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authorDannyArends2016-03-22 23:38:18 +0100
committerPjotr Prins2016-04-20 10:17:27 +0000
commit179b8eab7528db15f5c97733c94a5e24dbfed661 (patch)
tree7abd8dede9c429cafb160b88ee7dfcf82d5ee124 /wqflask
parenta13baa5fb98d8167e70df7008d0d07b40a05a6b9 (diff)
downloadgenenetwork2-179b8eab7528db15f5c97733c94a5e24dbfed661.tar.gz
Using the geno parser to get/parse the genotypes for the dataset
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/ctl/ctl_analysis.py19
1 files changed, 17 insertions, 2 deletions
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 3159ad7f..8a2f1954 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -8,11 +8,14 @@ import rpy2.rinterface as ri
from base.webqtlConfig import GENERATED_IMAGE_DIR
from utility import webqtlUtil # Random number for the image
+from utility import genofile_parser # genofile_parser
import base64
import array
+import csv
from utility import helper_functions
+from utility.tools import locate
from rpy2.robjects.packages import importr
utils = importr("utils")
@@ -43,13 +46,17 @@ r_dev_off = ro.r["dev.off"] # Map the dev.off function
class CTL(object):
def __init__(self):
print("Initialization of CTL")
- #log = r_file("/tmp/genenetwork_wcgna.log", open = "wt")
+ #log = r_file("/tmp/genenetwork_ctl.log", open = "wt")
#r_sink(log) # Uncomment the r_sink() commands to log output from stdout/stderr to a file
#r_sink(log, type = "message")
r_library("ctl") # Load CTL - Should only be done once, since it is quite expensive
r_options(stringsAsFactors = False)
print("Initialization of CTL done, package loaded in R session")
- self.r_CTLscan = ro.r["CTLscan"] # Map the CTLscan function
+ self.r_CTLscan = ro.r["CTLscan"] # Map the CTLscan function
+ self.r_CTLsignificant = ro.r["CTLsignificant"] # Map the CTLsignificant function
+ self.r_lineplot = ro.r["ctl.lineplot"] # Map the ctl.lineplot function
+ self.r_CTLnetwork = ro.r["CTLnetwork"] # Map the CTLnetwork function
+ self.r_CTLprofiles = ro.r["CTLprofiles"] # Map the CTLprofiles function
print("Obtained pointers to CTL functions")
def run_analysis(self, requestform):
@@ -57,18 +64,26 @@ class CTL(object):
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")
+ parser = genofile_parser.ConvertGenoFile(genofilelocation)
+ parser.process_csv()
+ print(parser.markers)
self.results = {}
sys.stdout.flush()