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src/b/i/biopython-1.63/Tests/test_SearchIO_write.py   biopython(Download)
    def read_write_and_compare(self, source_file, source_format, out_file,
            out_format, **kwargs):
        """Compares read QueryResults after it has been written to a file."""
        source_qresult = SearchIO.read(source_file, source_format, **kwargs)
        SearchIO.write(source_qresult, out_file, out_format, **kwargs)
        out_qresult = SearchIO.read(out_file, out_format, **kwargs)

src/b/i/biopython-HEAD/Tests/test_SearchIO_write.py   biopython(Download)
    def read_write_and_compare(self, source_file, source_format, out_file,
            out_format, **kwargs):
        """Compares read QueryResults after it has been written to a file."""
        source_qresult = SearchIO.read(source_file, source_format, **kwargs)
        SearchIO.write(source_qresult, out_file, out_format, **kwargs)
        out_qresult = SearchIO.read(out_file, out_format, **kwargs)

src/b/i/biopython-1.63/Tests/test_SearchIO_exonerate.py   biopython(Download)
import unittest
 
from Bio.SearchIO import parse, read
 
# test case files are in the Blast directory
        tfile = get_file(text)
 
        vqres = read(vfile, 'exonerate-vulgar')
        tqres = read(tfile, 'exonerate-text')
 
    def test_exn_22_m_affine_local(self):
        """Test parsing exonerate output (exn_22_m_affine_local.exn)"""
 
        exn_file = get_file('exn_22_m_affine_local.exn')
        qresult = read(exn_file, self.fmt)
    def test_exn_22_m_cdna2genome(self):
        """Test parsing exonerate output (exn_22_m_cdna2genome.exn)"""
 
        exn_file = get_file('exn_22_m_cdna2genome.exn')
        qresult = read(exn_file, self.fmt)

src/b/i/biopython-HEAD/Tests/test_SearchIO_exonerate.py   biopython(Download)
with warnings.catch_warnings():
   warnings.simplefilter('ignore', BiopythonExperimentalWarning)
   from Bio.SearchIO import parse, read
 
# test case files are in the Blast directory
        tfile = get_file(text)
 
        vqres = read(vfile, 'exonerate-vulgar')
        tqres = read(tfile, 'exonerate-text')
 
    def test_exn_22_m_affine_local(self):
        """Test parsing exonerate output (exn_22_m_affine_local.exn)"""
 
        exn_file = get_file('exn_22_m_affine_local.exn')
        qresult = read(exn_file, self.fmt)
    def test_exn_22_m_cdna2genome(self):
        """Test parsing exonerate output (exn_22_m_cdna2genome.exn)"""
 
        exn_file = get_file('exn_22_m_cdna2genome.exn')
        qresult = read(exn_file, self.fmt)

src/b/i/biopython-1.63/Tests/test_SearchIO_hmmer2_text.py   biopython(Download)
from os import path
 
from Bio.SearchIO import parse, read
 
 
    def test_hmmsearch_20(self):
        """Test parsing hmmsearch 2.0 file (text_20_hmmsearch_001.out)"""
        res = read(path.join("Hmmer", "text_20_hmmsearch_001.out"), self.fmt)
 
        # first query
    def test_hmmsearch_22(self):
        """Test parsing hmmsearch 2.2 file (text_22_hmmsearch_001.out)"""
        res = read(path.join("Hmmer", "text_22_hmmsearch_001.out"), self.fmt)
 
        # first query

src/b/i/biopython-HEAD/Tests/test_SearchIO_hmmer2_text.py   biopython(Download)
with warnings.catch_warnings():
   warnings.simplefilter('ignore', BiopythonExperimentalWarning)
   from Bio.SearchIO import parse, read
 
 
    def test_hmmsearch_20(self):
        """Test parsing hmmsearch 2.0 file (text_20_hmmsearch_001.out)"""
        res = read(path.join("Hmmer", "text_20_hmmsearch_001.out"), self.fmt)
 
        # first query
    def test_hmmsearch_22(self):
        """Test parsing hmmsearch 2.2 file (text_22_hmmsearch_001.out)"""
        res = read(path.join("Hmmer", "text_22_hmmsearch_001.out"), self.fmt)
 
        # first query