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authorDannyArends2016-03-23 23:08:12 +0100
committerPjotr Prins2016-04-20 10:17:51 +0000
commit210d8109a4171ddf6ea6a3f70a1bfbea7b327722 (patch)
treea655cc1eda7be8ffe0a2a71e27d37545e1c0675a
parent3d505d997511cd8f7b9f14510059cb2983edc6d4 (diff)
downloadgenenetwork2-210d8109a4171ddf6ea6a3f70a1bfbea7b327722.tar.gz
Adding code to do initial CTL mapping (working on the BXD)
-rw-r--r--wqflask/wqflask/ctl/ctl_analysis.py99
1 files changed, 77 insertions, 22 deletions
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 8a2f1954..f998dc59 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -13,6 +13,10 @@ from utility import genofile_parser # genofile_parser
import base64
import array
import csv
+import itertools
+
+from base import data_set
+from base import trait as TRAIT
from utility import helper_functions
from utility.tools import locate
@@ -26,9 +30,11 @@ r_options = ro.r["options"] # Map the options function
r_read_csv = ro.r["read.csv"] # Map the read.csv function
r_dim = ro.r["dim"] # Map the dim function
r_c = ro.r["c"] # Map the c function
+r_t = ro.r["t"] # Map the t function
r_cat = ro.r["cat"] # Map the cat function
r_paste = ro.r["paste"] # Map the paste function
r_unlist = ro.r["unlist"] # Map the unlist function
+r_head = ro.r["head"] # Map the unlist function
r_unique = ro.r["unique"] # Map the unique function
r_length = ro.r["length"] # Map the length function
r_unlist = ro.r["unlist"] # Map the unlist function
@@ -42,6 +48,12 @@ r_is_NA = ro.r["is.na"] # Map the is.na function
r_file = ro.r["file"] # Map the file function
r_png = ro.r["png"] # Map the png function for plotting
r_dev_off = ro.r["dev.off"] # Map the dev.off function
+r_save_image = ro.r["save.image"] # Map the save.image function
+r_class = ro.r["class"] # Map the class function
+r_save = ro.r["save"] # Map the save function
+r_write_table = ro.r["write.table"] # Map the write.table function
+r_as_data_frame = ro.r["as.data.frame"] # Map the write.table function
+r_data_frame = ro.r["data.frame"] # Map the write.table function
class CTL(object):
def __init__(self):
@@ -61,31 +73,73 @@ class CTL(object):
def run_analysis(self, requestform):
print("Starting CTL analysis on dataset")
-
self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')]
- print("Retrieved phenotype data from database", requestform['trait_list'])
-
- helper_functions.get_trait_db_obs(self, self.trait_db_list)
-
- self.input = {} # self.input contains the phenotype values we need to send to R
- strains = [] # All the strains we have data for (contains duplicates)
- traits = [] # All the traits we have data for (should not contain duplicates)
- genotypebasename = ""
- for trait in self.trait_list:
- traits.append(trait[0].name)
- if genotypebasename == "":
- genotypebasename = trait[1].group.name
- self.input[trait[0].name] = {}
- for strain in trait[0].data:
- strains.append(strain)
- self.input[trait[0].name][strain] = trait[0].data[strain].value
-
- genofilelocation = locate(genotypebasename + ".geno", "genotype")
+ self.trait_db_list = [x for x in self.trait_db_list if x]
+
+ datasetname = self.trait_db_list[0].split(":")[1]
+ dataset = data_set.create_dataset(datasetname)
+
+ genofilelocation = locate(dataset.group.name + ".geno", "genotype")
parser = genofile_parser.ConvertGenoFile(genofilelocation)
parser.process_csv()
- print(parser.markers)
+
+ 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)
+
+
+ traits = []
+ for trait in self.trait_db_list:
+ print("retrieving data for", trait)
+ if trait != "":
+ ts = trait.split(':')
+ gt = TRAIT.GeneralTrait(name = ts[0], dataset_name = ts[1])
+ gt.retrieve_sample_data(individuals)
+ for ind in individuals:
+ if ind in gt.data.keys():
+ traits.append(gt.data[ind].value)
+ 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))
+
+ 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")
+ res = self.r_CTLscan(rGeno, rPheno)
+
self.results = {}
- sys.stdout.flush()
+ 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()
def render_image(self, results):
print("pre-loading imgage results:", self.results['imgloc'])
@@ -98,7 +152,8 @@ class CTL(object):
def process_results(self, results):
print("Processing CTL output")
template_vars = {}
- template_vars["input"] = self.input
+ template_vars["results"] = self.results
+ self.render_image(self.results)
sys.stdout.flush()
return(dict(template_vars))