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
