diff options
Diffstat (limited to 'gn3/computations/heatmap.py')
| -rw-r--r-- | gn3/computations/heatmap.py | 79 |
1 files changed, 40 insertions, 39 deletions
diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py index 1b7dfb7..a0e778a 100644 --- a/gn3/computations/heatmap.py +++ b/gn3/computations/heatmap.py @@ -57,26 +57,24 @@ def export_trait_data( return tuple(sample_data) def __exporter(accumulator, strain): - if tdata.has_key(strain): + # pylint: disable=[R0911] + if trait_data.has_key(strain): if dtype == "val": - return accumulator + (tdata[strain]["val"], ) + return accumulator + (trait_data[strain]["val"], ) if dtype == "var": - return accumulator + (tdata[strain]["var"], ) + return accumulator + (trait_data[strain]["var"], ) if dtype == "N": - return tdata[strain]["ndata"] + return trait_data[strain]["ndata"] if dtype == "all": - return accumulator + __export_all_types( - accumulator, tdata, strain) - else: - raise KeyError("Type `%s` is incorrect" % dtype) - else: - if var_exists and n_exists: - return accumulator + (None, None, None) - if var_exists or n_exists: - return accumulator + (None, None) - return accumulator + (None,) + return accumulator + __export_all_types(trait_data, strain) + raise KeyError("Type `%s` is incorrect" % dtype) + if var_exists and n_exists: + return accumulator + (None, None, None) + if var_exists or n_exists: + return accumulator + (None, None) + return accumulator + (None,) - return reduce(__exporter(strain), strainlist, tuple()) + return reduce(__exporter, strainlist, tuple()) def trait_display_name(trait: Dict): """ @@ -96,12 +94,11 @@ def trait_display_name(trait: Dict): return "%s::%s" % ( trait["db"]["displayname"], desc[:desc.index('entered')].strip()) - else: - prefix = "%s::%s" % ( - trait["db"]["dataset_name"], trait["trait_name"]) - if trait["cellid"]: - return "%s::%s" % (prefix, trait["cellid"]) - return prefix + prefix = "%s::%s" % ( + trait["db"]["dataset_name"], trait["trait_name"]) + if trait["cellid"]: + return "%s::%s" % (prefix, trait["cellid"]) + return prefix return trait["description"] def cluster_traits(traits_data_list: Sequence[Dict]): @@ -114,21 +111,21 @@ def cluster_traits(traits_data_list: Sequence[Dict]): """ def __compute_corr(tdata_i, tdata_j): if tdata_j[0] < tdata_i[0]: - corr, nOverlap = compute_correlation(tdata_i, tdata_j) + corr_vals = compute_correlation(tdata_i, tdata_j) + corr = corr_vals[0] if (1 - corr) < 0: return 0.0 return 1 - corr return 0.0 def __cluster(tdata_i): - res2 = tuple( - __compute_corr(tdata_i, tdata_j) for tdata_j in enumerate(traits)) + return tuple( + __compute_corr(tdata_i, tdata_j) + for tdata_j in enumerate(traits_data_list)) return tuple(__cluster(tdata_i) for tdata_i in enumerate(traits_data_list)) -def heatmap_data( - fd, search_result, conn: Any, colorScheme=None, userPrivilege=None, - userName=None): +def heatmap_data(formd, search_result, conn: Any): """ heatmap function @@ -144,13 +141,17 @@ def heatmap_data( PARAMETERS: TODO: Elaborate on the parameters here... """ - cluster_checked = fd.formdata.getvalue("clusterCheck", "") - strainlist = [strain for strain in fd.strainlist if strain not in fd.parlist] - genotype = fd.genotype + threshold = 0 # webqtlConfig.PUBLICTHRESH + cluster_checked = formd.formdata.getvalue("clusterCheck", "") + strainlist = [ + strain for strain in formd.strainlist if strain not in formd.parlist] + genotype = formd.genotype def __retrieve_traitlist_and_datalist(threshold, fullname): trait = retrieve_trait_info(threshold, fullname, conn) - return (trait, export_trait_data(retrieve_trait_data(trait), strainlist)) + return ( + trait, + export_trait_data(retrieve_trait_data(trait, conn), strainlist)) traits_details = [ __retrieve_traitlist_and_datalist(threshold, fullname) @@ -159,18 +160,18 @@ def heatmap_data( traits_data_list = map(lambda x: x[1], traits_details) return { - "target_description_checked": fd.formdata.getvalue( + "target_description_checked": formd.formdata.getvalue( "targetDescriptionCheck", ""), "cluster_checked": cluster_checked, "slink_data": ( - slink(cluster_traits(traits_list, strainlist)) - if cluster_checked else False) - "sessionfile": fd.formdata.getvalue("session"), + slink(cluster_traits(traits_data_list)) + if cluster_checked else False), + "sessionfile": formd.formdata.getvalue("session"), "genotype": genotype, - "nLoci": sum(map(lambda x: len(x), genotype)) + "nLoci": sum(map(len, genotype)), "strainlist": strainlist, - "ppolar": fd.ppolar, - "mpolar":fd.mpolar, - "traits_list": traits_list + "ppolar": formd.ppolar, + "mpolar":formd.mpolar, + "traits_list": traits_list, "traits_data_list": traits_data_list } |