diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/ctl/ctl_analysis.py | 28 |
1 files changed, 9 insertions, 19 deletions
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index f998dc59..71c41135 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -76,6 +76,7 @@ class CTL(object): self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')] self.trait_db_list = [x for x in self.trait_db_list if x] + # Get the name of the .geno file belonging to the first phenotype datasetname = self.trait_db_list[0].split(":")[1] dataset = data_set.create_dataset(datasetname) @@ -83,28 +84,20 @@ class CTL(object): parser = genofile_parser.ConvertGenoFile(genofilelocation) parser.process_csv() + # Create a genotype matrix individuals = parser.individuals markers = [] markernames = [] - x = 1 for marker in parser.markers: markernames.append(marker["name"]) markers.append(marker["genotypes"]) - if x == 1: - print marker["genotypes"] - x = x +1 - genotypes = list(itertools.chain(*markers)) print(len(genotypes) / len(individuals), "==", len(parser.markers)) rGeno = r_t(ro.r.matrix(r_unlist(genotypes), nrow=len(markernames), ncol=len(individuals), dimnames = r_list(markernames, individuals), byrow=True)) - print(r_dim(rGeno)) - #self.trait_names = [trait.split(':')[0].strip() for trait in self.trait_db_list] - #print(self.trait_names) - - + # Create a phenotype matrix traits = [] for trait in self.trait_db_list: print("retrieving data for", trait) @@ -118,28 +111,25 @@ class CTL(object): else: traits.append("-999") - print len(traits) / len(individuals), "==", len(self.trait_db_list) rPheno = r_t(ro.r.matrix(r_unlist(traits), nrow=len(self.trait_db_list), ncol=len(individuals), dimnames = r_list(self.trait_db_list, individuals), byrow=True)) + # Use a data frame to store the objects rPheno = r_data_frame(rPheno) rGeno = r_data_frame(rGeno) - print(r_class(rPheno)) - print(r_class(rGeno)) - - - - r_write_table(rPheno, "~/pheno.csv") - r_write_table(rGeno, "~/geno.csv") + # Perform the CTL scan res = self.r_CTLscan(rGeno, rPheno) + # Create an image for output self.results = {} self.results['imgurl'] = webqtlUtil.genRandStr("WGCNAoutput_") + ".png" self.results['imgloc'] = GENERATED_IMAGE_DIR + self.results['imgurl'] r_png(self.results['imgloc'], width=1000, height=600) self.r_lineplot(res, significance = 1) r_dev_off() - # sys.stdout.flush() + + # Flush any output from R + sys.stdout.flush() def render_image(self, results): print("pre-loading imgage results:", self.results['imgloc']) |