diff options
| -rw-r--r-- | gn3/api/rqtl.py | 2 | ||||
| -rw-r--r-- | gn3/computations/rqtl.py | 6 |
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) |