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src/c/o/cogent-1.5.3/cogent/app/blast.py   cogent(Download)
    get_tmp_filename, guess_input_handler, ApplicationNotFoundError
from cogent.parse.fasta import FastaFinder, LabeledRecordFinder, is_fasta_label
from cogent.parse.blast import LastProteinIds9, QMEBlast9, QMEPsiBlast9, BlastResult
from cogent.util.misc import app_path
from random import choice
    if blast_res['StdOut']:
        lines = [x for x in blast_res['StdOut']]
        return BlastResult(lines)
 
    return None 
    if blast_res['StdOut']:
        lines = [x for x in blast_res['StdOut']]
        return BlastResult(lines)
 
    return None 

src/p/y/pycogent-HEAD/cogent/app/blast.py   pycogent(Download)
    get_tmp_filename, guess_input_handler, ApplicationNotFoundError
from cogent.parse.fasta import FastaFinder, LabeledRecordFinder, is_fasta_label
from cogent.parse.blast import LastProteinIds9, QMEBlast9, QMEPsiBlast9, BlastResult
from cogent.util.misc import app_path
from random import choice
    if blast_res['StdOut']:
        lines = [x for x in blast_res['StdOut']]
        return BlastResult(lines)
 
    return None 
    if blast_res['StdOut']:
        lines = [x for x in blast_res['StdOut']]
        return BlastResult(lines)
 
    return None 

src/q/i/qiime-1.8.0/qiime/util.py   qiime(Download)
from cogent.app.util import (ApplicationError, CommandLineApplication,
    get_tmp_filename as cogent_get_tmp_filename, FilePath)
from cogent.parse.blast import BlastResult
from cogent.parse.fasta import MinimalFastaParser
from cogent.util.misc import remove_files
 
    current_seqs = []
    blast_results = BlastResult([])
    for seq in seqs:
        current_seqs.append(seq)
        if len(current_seqs) % seqs_per_blast_run == 0:
            if blast_results:
                blast_results.update(\
                 BlastResult(blast_app(current_seqs)['StdOut']))
                 BlastResult(blast_app(current_seqs)['StdOut']))
            else:
                blast_results = BlastResult(blast_app(current_seqs)['StdOut'])
            current_seqs = []
 
    # clean-up run: blast the remaining sequences
    blast_results.update(\
     BlastResult(blast_app(current_seqs)['StdOut']))

src/c/o/cogent-1.5.3/cogent/parse/blast_xml.py   cogent(Download)
"""
 
from cogent.parse.blast import BlastResult
 
# field names used to parse tags and create dict.
class BlastXMLResult(BlastResult):
    """the BlastResult objects have the query sequence as keys,
    and the values are lists of lists of dictionaries.
    The FIELD NAMES given are the keys of the dict.
    """

src/p/y/pycogent-HEAD/cogent/parse/blast_xml.py   pycogent(Download)
"""
 
from cogent.parse.blast import BlastResult
 
# field names used to parse tags and create dict.
class BlastXMLResult(BlastResult):
    """the BlastResult objects have the query sequence as keys,
    and the values are lists of lists of dictionaries.
    The FIELD NAMES given are the keys of the dict.
    """

src/p/y/pynast-1.2.2/pynast/util.py   pynast(Download)
from cogent.app.mafft import align_unaligned_seqs as mafft_align_unaligned_seqs
from cogent.app.clustalw import align_unaligned_seqs as clustal_align_unaligned_seqs
from cogent.parse.blast import BlastResult
from cogent.parse.fasta import MinimalFastaParser
 

src/q/i/qiime-1.8.0/tests/test_exclude_seqs_by_blast.py   qiime(Download)
from numpy import array, arange, log, log10
from cogent.util.unit_test import TestCase, main
from cogent.parse.blast import BlastResult
from qiime.exclude_seqs_by_blast import blast_genome,\
                                        find_homologs,\
    def setUp(self):
 
        self.blast_lines = BLAST_LINES
        self.blast_result=BlastResult(self.blast_lines)