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-rw-r--r--gn3/api/rqtl.py8
-rw-r--r--gn3/computations/rqtl.py17
2 files changed, 21 insertions, 4 deletions
diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index b5627c5..ed01a97 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -25,7 +25,7 @@ run the rqtl_wrapper script and return the results as JSON
# Split kwargs by those with values and boolean ones that just convert to True/False
kwargs = ["covarstruct", "model", "method", "nperm", "scale", "control_marker"]
- boolean_kwargs = ["addcovar", "interval", "pstrata"]
+ boolean_kwargs = ["addcovar", "interval", "pstrata", "pairscan"]
all_kwargs = kwargs + boolean_kwargs
rqtl_kwargs = {"geno": genofile, "pheno": phenofile}
@@ -48,9 +48,11 @@ run the rqtl_wrapper script and return the results as JSON
"output", rqtl_cmd.get('output_file'))):
os.system(rqtl_cmd.get('rqtl_cmd'))
- rqtl_output['results'] = process_rqtl_output(rqtl_cmd.get('output_file'))
+ if "pairscan" in boolean_kwargs:
+ rqtl_output['results'] = process_rqtl_pairscan(rqtl_cmd.get('output_file'))
+ else:
+ rqtl_output['results'] = process_rqtl_mapping(rqtl_cmd.get('output_file'))
- rqtl_output['results'] = process_rqtl_output(rqtl_cmd.get('output_file'))
if int(rqtl_kwargs['nperm']) > 0:
rqtl_output['perm_results'], rqtl_output['suggestive'], rqtl_output['significant'] = \
process_perm_output(rqtl_cmd.get('output_file'))
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index b3539a9..b9e715a 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -47,7 +47,7 @@ output filename generated from a hash of the genotype and phenotype files
}
-def process_rqtl_output(file_name: str) -> List:
+def process_rqtl_mapping(file_name: str) -> List:
"""Given an output file name, read in R/qtl results and return
a List of marker objects
@@ -80,6 +80,21 @@ def process_rqtl_output(file_name: str) -> List:
return marker_obs
+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
+
+ """
+ results = []
+ 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):
+ if i == 0: # Skip first line
+ continue
+ line_items = line.split(",")
+ results.append(line_items[1:]) # Append all but first item in line
+
+ return results
def process_perm_output(file_name: str):
"""Given base filename, read in R/qtl permutation output and calculate