aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask')
-rwxr-xr-xwqflask/wqflask/ctl/__init__.py0
-rw-r--r--wqflask/wqflask/ctl/ctl_analysis.py87
2 files changed, 87 insertions, 0 deletions
diff --git a/wqflask/wqflask/ctl/__init__.py b/wqflask/wqflask/ctl/__init__.py
new file mode 100755
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/wqflask/ctl/__init__.py
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
new file mode 100644
index 00000000..13f08a0f
--- /dev/null
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -0,0 +1,87 @@
+# CTL analysis for GN2
+# Author / Maintainer: Danny Arends <Danny.Arends@gmail.com>
+import sys
+from numpy import *
+import scipy as sp # SciPy
+import rpy2.robjects as ro # R Objects
+import rpy2.rinterface as ri
+
+from base.webqtlConfig import GENERATED_IMAGE_DIR
+from utility import webqtlUtil # Random number for the image
+
+import base64
+import array
+
+from utility import helper_functions
+
+from rpy2.robjects.packages import importr
+utils = importr("utils")
+
+## Get pointers to some common R functions
+r_library = ro.r["library"] # Map the library function
+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_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_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
+r_list = ro.r.list # Map the list function
+r_matrix = ro.r.matrix # Map the matrix function
+r_seq = ro.r["seq"] # Map the seq function
+r_table = ro.r["table"] # Map the table function
+r_names = ro.r["names"] # Map the names function
+r_sink = ro.r["sink"] # Map the sink function
+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
+
+class CTL(object):
+ def __init__(self):
+ print("Initialization of CTL")
+ #log = r_file("/tmp/genenetwork_wcgna.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 WGCNA - 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
+ print("Obtained pointers to CTL functions")
+
+ 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)
+ for trait in self.trait_list:
+ traits.append(trait[0].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
+ sys.stdout.flush()
+
+ def render_image(self, results):
+ print("pre-loading imgage results:", self.results['imgloc'])
+ imgfile = open(self.results['imgloc'], 'rb')
+ imgdata = imgfile.read()
+ imgB64 = imgdata.encode("base64")
+ bytesarray = array.array('B', imgB64)
+ self.results['imgdata'] = bytesarray
+
+ def process_results(self, results):
+ print("Processing WGCNA output")
+ template_vars = {}
+ template_vars["input"] = self.input
+ sys.stdout.flush()
+ return(dict(template_vars))
+