diff options
Diffstat (limited to 'gn3/computations/rqtl.py')
| -rw-r--r-- | gn3/computations/rqtl.py | 38 |
1 files changed, 11 insertions, 27 deletions
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py index 38c5000..45232e3 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 @@ -129,9 +120,7 @@ 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 @@ -181,11 +170,9 @@ 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() @@ -211,10 +198,8 @@ 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]] @@ -228,9 +213,8 @@ 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") as the_file: |