diff options
| -rw-r--r-- | gn3/computations/rqtl.py | 10 |
1 files changed, 5 insertions, 5 deletions
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py index d6fcd3f..4f2709c 100644 --- a/gn3/computations/rqtl.py +++ b/gn3/computations/rqtl.py @@ -1,7 +1,7 @@ """Procedures related rqtl computations""" import os from bisect import bisect -from typing import Dict, List, Union +from typing import Dict, List, Tuple, Union import numpy as np @@ -150,7 +150,7 @@ def pairscan_for_table(file_name: str, geno_file: str) -> List: marker_list.append(this_marker) # Get the list of original markers from the .geno file - original_markers = build_marker_pos_list(geno_file) + original_markers = build_marker_pos_dict(geno_file) # Open the file with the actual results and write the results as # they will be displayed in the results table @@ -181,7 +181,7 @@ def pairscan_for_table(file_name: str, geno_file: str) -> List: return sorted(table_data, key = lambda i: float(i['lod']), reverse=True)[:500] -def build_marker_pos_list(genotype_file): +def build_marker_pos_dict(genotype_file: str) -> Dict: """ Gets list of markers and their positions from .geno file @@ -211,7 +211,7 @@ def build_marker_pos_list(genotype_file): return the_markers -def find_nearest_marker(the_chr, the_pos, marker_list): +def find_nearest_marker(the_chr: str, the_pos: str, marker_list: Dict) -> Tuple[str, str]: """ Given a chromosome and position of a pseudomarker (from R/qtl pair-scan results), return the nearest real marker @@ -227,7 +227,7 @@ def find_nearest_marker(the_chr, the_pos, marker_list): return proximal_marker, distal_marker -def process_perm_output(file_name: str): +def process_perm_output(file_name: str) -> Tuple[List, float, float]: """Given base filename, read in R/qtl permutation output and calculate suggestive and significant thresholds |