HSPFragment
                frag = HSPFragment(prev_hid, prev_qid)
                for attr, value in prev['frag'].items():
                    setattr(frag, 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 fragment and HSP and set their attributes
                frag = HSPFragment(prev_hid, prev_qid)
                for attr, value in prev['frag'].items():
                    setattr(frag, 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
            if prev is not None:
                # each line is basically an HSP with one HSPFragment
                frag = HSPFragment(prev_hid, prev_qid)
                for attr, value in prev['frag'].items():
                    setattr(frag, attr, value)

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