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authorzsloan2021-08-03 20:34:06 +0000
committerzsloan2022-03-22 19:08:01 +0000
commit019f196f21cbfd7bb3d91838313aad1d29ea98cb (patch)
treec7e28cf82b336159c0077059587dc27d7d171b3f /gn3
parent4c3359082fbb1eef93a9e54c633f938606cba5f6 (diff)
downloadgenenetwork3-019f196f21cbfd7bb3d91838313aad1d29ea98cb.tar.gz
Create pairscan_for_figure and pairscan_for_table functions that return the Dict and List respectively used for the pair scan figure and the table showing the results
Diffstat (limited to 'gn3')
-rw-r--r--gn3/computations/rqtl.py87
1 files changed, 82 insertions, 5 deletions
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index b9e715a..87c9ae8 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -82,19 +82,96 @@ def process_rqtl_mapping(file_name: str) -> List:
def process_rqtl_pairscan(file_name: str) -> List:
"""Given an output file name, read in R/qtl pair-scan results and return
- a List of Lists representing the matrix of results
+ a list of both the JSON needed for the d3panels figure and a list of results
+ to be used when generating the results table (which will include marker names)
"""
- results = []
+
+ figure_data = pairscan_results_for_figure(file_name)
+ table_data = pairscan_results_for_table(file_name)
+
+ return [figure_data, table_data]
+
+def pairscan_for_figure(file_name: str) -> Dict:
+ """Given an output file name, read in R/qtl pair-scan results and return
+ the JSON needed for the d3panels figure
+
+ """
+ figure_data = {}
+
+ # Open the file with the actual results, written as a list of lists
with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"),
"output", file_name), "r") as the_file:
+ lod_results = []
for i, line in enumerate(the_file):
if i == 0: # Skip first line
continue
- line_items = line.split(",")
- results.append(line_items[1:]) # Append all but first item in line
+ line_items = [item.rstrip('\n') for item in line.split(",")]
+ lod_results.append(line_items[1:]) # Append all but first item in line
+ figure_data['lod'] = lod_results
+
+ # Open the map file with the list of markers/pseudomarkers and their positions
+ with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"),
+ "output", "MAP_" + file_name), "r") as the_file:
+ chr_list = []
+ pos_list = []
+ for i, line in enumerate(the_file):
+ if i == 0: # Skip first line
+ continue
+ line_items = [item.rstrip('\n') for item in line.split(",")]
+ chr_list.append(line_items[1])
+ pos_list.append(line_items[2])
+ figure_data['chr'] = chr_list
+ figure_data['pos'] = pos_list
+
+ return figure_data
+
+
+def pairscan_for_table(file_name: str) -> List:
+ """Given an output file name, read in R/qtl pair-scan results and return
+ a list of results to be used when generating the results table (which will include marker names)
+
+ """
+ table_data = []
+
+ # Open the map file with the list of markers/pseudomarkers and create list of marker obs
+ with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"),
+ "output", "MAP_" + file_name), "r") as the_file:
+ marker_list = []
+ for i, line in enumerate(the_file.readlines()[1:]):
+ line_items = [item.rstrip('\n') for item in line.split(",")]
+ this_marker = {
+ 'name': line_items[0],
+ 'chr': line_items[1][1:-1], # Strip quotes from beginning and end of chr string
+ 'pos': line_items[2]
+ }
+
+ marker_list.append(this_marker)
+
+ # Open the file with the actual results and write the results as
+ # they will be displayed in the results table
+ with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"),
+ "output", file_name), "r") as the_file:
+ for i, line in enumerate(the_file.readlines()[1:]):
+ marker_1 = marker_list[i]
+ line_items = [item.rstrip('\n') for item in line.split(",")]
+ for j, item in enumerate(line_items[1:]):
+ marker_2 = marker_list[j]
+ try:
+ lod_score = f"{float(item):.3f}"
+ except:
+ lod_score = f"{item}"
+ this_line = {
+ 'marker1': f"{marker_1['name']}",
+ 'pos1': f"Chr {marker_1['chr']} @ {float(marker_1['pos']):.1f} cM",
+ 'lod': lod_score,
+ 'marker2': f"{marker_2['name']}",
+ 'pos2': f"Chr {marker_2['chr']} @ {float(marker_2['pos']):.1f} cM"
+ }
+ table_data.append(this_line)
+
+ return table_data
- return results
def process_perm_output(file_name: str):
"""Given base filename, read in R/qtl permutation output and calculate