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python-biopython  1.60
Public Member Functions
test_SeqIO_QualityIO.TestReferenceSffConversions Class Reference

List of all members.

Public Member Functions

def check
def check_sff
def test_original
def test_no_manifest
def test_alt_index_at_start
def test_alt_index_in_middle
def test_alt_index_at_end
def test_index_at_start
def test_index_at_end

Detailed Description

Definition at line 217 of file test_SeqIO_QualityIO.py.


Member Function Documentation

def test_SeqIO_QualityIO.TestReferenceSffConversions.check (   self,
  sff_name,
  sff_format,
  out_name,
  format 
)

Definition at line 218 of file test_SeqIO_QualityIO.py.

00218 
00219     def check(self, sff_name, sff_format, out_name, format) :
00220         wanted = list(SeqIO.parse(open(out_name), format))
00221         data = StringIO()
00222         count = SeqIO.convert(sff_name, sff_format, data, format)
00223         self.assertEqual(count, len(wanted))
00224         data.seek(0)
00225         converted = list(SeqIO.parse(data, format))
00226         self.assertEqual(len(wanted), len(converted))
00227         for old, new in zip(wanted, converted) :
00228             self.assertEqual(old.id, new.id)
00229             self.assertEqual(old.name, new.name)
00230             if format!="qual" :
00231                 self.assertEqual(str(old.seq), str(new.seq))
00232             elif format!="fasta" :
00233                 self.assertEqual(old.letter_annotations["phred_quality"],
00234                                  new.letter_annotations["phred_quality"])

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Definition at line 235 of file test_SeqIO_QualityIO.py.

00235 
00236     def check_sff(self, sff_name):
00237         self.check(sff_name, "sff", "Roche/E3MFGYR02_random_10_reads_no_trim.fasta", "fasta")
00238         self.check(sff_name, "sff", "Roche/E3MFGYR02_random_10_reads_no_trim.qual", "qual")
00239         self.check(sff_name, "sff-trim", "Roche/E3MFGYR02_random_10_reads.fasta", "fasta")
00240         self.check(sff_name, "sff-trim", "Roche/E3MFGYR02_random_10_reads.qual", "qual")

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Test converting E3MFGYR02_alt_index_at_end into FASTA+QUAL

Definition at line 257 of file test_SeqIO_QualityIO.py.

00257 
00258     def test_alt_index_at_end(self) :
00259         """Test converting E3MFGYR02_alt_index_at_end into FASTA+QUAL"""
00260         self.check_sff("Roche/E3MFGYR02_alt_index_at_end.sff")

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Test converting E3MFGYR02_alt_index_at_start into FASTA+QUAL

Definition at line 249 of file test_SeqIO_QualityIO.py.

00249 
00250     def test_alt_index_at_start(self) :
00251         """Test converting E3MFGYR02_alt_index_at_start into FASTA+QUAL"""
00252         self.check_sff("Roche/E3MFGYR02_alt_index_at_start.sff")

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Test converting E3MFGYR02_alt_index_in_middle into FASTA+QUAL

Definition at line 253 of file test_SeqIO_QualityIO.py.

00253 
00254     def test_alt_index_in_middle(self) :
00255         """Test converting E3MFGYR02_alt_index_in_middle into FASTA+QUAL"""
00256         self.check_sff("Roche/E3MFGYR02_alt_index_in_middle.sff")

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Test converting E3MFGYR02_index_in_middle into FASTA+QUAL

Definition at line 265 of file test_SeqIO_QualityIO.py.

00265 
00266     def test_index_at_end(self) :
00267         """Test converting E3MFGYR02_index_in_middle into FASTA+QUAL"""
00268         self.check_sff("Roche/E3MFGYR02_index_in_middle.sff")

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Test converting E3MFGYR02_index_at_start into FASTA+QUAL

Definition at line 261 of file test_SeqIO_QualityIO.py.

00261 
00262     def test_index_at_start(self) :
00263         """Test converting E3MFGYR02_index_at_start into FASTA+QUAL"""
00264         self.check_sff("Roche/E3MFGYR02_index_at_start.sff")

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Test converting E3MFGYR02_no_manifest.sff into FASTA+QUAL

Definition at line 245 of file test_SeqIO_QualityIO.py.

00245 
00246     def test_no_manifest(self) :
00247         """Test converting E3MFGYR02_no_manifest.sff into FASTA+QUAL"""
00248         self.check_sff("Roche/E3MFGYR02_no_manifest.sff")
        

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Test converting E3MFGYR02_random_10_reads.sff into FASTA+QUAL

Definition at line 241 of file test_SeqIO_QualityIO.py.

00241 
00242     def test_original(self) :
00243         """Test converting E3MFGYR02_random_10_reads.sff into FASTA+QUAL"""
00244         self.check_sff("Roche/E3MFGYR02_random_10_reads.sff")
        

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The documentation for this class was generated from the following file: