From 694cd889016d27eb9a81946dc39b07892aa26f03 Mon Sep 17 00:00:00 2001 From: Eric Weitz Date: Thu, 29 Mar 2018 14:11:25 -0400 Subject: [PATCH 1/2] Add --infercnv_delimiter argument Former-commit-id: d2573fa90efdeb54c94f16a3852f269f5bb0be84 --- scripts/matrix_to_ideogram_annots.py | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/scripts/matrix_to_ideogram_annots.py b/scripts/matrix_to_ideogram_annots.py index 6ac4f060..4bd45de4 100755 --- a/scripts/matrix_to_ideogram_annots.py +++ b/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', @@ -250,6 +255,7 @@ 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 @@ -257,4 +263,4 @@ def get_clusters_meta(names, paths): 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) From f216e03286afa4b753817455b1615c84b0743973 Mon Sep 17 00:00:00 2001 From: Eric Weitz Date: Thu, 29 Mar 2018 14:19:12 -0400 Subject: [PATCH 2/2] Improve argument documentation Former-commit-id: ba07b1c13c88cf43921a8e56ed8ce8008add5773 --- scripts/matrix_to_ideogram_annots.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/matrix_to_ideogram_annots.py b/scripts/matrix_to_ideogram_annots.py index 4bd45de4..7f327d57 100755 --- a/scripts/matrix_to_ideogram_annots.py +++ b/scripts/matrix_to_ideogram_annots.py @@ -239,7 +239,7 @@ def get_clusters_meta(names, paths): 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', + help='Delimiter in pre_vis_transform.txt output from inferCNV. Default: \\t', default='\t') ap.add_argument('--gen_pos_file', help='Path to gen_pos.txt genomic positions file from inferCNV ')