Namespace all modules under gn2.

We move all modules under a gn2 directory. This is important for
"correct" packaging and deployment as a Guix service.

2 files changed, 191 insertions, 0 deletions

diff --git a/gn2/wqflask/heatmap/__init__.py b/gn2/wqflask/heatmap/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/gn2/wqflask/heatmap/__init__.py
diff --git a/gn2/wqflask/heatmap/heatmap.py b/gn2/wqflask/heatmap/heatmap.py
new file mode 100644
index 00000000..c2dd55bd
--- /dev/null
+++ b/gn2/wqflask/heatmap/heatmap.py
@@ -0,0 +1,191 @@
+import string
+import os
+import random
+from gn2.base import species
+from gn2.base import webqtlConfig
+from gn2.utility import helper_functions
+
+from gn2.utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
+from redis import Redis
+from flask import Flask, g
+
+from gn2.wqflask.database import database_connection
+from gn2.utility.tools import get_setting
+
+Redis = Redis()
+
+
+class Heatmap:
+
+    def __init__(self, db_cursor, start_vars, temp_uuid):
+        trait_db_list = [trait.strip()
+                         for trait in start_vars['trait_list'].split(',')]
+        helper_functions.get_trait_db_obs(self, trait_db_list)
+
+        self.temp_uuid = temp_uuid
+        self.num_permutations = 5000
+        self.dataset = self.trait_list[0][1]
+
+        self.json_data = {}  # The dictionary that will be used to create the json object that contains all the data needed to create the figure
+
+        self.all_sample_list = []
+        self.traits = []
+
+        chrnames = []
+        self.species = species.TheSpecies(dataset=self.trait_list[0][1])
+
+        with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as db_cursor:
+            for this_chr in self.species.chromosomes.chromosomes(db_cursor):
+                chrnames.append([self.species.chromosomes.chromosomes(db_cursor)[this_chr].name,
+                                self.species.chromosomes.chromosomes(db_cursor)[this_chr].mb_length])
+
+        for trait_db in self.trait_list:
+
+            this_trait = trait_db[0]
+            self.traits.append(this_trait.name)
+            this_sample_data = this_trait.data
+
+            for sample in this_sample_data:
+                if sample not in self.all_sample_list:
+                    self.all_sample_list.append(sample)
+
+        self.sample_data = []
+        for trait_db in self.trait_list:
+            this_trait = trait_db[0]
+            this_sample_data = this_trait.data
+
+            this_trait_vals = []
+            for sample in self.all_sample_list:
+                if sample in this_sample_data:
+                    this_trait_vals.append(this_sample_data[sample].value)
+                else:
+                    this_trait_vals.append('')
+            self.sample_data.append(this_trait_vals)
+
+        self.gen_reaper_results()
+
+        lodnames = []
+        chr_pos = []
+        pos = []
+        markernames = []
+
+        for trait in list(self.trait_results.keys()):
+            lodnames.append(trait)
+
+        self.dataset.group.get_markers()
+        for marker in self.dataset.group.markers.markers:
+            chr_pos.append(marker['chr'])
+            pos.append(marker['Mb'])
+            markernames.append(marker['name'])
+
+        self.json_data['chrnames'] = chrnames
+        self.json_data['lodnames'] = lodnames
+        self.json_data['chr'] = chr_pos
+        self.json_data['pos'] = pos
+        self.json_data['markernames'] = markernames
+
+        for trait in self.trait_results:
+            self.json_data[trait] = self.trait_results[trait]
+
+        self.js_data = dict(
+            json_data=self.json_data
+        )
+
+    def gen_reaper_results(self):
+        self.trait_results = {}
+        for trait_db in self.trait_list:
+            self.dataset.group.get_markers()
+            this_trait = trait_db[0]
+
+            genotype = self.dataset.group.read_genotype_file(use_reaper=False)
+            samples, values, variances, sample_aliases = this_trait.export_informative()
+
+            if self.dataset.group.genofile != None:
+                genofile_name = self.dataset.group.genofile[:-5]
+            else:
+                genofile_name = self.dataset.group.name
+
+            trimmed_samples = []
+            trimmed_values = []
+            for i in range(0, len(samples)):
+                if samples[i] in self.dataset.group.samplelist:
+                    trimmed_samples.append(str(samples[i]))
+                    trimmed_values.append(values[i])
+
+            trait_filename = str(this_trait.name) + "_" + \
+                str(self.dataset.name) + "_pheno"
+            gen_pheno_txt_file(trimmed_samples, trimmed_values, trait_filename)
+
+            output_filename = self.dataset.group.name + "_GWA_" + \
+                ''.join(random.choice(string.ascii_uppercase + string.digits)
+                        for _ in range(6))
+
+            reaper_command = REAPER_COMMAND + ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt -n 1000 -o {4}{5}.txt'.format(flat_files('genotype'),
+                                                                                                                           genofile_name,
+                                                                                                                           TEMPDIR,
+                                                                                                                           trait_filename,
+                                                                                                                           webqtlConfig.GENERATED_IMAGE_DIR,
+                                                                                                                           output_filename)
+
+            os.system(reaper_command)
+
+            reaper_results = parse_reaper_output(output_filename)
+
+            lrs_values = [float(qtl['lrs_value']) for qtl in reaper_results]
+
+            self.trait_results[this_trait.name] = []
+            for qtl in reaper_results:
+                if qtl['additive'] > 0:
+                    self.trait_results[this_trait.name].append(
+                        -float(qtl['lrs_value']))
+                else:
+                    self.trait_results[this_trait.name].append(
+                        float(qtl['lrs_value']))
+
+
+def gen_pheno_txt_file(samples, vals, filename):
+    """Generates phenotype file for GEMMA"""
+
+    with open("{0}/gn2/{1}.txt".format(TEMPDIR, filename), "w") as outfile:
+        outfile.write("Trait\t")
+
+        filtered_sample_list = []
+        filtered_vals_list = []
+        for i, sample in enumerate(samples):
+            if vals[i] != "x":
+                filtered_sample_list.append(sample)
+                filtered_vals_list.append(str(vals[i]))
+
+        samples_string = "\t".join(filtered_sample_list)
+        outfile.write(samples_string + "\n")
+        outfile.write("T1\t")
+        values_string = "\t".join(filtered_vals_list)
+        outfile.write(values_string)
+
+
+def parse_reaper_output(gwa_filename):
+    included_markers = []
+    p_values = []
+    marker_obs = []
+
+    with open("{}{}.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, gwa_filename)) as output_file:
+        for line in output_file:
+            if line.startswith("ID\t"):
+                continue
+            else:
+                marker = {}
+                marker['name'] = line.split("\t")[1]
+                try:
+                    marker['chr'] = int(line.split("\t")[2])
+                except:
+                    marker['chr'] = line.split("\t")[2]
+                marker['cM'] = float(line.split("\t")[3])
+                marker['Mb'] = float(line.split("\t")[4])
+                if float(line.split("\t")[7]) != 1:
+                    marker['p_value'] = float(line.split("\t")[7])
+                marker['lrs_value'] = float(line.split("\t")[5])
+                marker['lod_score'] = marker['lrs_value'] / 4.61
+                marker['additive'] = float(line.split("\t")[6])
+                marker_obs.append(marker)
+
+    return marker_obs