def test_remove_gap_matrix(self): raw_matrix = ["aaa--a", "bbbcac"] fileterd_matrix = ["aaa", "bbb"] self.assertEqual(fileterd_matrix, dh.remove_gaps_matrix(raw_matrix))
def test_remove_gap_matrix(self): raw_matrix = ["aaa--a", "bbbcac"] fileterd_matrix = ["aaa", "bbb"] self.assertEqual(fileterd_matrix, dh.remove_gaps_matrix(raw_matrix))
current_dir = os.path.abspath(os.curdir) os.chdir(path_aln_file) species_list = check_gene_order_in_alignments(path_aln_file) inputfile_header = [">%s" % species_name for species_name in species_list] matrix_sequence = ["" for species_name in species_list] aln_files = [single_file for single_file in os.listdir(path_aln_file) if ".aln" == os.path.splitext(single_file)[-1]] for single_aln_file in aln_files: # single file operation # rejection : 1. length not enough 2 two many gaps try: <<<<<<< HEAD matrix_sequence = paste_matrix(matrix_sequence,DH.remove_gaps_matrix(extract_TIR_single_file(single_aln_file, length_of_TIR, start_point))) ======= if remove_gap: gene_seq_matrix_addition = DH.remove_gaps_matrix(extract_TIR_single_file(single_aln_file, length_of_TIR, start_point)) else: gene_seq_matrix_addition = extract_TIR_single_file(single_aln_file, length_of_TIR, start_point) matrix_sequence = paste_matrix(matrix_sequence, gene_seq_matrix_addition) >>>>>>> f0acd743d1106c96b88083b2df2cb3526b388aec except SequenceTooShort: print "Too short in %s" % single_aln_file continue except DimNotSame: print "Error of Dimisions %s" % single_aln_file