diff options
| -rwxr-xr-x | wqflask/wqflask/ctl/__init__.py | 0 | ||||
| -rw-r--r-- | wqflask/wqflask/ctl/ctl_analysis.py | 87 |
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)) + |