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authorzsloan2021-05-25 20:19:37 +0000
committerzsloan2021-05-25 20:19:37 +0000
commit4d15c32e7d86885cffce1720db0df394bd6a02ff (patch)
treec1e12fa332d6ad6157a6d38333f2500a4dbc036e
parentcf9f0bef4454f97270bcacd16080f9d7f6bbb5e6 (diff)
downloadgenenetwork2-4d15c32e7d86885cffce1720db0df394bd6a02ff.tar.gz
Removed code that processes output files, since this functionality is moved to GN3
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py67
1 files changed, 4 insertions, 63 deletions
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index d18f6a7b..495678e9 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -46,70 +46,11 @@ def run_rqtl(trait_name, vals, samples, dataset, mapping_scale, model, method, n
if cofactors:
post_data["addcovar"] = True
- out_file = requests.post(GN3_RQTL_URL, data=post_data).json()['output_file']
-
+ rqtl_output = requests.post(GN3_RQTL_URL, data=post_data).json()
if num_perm > 0:
- perm_results, suggestive, significant = process_perm_results(out_file)
- return perm_results, suggestive, significant, process_rqtl_results(out_file)
+ return rqtl_output['perm_results'], rqtl_output['suggestive'], rqtl_output['significant'], rqtl_output['results']
else:
- return process_rqtl_results(out_file)
-
-
-def process_rqtl_results(out_file: str) -> List:
- """Given the output filename, read in results and
- return as a list of dictionaries representing each
- marker
-
- """
-
- marker_obs = []
- # Later I should probably redo this using csv.read to avoid the
- # awkwardness with removing quotes with [1:-1]
- with open(GN3_TMP_PATH + "/output/" + out_file, "r") as the_file:
- for line in the_file:
- line_items = line.split(",")
- if line_items[1][1:-1] == "chr" or not line_items:
- # Skip header line
- continue
- else:
- # Convert chr to int if possible
- try:
- the_chr = int(line_items[1][1:-1])
- except:
- the_chr = line_items[1][1:-1]
- this_marker = {
- "name": line_items[0][1:-1],
- "chr": the_chr,
- "cM": float(line_items[2]),
- "Mb": float(line_items[2]),
- "lod_score": float(line_items[3])
- }
- marker_obs.append(this_marker)
-
- return marker_obs
-
-
-def process_perm_results(out_file: str):
- """Given base filename, read in R/qtl permutation output and calculate
- suggestive and significant thresholds
-
- """
- perm_results = []
- with open(GN3_TMP_PATH + "/output/PERM_" + out_file, "r") as the_file:
- for i, line in enumerate(the_file):
- if i == 0:
- # Skip header line
- continue
- else:
- line_items = line.split(",")
- perm_results.append(float(line_items[1]))
-
- logger.debug("PERM RESULTS:", perm_results)
-
- suggestive = np.percentile(np.array(perm_results), 67)
- significant = np.percentile(np.array(perm_results), 95)
-
- return perm_results, suggestive, significant
+ return rqtl_output['results']
def get_hash_of_textio(the_file: TextIO) -> str:
@@ -182,4 +123,4 @@ def cofactors_to_dict(cofactors: str, dataset_ob, samples) -> Dict:
cofactors[cofactor_name].append(sample_value)
else:
cofactors[cofactor_name].append("NA")
- return cofactors \ No newline at end of file
+ return cofactors