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src/c/o/cogent-1.5.3/cogent/app/infernal.py   cogent(Download)
from cogent.parse.rfam import MinimalRfamParser, ChangedSequence, \
    ChangedRnaSequence, ChangedDnaSequence
from cogent.parse.infernal import CmsearchParser
from cogent.core.moltype import DNA, RNA
from cogent.core.alignment import SequenceCollection, Alignment, DataError
    res = app(paths)
 
    search_results = list(CmsearchParser(res['SearchResults'].readlines()))
    if search_results:
        for i,line in enumerate(search_results):
    res = app(paths)
 
    search_results = list(CmsearchParser(res['SearchResults'].readlines()))
 
    if search_results:    

src/p/y/pycogent-HEAD/cogent/app/infernal.py   pycogent(Download)
from cogent.parse.rfam import MinimalRfamParser, ChangedSequence, \
    ChangedRnaSequence, ChangedDnaSequence
from cogent.parse.infernal import CmsearchParser
from cogent.core.moltype import DNA, RNA
from cogent.core.alignment import SequenceCollection, Alignment, DataError
    res = app(paths)
 
    search_results = list(CmsearchParser(res['SearchResults'].readlines()))
    if search_results:
        for i,line in enumerate(search_results):
    res = app(paths)
 
    search_results = list(CmsearchParser(res['SearchResults'].readlines()))
 
    if search_results:    

src/c/o/cogent-1.5.3/tests/test_parse/test_infernal.py   cogent(Download)
#!/usr/bin/env python
# test_infernal.py
 
from cogent.util.unit_test import TestCase, main
from cogent.parse.infernal import CmsearchParser,CmalignScoreParser
    def test_cmsearch_parser_no_data(self):
        """CmsearchParser should return correct result given no data.
        """
        parser = CmsearchParser([])
        self.assertEqual(list(parser),[])
 
    def test_cmsearch_parser_no_res(self):
        """CmsearchParser should return correct result given no hits in result.
        """
        parser = CmsearchParser(self.basic_results_empty.split('\n'))
    def test_cmsearch_parser_basic(self):
        """CmsearchParser should return correct result given basic output.
        """
        parser = CmsearchParser(self.basic_results_hits.split('\n'))
        self.assertEqual(list(parser),self.basic_res)
 
    def test_cmsearch_parser_full(self):
        """CmsearchParser should return correct result given cmsearch output.
        """
        parser = CmsearchParser(SEARCH_DATA.split('\n'))

src/p/y/pycogent-HEAD/tests/test_parse/test_infernal.py   pycogent(Download)
#!/usr/bin/env python
# test_infernal.py
 
from cogent.util.unit_test import TestCase, main
from cogent.parse.infernal import CmsearchParser,CmalignScoreParser
    def test_cmsearch_parser_no_data(self):
        """CmsearchParser should return correct result given no data.
        """
        parser = CmsearchParser([])
        self.assertEqual(list(parser),[])
 
    def test_cmsearch_parser_no_res(self):
        """CmsearchParser should return correct result given no hits in result.
        """
        parser = CmsearchParser(self.basic_results_empty.split('\n'))
    def test_cmsearch_parser_basic(self):
        """CmsearchParser should return correct result given basic output.
        """
        parser = CmsearchParser(self.basic_results_hits.split('\n'))
        self.assertEqual(list(parser),self.basic_res)
 
    def test_cmsearch_parser_full(self):
        """CmsearchParser should return correct result given cmsearch output.
        """
        parser = CmsearchParser(SEARCH_DATA.split('\n'))