def testfasta_iter(self):
fasta = open( self.seqfile ,'r' )
fasta_i = fasta_iter( fasta )
i= 0
for sequences in fasta_i:
header, seq = sequences
self.assertEqual( header , self.seqs[i][0] )
self.assertEqual( seq , self.seqs[i][1] )
i +=1
fasta.close()
def testrename_fasta(self):
fasta_file = open( self.seqfile ,'r' )
renamed_fasta_name = os.path.join( TEST_DIR , 'fasta_renamed' )
renamed_fasta = open( renamed_fasta_name , 'w' )
mapping_file_name = os.path.join( TEST_DIR , 'mapping' )
mapping_file = open( mapping_file_name , 'w' )
rename_fasta(fasta_file , renamed_fasta , mapping_file )
fasta_file.close()
renamed_fasta.close()
mapping_file.close()
old_fasta = open( self.seqfile ,'r' )
old_fasta_iter = fasta_iter( old_fasta )
new_fasta = open( renamed_fasta_name , 'r')
new_fasta_iter = fasta_iter( new_fasta )
mapping_file = open( mapping_file_name , 'r')
for l in mapping_file:
old_header , old_seq = old_fasta_iter.next()
new_header , new_seq = new_fasta_iter.next()
new_map , old_map = l[:-1].split('\t')
self.assertEqual( old_header , old_map )
self.assertEqual( new_header , new_map )
self.assertEqual( old_seq , new_seq )
