Add --infercnv_delimiter argument

Former-commit-id: d2573fa

scripts/matrix_to_ideogram_annots.py

@@ -18,11 +18,12 @@
 
 class MatrixToIdeogramAnnots:
 
- def __init__(self, infercnv_output, gen_pos_file, clusters_meta,
- output_file):
+ def __init__(self, infercnv_output, infercnv_delimiter, gen_pos_file,
+ clusters_meta, output_file):
  """Class and parameter docs in module summary and argument parser"""
 
  self.infercnv_output = infercnv_output
+ self.infercnv_delimiter = infercnv_delimiter
  self.clusters = self.get_clusters(clusters_meta)
  self.output_file = output_file
  self.genomic_position_file_path = gen_pos_file
@@ -121,7 +122,8 @@ def get_expression_matrix_dict(self):
 
  cells_dict = {}
 
- cells_list = lines[0].strip().split()
+ cells_list = lines[0].strip().split(self.infercnv_delimiter)
+
  for i, cell in enumerate(cells_list):
  cell = cell.strip('"').split('PREVIZ.')[1].replace('.', '-') # "PREVIZ.AAACATACAAGGGC.1" -> AAACATACAAGGGC-1
  cells_dict[cell] = i
@@ -130,7 +132,7 @@ def get_expression_matrix_dict(self):
  genes = {}
 
  for line in lines[1:]:
- columns = line.strip().split()
+ columns = line.strip().split(self.infercnv_delimiter)
  gene = columns[0].strip('"')
  expression_by_cell = list(map(float, columns[1:]))
 
@@ -236,6 +238,9 @@ def get_clusters_meta(names, paths):
  formatter_class=RawDescriptionHelpFormatter)
  ap.add_argument('--infercnv_output',
  help='Path to pre_vis_transform.txt output from inferCNV')
+ ap.add_argument('--infercnv_delimiter',
+ help='Delimiter in pre_vis_transform.txt output from inferCNV',
+ default='\t')
  ap.add_argument('--gen_pos_file',
  help='Path to gen_pos.txt genomic positions file from inferCNV ')
  ap.add_argument('--cluster_names',
@@ -250,11 +255,12 @@ def get_clusters_meta(names, paths):
  args = ap.parse_args()
 
  infercnv_output = args.infercnv_output
+ infercnv_delimiter = args.infercnv_delimiter
  gen_pos_file = args.gen_pos_file
  cluster_names = args.cluster_names
  cluster_paths = args.cluster_paths
  output_file = args.output_file
 
  clusters_meta = get_clusters_meta(cluster_names, cluster_paths)
 
- MatrixToIdeogramAnnots(infercnv_output, gen_pos_file, clusters_meta, output_file)
+ MatrixToIdeogramAnnots(infercnv_output, infercnv_delimiter, gen_pos_file, clusters_meta, output_file)