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-rw-r--r--gn3/computations/rqtl.py38
1 files changed, 11 insertions, 27 deletions
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index cfa58a8..8d066ef 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -16,9 +16,7 @@ def generate_rqtl_cmd(rqtl_wrapper_cmd: str,
rqtl_wrapper_bool_kwargs: list) -> Dict:
"""Given the base rqtl_wrapper command and
dict of keyword arguments, return the full rqtl_wrapper command and an
-output filename generated from a hash of the genotype and phenotype files
-
- """
+output filename generated from a hash of the genotype and phenotype files"""
# Generate a hash from contents of the genotype and phenotype files
_hash = get_hash_of_files(
@@ -50,9 +48,7 @@ output filename generated from a hash of the genotype and phenotype files
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
-
- """
+ a List of marker objects"""
marker_obs = []
# Later I should probably redo this using csv.read to avoid the
# awkwardness with removing quotes with [1:-1]
@@ -83,11 +79,8 @@ def process_rqtl_mapping(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)
-
- """
-
+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)"""
figure_data = pairscan_for_figure(file_name)
table_data = pairscan_for_table(file_name, geno_file)
@@ -95,9 +88,7 @@ def process_rqtl_pairscan(file_name: str, geno_file: str) -> List:
def pairscan_for_figure(file_name: str) -> Dict:
"""Given an output file name, read in R/qtl pair-scan results and return
- the JSON needed for the d3panels figure
-
- """
+ the JSON needed for the d3panels figure"""
figure_data = {}
# Open the file with the actual results, written as a list of lists
@@ -130,9 +121,7 @@ def pairscan_for_figure(file_name: str) -> Dict:
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)
-
- """
+ a list of results to be used when generating the results table (which will include marker names)"""
table_data = []
# Open the map file with the list of markers/pseudomarkers and create list of marker obs
@@ -182,11 +171,9 @@ 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_dict(genotype_file: str) -> Dict:
- """
- Gets list of markers and their positions from .geno file
+ """Gets list of markers and their positions from .geno file
- Basically a pared-down version of parse_genotype_file for R/qtl pair-scan
- """
+ Basically a pared-down version of parse_genotype_file for R/qtl pair-scan"""
with open(genotype_file, "r") as infile:
contents = infile.readlines()
@@ -212,10 +199,8 @@ def build_marker_pos_dict(genotype_file: str) -> Dict:
return the_markers
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
- """
+ """Given a chromosome and position of a pseudomarker (from R/qtl pair-scan results),
+ return the nearest real marker"""
pos_list = [float(pos) for pos in marker_list[the_chr]]
@@ -229,9 +214,8 @@ def find_nearest_marker(the_chr: str, the_pos: str, marker_list: Dict) -> Tuple[
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
+ suggestive and significant thresholds"""
- """
perm_results = []
with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"),
"output", "PERM_" + file_name), "r", encoding="utf-8") as the_file: