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All Samples(6)  |  Call(3)  |  Derive(0)  |  Import(3)
It matches the given SeqRecords against the reads in the file.

This class uses Blast to do the matching and it is optimized for having
few SeqRecords to match against a medium sized sequence file.

In this class the seqs_fpath, that in the API acts as the query, it's
internally indexed into a blast database and the seqrecords are blasted
against it. This is done because in the case of having lots of queries to
blast against few subjects it is more efficient to do the blast backwards.
This class behaves as if the seqs_fpath were the query and the seqrecords(more...)

src/s/e/seq_crumbs-HEAD/crumbs/filters.py   seq_crumbs(Download)
    SeqItem
from crumbs.exceptions import WrongFormatError
from crumbs.blast import Blaster, BlasterForFewSubjects
from crumbs.statistics import calculate_dust_score, IntCounter, draw_histogram
from crumbs.settings import get_setting
                   {'kind': 'min_length', 'min_num_residues': 13,
                    'length_in_query': False}]
        self._matcher = BlasterForFewSubjects(db_fhand.name, self.oligos,
                                             program='blastn', filters=filters,
                                             params=params,

src/s/e/seq_crumbs-HEAD/crumbs/trim.py   seq_crumbs(Download)
from crumbs.utils.tags import SEQRECORD
from crumbs.iterutils import rolling_window
from crumbs.blast import BlasterForFewSubjects
from crumbs.seqio import write_seqs
from crumbs.pairs import group_pairs_by_name, group_pairs
                   {'kind': 'min_length', 'min_num_residues': 13,
                    'length_in_query': False}]
        self._matcher = BlasterForFewSubjects(db_fhand.name, self.oligos,
                                             program='blastn', filters=filters,
                                             params=params,

src/s/e/seq_crumbs-HEAD/test/test_blast.py   seq_crumbs(Download)
from Bio.Seq import Seq
 
from crumbs.blast import (do_blast, BlasterForFewSubjects,
                          get_or_create_blastdb, _blastdb_exists, Blaster)
from crumbs.utils.file_utils import TemporaryDir
 
        expected_region = (len(seq_5), len(seq_5 + TITANIUM_LINKER) - 1)
        matcher = BlasterForFewSubjects(mate_fhand.name, linkers,
                                             program='blastn',
                                             elongate_for_global=True)