diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/computations/heatmap.py | 49 |
1 files changed, 48 insertions, 1 deletions
diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py index 1143450..ccce385 100644 --- a/gn3/computations/heatmap.py +++ b/gn3/computations/heatmap.py @@ -30,7 +30,7 @@ def export_trait_data( The dictionary of key-value pairs representing a trait strainlist: (list) A list of strain names - type: (str) + dtype: (str) ... verify what this is ... var_exists: (bool) A flag indicating existence of variance @@ -232,3 +232,50 @@ def retrieve_strains_and_values(orders, strainlist, traits_data_list): values = [] return rets + +def nearest_marker_finder(genotype): + """ + Returns a function to be used with `genotype` to compute the nearest marker + to the trait passed to the returned function. + + https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L425-434 + """ + def __compute_distances(chromo, trait): + loci = chromo.get("loci", None) + if not loci: + return None + return tuple( + { + "name": locus["name"], + "distance": abs(locus["Mb"] - trait["mb"]) + } for locus in loci) + + def __finder(trait): + _chrs = tuple( + _chr for _chr in genotype["chromosomes"] + if str(_chr["name"]) == str(trait["chr"])) + if len(_chrs) == 0: + return None + distances = tuple( + distance for dists in + filter( + lambda x: x is not None, + (__compute_distances(_chr, trait) for _chr in _chrs)) + for distance in dists) + nearest = min(distances, key=lambda d: d["distance"]) + return nearest["name"] + return __finder + +def get_nearest_marker(traits_list, genotype): + """ + Retrieves the nearest marker for each of the traits in the list. + + DESCRIPTION: + This migrates the code in + https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L419-L438 + """ + if not genotype["Mbmap"]: + return [None] * len(trait_list) + + marker_finder = nearest_marker_finder(genotype) + return [marker_finder(trait) for trait in traits_list] |