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-rw-r--r--gn3/api/rqtl.py2
-rw-r--r--gn3/computations/rqtl.py6
2 files changed, 4 insertions, 4 deletions
diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index abce705..9aab9fa 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -49,7 +49,7 @@ run the rqtl_wrapper script and return the results as JSON
os.system(rqtl_cmd.get('rqtl_cmd'))
if "pairscan" in boolean_kwargs:
- rqtl_output['results'] = process_rqtl_pairscan(rqtl_cmd.get('output_file'))
+ rqtl_output['results'] = process_rqtl_pairscan(rqtl_cmd.get('output_file'), genofile)
else:
rqtl_output['results'] = process_rqtl_mapping(rqtl_cmd.get('output_file'))
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index 36c9fa2..b05a577 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -80,7 +80,7 @@ def process_rqtl_mapping(file_name: str) -> List:
return marker_obs
-def process_rqtl_pairscan(file_name: str) -> List:
+def process_rqtl_pairscan(file_name: str, geno_file: str) -> List:
"""Given an output file name, read in R/qtl pair-scan results and return
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)
@@ -88,7 +88,7 @@ def process_rqtl_pairscan(file_name: str) -> List:
"""
figure_data = pairscan_for_figure(file_name)
- table_data = pairscan_for_table(file_name)
+ table_data = pairscan_for_table(file_name, geno_file)
return [figure_data, table_data]
@@ -127,7 +127,7 @@ def pairscan_for_figure(file_name: str) -> Dict:
return figure_data
-def pairscan_for_table(file_name: str) -> List:
+def pairscan_for_table(file_name: str, geno_file: 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)