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authorzsloan2021-05-21 19:43:23 +0000
committerzsloan2021-05-21 19:43:23 +0000
commitefbe47b58f6e0b9a4b509a28ec8788a1c6dae343 (patch)
treed09eea867e29a6f1333b2bf0c8625762719babb0
parentc2fac869f5ac1a398677d5646d34a1a0704e29e4 (diff)
downloadgenenetwork2-efbe47b58f6e0b9a4b509a28ec8788a1c6dae343.tar.gz
run_rqtl now reads in permutation output
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py34
1 files changed, 32 insertions, 2 deletions
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 3f4899b0..c3f047fc 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -8,6 +8,8 @@ from typing import List
from typing import Optional
from typing import TextIO
+import numpy as np
+
from base.webqtlConfig import TMPDIR
from base.trait import create_trait
from utility.tools import locate
@@ -46,7 +48,11 @@ def run_rqtl(trait_name, vals, samples, dataset, mapping_scale, method, model, p
out_file = requests.post(GN3_RQTL_URL, data=post_data).json()['output_file']
- return process_rqtl_results(out_file)
+ if num_perm > 0:
+ perm_results, suggestive, significant = process_perm_results(out_file)
+ return perm_results, suggestive, significant, process_rqtl_results(out_file)
+ else:
+ return process_rqtl_results(out_file)
def process_rqtl_results(out_file: str) -> List:
@@ -63,6 +69,7 @@ def process_rqtl_results(out_file: str) -> List:
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
@@ -81,6 +88,30 @@ def process_rqtl_results(out_file: str) -> List:
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
+
+
def get_hash_of_textio(the_file: TextIO) -> str:
"""Given a StringIO, return the hash of its contents"""
@@ -146,7 +177,6 @@ def cofactors_to_dict(cofactors: str, dataset_ob, samples) -> Dict:
name=cofactor_name)
sample_data = trait_ob.data
for index, sample in enumerate(samples):
- #if (sample in sample_list) and (sample in sample_data):
if sample in sample_data:
sample_value = sample_data[sample].value
cofactors[cofactor_name].append(sample_value)