diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/base/data_set.py | 40 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 15 | ||||
| -rw-r--r-- | wqflask/wqflask/collect.py | 35 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/corr_scatter_plot.py | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation_matrix/show_corr_matrix.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/docs.py | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/resource_manager.py | 20 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/correlation_matrix.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/correlation_page.html | 12 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/index_page_orig.html | 10 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/wgcna/wgcna_analysis.py | 87 |
12 files changed, 108 insertions, 134 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 295f5c48..0d4ac24b 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -150,10 +150,12 @@ Publish or ProbeSet. E.g. "geno": "Geno", } + group_name = name if t in ['pheno', 'other_pheno']: - name = name.replace("Publish", "") + group_name = name.replace("Publish", "") - if bool(len(g.db.execute(sql_query_mapping[t].format(name)).fetchone())): + results = g.db.execute(sql_query_mapping[t].format(group_name)).fetchone() + if results: self.datasets[name] = dataset_name_mapping[t] self.redis_instance.set("dataset_structure", json.dumps(self.datasets)) return True @@ -1154,40 +1156,6 @@ class TempDataSet(DataSet): self.fullname = 'Temporary Storage' self.shortname = 'Temp' - @staticmethod - def handle_pca(desc): - if 'PCA' in desc: - # Todo: Modernize below lines - desc = desc[desc.rindex(':')+1:].strip() - else: - desc = desc[:desc.index('entered')].strip() - return desc - - def get_desc(self): - query = 'SELECT description FROM Temp WHERE Name=%s' % self.name - logger.sql(query) - g.db.execute(query) - desc = g.db.fetchone()[0] - desc = self.handle_pca(desc) - return desc - - def retrieve_sample_data(self, trait): - query = """ - SELECT - Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id - FROM - TempData, Temp, Strain - WHERE - TempData.StrainId = Strain.Id AND - TempData.Id = Temp.DataId AND - Temp.name = '%s' - Order BY - Strain.Name - """ % escape(trait.name) - - logger.sql(query) - results = g.db.execute(query).fetchall() - def geno_mrna_confidentiality(ob): dataset_table = ob.type + "Freeze" diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index a493cfbf..cfc02f8b 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -132,7 +132,7 @@ class GeneralTrait(object): @property def description_fmt(self): - '''Return a text formated description''' + """Return a text formated description""" if self.dataset.type == 'ProbeSet': if self.description: formatted = self.description @@ -153,7 +153,7 @@ class GeneralTrait(object): @property def alias_fmt(self): - '''Return a text formatted alias''' + """Return a text formatted alias""" alias = 'Not available' if getattr(self, "alias", None): @@ -164,7 +164,7 @@ class GeneralTrait(object): @property def wikidata_alias_fmt(self): - '''Return a text formatted alias''' + """Return a text formatted alias""" alias = 'Not available' if self.symbol: @@ -194,12 +194,12 @@ class GeneralTrait(object): @property def location_fmt(self): - '''Return a text formatted location + """Return a text formatted location While we're at it we set self.location in case we need it later (do we?) - ''' + """ if self.chr and self.mb: self.location = 'Chr %s @ %s Mb' % (self.chr, self.mb) @@ -542,7 +542,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): if (str(description_display or "") != "" and description_display != 'N/A' and - str(target_string or "") != "" and target_string != 'None'): + str(target_string or "") != "" and target_string != 'None'): description_display = description_display + '; ' + target_string.strip() # Save it for the jinja2 template @@ -631,7 +631,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): else: trait.locus = trait.lrs = trait.additive = "" if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and str(trait.locus_chr or "") != "" and str(trait.locus_mb or "") != "": - trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb)) + trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % ( + trait.locus_chr, float(trait.locus_mb)) if str(trait.lrs or "") != "": trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs else: diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 9752c8b5..e074a3d8 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -1,38 +1,29 @@ -import os import hashlib import datetime -import time - -import uuid -import hashlib -import base64 - -import urllib.parse - import simplejson as json -from flask import (Flask, g, render_template, url_for, request, make_response, - redirect, flash, jsonify) +from flask import g +from flask import render_template +from flask import url_for +from flask import request +from flask import redirect +from flask import flash from wqflask import app - -from pprint import pformat as pf - -from wqflask.database import db_session - -from wqflask import model - -from utility import Bunch, Struct, hmac +from utility import hmac from utility.formatting import numify from utility.redis_tools import get_redis_conn -Redis = get_redis_conn() -from base.trait import create_trait, retrieve_trait_info, jsonable +from base.trait import create_trait +from base.trait import retrieve_trait_info +from base.trait import jsonable from base.data_set import create_dataset -import logging from utility.logger import getLogger + logger = getLogger(__name__) +Redis = get_redis_conn() + def process_traits(unprocessed_traits): if isinstance(unprocessed_traits, bytes): diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index 929cd2c9..6ab8c3d8 100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py @@ -15,8 +15,15 @@ class CorrScatterPlot(object): """Page that displays a correlation scatterplot with a line fitted to it""" def __init__(self, params): - self.dataset_1 = data_set.create_dataset(params['dataset_1']) - self.dataset_2 = data_set.create_dataset(params['dataset_2']) + if "Temp" in params['dataset_1']: + self.dataset_1 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_1'].split("_")[1]) + else: + self.dataset_1 = data_set.create_dataset(params['dataset_1']) + if "Temp" in params['dataset_2']: + self.dataset_2 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_2'].split("_")[1]) + else: + self.dataset_2 = data_set.create_dataset(params['dataset_2']) + #self.dataset_3 = data_set.create_dataset(params['dataset_3']) self.trait_1 = create_trait(name=params['trait_1'], dataset=self.dataset_1) self.trait_2 = create_trait(name=params['trait_2'], dataset=self.dataset_2) diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index f24b9f7f..a394f548 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -124,7 +124,7 @@ class CorrelationMatrix(object): if num_overlap < self.lowest_overlap: self.lowest_overlap = num_overlap - if num_overlap == 0: + if num_overlap < 2: corr_result_row.append([target_trait, 0, num_overlap]) pca_corr_result_row.append(0) else: diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py index 8628b81d..d653c269 100644 --- a/wqflask/wqflask/docs.py +++ b/wqflask/wqflask/docs.py @@ -9,7 +9,7 @@ class Docs(object): def __init__(self, entry, start_vars={}): sql = """ - SELECT Docs.title, Docs.content + SELECT Docs.title, CAST(Docs.content AS BINARY) FROM Docs WHERE Docs.entry LIKE %s """ @@ -20,7 +20,7 @@ class Docs(object): self.content = "" else: self.title = result[0] - self.content = result[1].encode("latin1") + self.content = result[1] self.editable = "false" # ZS: Removing option to edit to see if text still gets vandalized diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py index e883d5da..85cbb2fd 100644 --- a/wqflask/wqflask/resource_manager.py +++ b/wqflask/wqflask/resource_manager.py @@ -23,16 +23,16 @@ def manage_resource(): group_masks_with_names = get_group_names(group_masks) default_mask = resource_info['default_mask']['data'] owner_id = resource_info['owner_id'] - owner_info = get_user_by_unique_column("user_id", owner_id) - - if 'name' in owner_info: - owner_display_name = owner_info['full_name'] - elif 'user_name' in owner_info: - owner_display_name = owner_info['user_name'] - elif 'email_address' in owner_info: - owner_display_name = owner_info['email_address'] - else: - owner_display_name = None + + owner_display_name = None + if owner_id != "none": + owner_info = get_user_by_unique_column("user_id", owner_id) + if 'name' in owner_info: + owner_display_name = owner_info['full_name'] + elif 'user_name' in owner_info: + owner_display_name = owner_info['user_name'] + elif 'email_address' in owner_info: + owner_display_name = owner_info['email_address'] return render_template("admin/manage_resource.html", owner_name = owner_display_name, resource_id = resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names, admin_status=admin_status) diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index 9b96de1c..d556f31a 100644 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -51,7 +51,7 @@ {% if result[0].name == trait.name and result[0].dataset == trait.dataset %} <td nowrap="ON" align="center" bgcolor="#cccccc" style="padding: 3px; line-height: 1.1;"><a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><em>n</em><br>{{ result[2] }}</font></a></td> {% else %} - <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={{ trait.dataset.name }}&dataset_2={{ result[0].dataset.name }}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td> + <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&dataset_2={% if result[0].dataset.name == 'Temp' %}Temp_{{ result[0].dataset.group.name }}{% else %}{{ result[0].dataset.name }}{% endif %}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td> {% endif %} {% endfor %} </tr> diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index 435c0b37..134f15be 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -144,7 +144,7 @@ <td data-export="{{ trait.description_display }}">{{ trait.description_display }}</TD> <td data-export="{{ trait.location_repr }}" style="white-space: nowrap;">{{ trait.location_repr }}</td> <td data-export="{{ '%0.3f' % trait.mean|float }}" align="right">{{ '%0.3f' % trait.mean|float }}</td> - <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td> + <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td> <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td> <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td> {% if trait.lit_corr == "" or trait.lit_corr == 0.000 %} @@ -164,16 +164,16 @@ <td data-export={% if trait.additive != "" %}"{{ '%0.3f' % trait.additive|float }}"{% else %}"N/A"{% endif %} align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td> {% elif target_dataset.type == "Publish" %} {% if trait.abbreviation %} - <TD title="{{ trait.abbreviation }}" data-export="{{ trait.abbreviation }}">{% if trait.abbreviation|length > 20 %}{{ trait.abbreviation[:20] }}...{% else %}{{ trait.abbreviation }}{% endif %}</TD> + <td title="{{ trait.abbreviation }}" data-export="{{ trait.abbreviation }}">{% if trait.abbreviation|length > 20 %}{{ trait.abbreviation[:20] }}...{% else %}{{ trait.abbreviation }}{% endif %}</td> {% else %} - <TD data-export="N/A">N/A</TD> + <td data-export="N/A">N/A</td> {% endif %} <td data-export="{{ trait.description_display }}">{% if trait.description_display|length > 70 %}{{ trait.description_display[:70] }}...{% else %}{{ trait.description_display }}{% endif %}</td> {% if trait.authors %} {% set authors_list = trait.authors.split(',') %} <td data-export="{{ trait.authors }}">{% if authors_list|length > 6 %}{{ authors_list[:6]|join(', ') }}, et al.{% else %}{{ trait.authors }}{% endif %}</td> {% else %} - <TD data-export="N/A">N/A</TD> + <td data-export="N/A">N/A</td> {% endif %} <td data-export="{{ trait.pubmed_text }}"> {% if trait.pubmed_text != "N/A" %} @@ -184,7 +184,7 @@ {{ trait.pubmed_text }} {% endif %} </td> - <td data-export="{{ '%0.3f'|format(trait.sample_r) }}" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td> + <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={{ trait.dataset.name }}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td> <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td> <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td> <td data-export="{{ trait.LRS_score_repr }}" align="right">{{ trait.LRS_score_repr }}</td> @@ -192,7 +192,7 @@ <td data-export={% if trait.additive != "" %}"{{ '%0.3f' % trait.additive|float }}"{% else %}"N/A"{% endif %} align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td> {% elif target_dataset.type == "Geno" %} <td data-export="{{ trait.location_repr }}" align="right">{{ trait.location_repr }}</TD> - <td data-export="{{ '%0.3f'|format(trait.sample_r) }}" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td> + <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={{ trait.dataset.name }}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td> <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td> <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td> {% endif %} diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html index 06b71f53..6b3bec9a 100755 --- a/wqflask/wqflask/templates/index_page_orig.html +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -17,13 +17,13 @@ </header> --> - <div class="container-fluid" style="min-width: 1200px;"> + <div class="container-fluid" style="min-width: 1210px;"> {{ flash_me() }} <div class="row" style="width: 100%;"> - <div class="col-xs-5" style="min-width: 530px; max-width: 550px;"> + <div class="col-xs-4" style="margin-right:50px; min-width: 530px; max-width: 550px;"> <section id="search"> <div> <h1>Select and search</h1> @@ -84,7 +84,7 @@ <label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label> <div class="col-xs-10 controls" style="padding-left: 20px;"> <div class="col-8"> - <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea> + <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="or_search"></textarea> </div> </div> </div> @@ -105,7 +105,7 @@ <label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label> <div class="col-xs-10 controls" style="padding-left: 20px;"> <div class="col-8"> - <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea> + <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="and_search"></textarea> </div> </div> </div> @@ -184,7 +184,7 @@ </section> </div> - <div style="padding-left:80px" class="col-xs-4" style="width: 600px !important;"> + <div class="col-xs-4" style="width: 600px !important;"> <section id="affiliates"> <div class="page-header"> <h1>Affiliates</h1> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index c37be418..08673f79 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -48,7 +48,7 @@ from wqflask.search_results import SearchResultPage from wqflask.export_traits import export_search_results_csv from wqflask.gsearch import GSearch from wqflask.update_search_results import GSearch as UpdateGSearch -from wqflask.docs import Docs +from wqflask.docs import Docs, update_text from wqflask.db_info import InfoPage from utility import temp_data @@ -346,7 +346,7 @@ def environments(): @app.route("/update_text", methods=('POST',)) def update_page(): - docs.update_text(request.form) + update_text(request.form) doc = Docs(request.form['entry_type'], request.form) return render_template("docs.html", **doc.__dict__) diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py index 93742daf..c6e03ec5 100644 --- a/wqflask/wqflask/wgcna/wgcna_analysis.py +++ b/wqflask/wqflask/wgcna/wgcna_analysis.py @@ -1,5 +1,8 @@ -# WGCNA analysis for GN2 -# Author / Maintainer: Danny Arends <Danny.Arends@gmail.com> +""" +WGCNA analysis for GN2 + +Author / Maintainer: Danny Arends <Danny.Arends@gmail.com> +""" import base64 import sys import rpy2.robjects as ro # R Objects @@ -16,35 +19,34 @@ from utility import helper_functions 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 +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 WGCNA(object): def __init__(self): + # To log output from stdout/stderr to a file add `r_sink(log)` print("Initialization of WGCNA") - #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") + # Load WGCNA - Should only be done once, since it is quite expensive r_library("WGCNA") r_options(stringsAsFactors=False) @@ -67,11 +69,12 @@ class WGCNA(object): self.r_enableWGCNAThreads() self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')] - print(("Retrieved phenotype data from database", - requestform['trait_list'])) + 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 + # self.input contains the phenotype values we need to send to R + self.input = {} # All the strains we have data for (contains duplicates) strains = [] # All the traits we have data for (should not contain duplicates) @@ -91,7 +94,8 @@ class WGCNA(object): r_cat("The number of unique strains:", r_length(uStrainsR), "\n") r_cat("The number of unique traits:", r_length(uTraitsR), "\n") - # rM is the datamatrix holding all the data in R /rows = strains columns = traits + # rM is the datamatrix holding all the data in + # R /rows = strains columns = traits rM = ro.r.matrix(ri.NA_Real, nrow=r_length(uStrainsR), ncol=r_length( uTraitsR), dimnames=r_list(uStrainsR, uTraitsR)) for t in uTraitsR: @@ -100,7 +104,6 @@ class WGCNA(object): for s in uStrainsR: # R uses vectors every single element is a vector strain = s[0] - #DEBUG: print(trait, strain, " in python: ", self.input[trait].get(strain), "in R:", rM.rx(strain,trait)[0]) rM.rx[strain, trait] = self.input[trait].get( strain) # Update the matrix location sys.stdout.flush() @@ -116,19 +119,20 @@ class WGCNA(object): # Store the user specified parameters for the output page self.results['requestform'] = requestform - # Calculate soft threshold if the user specified the SoftThreshold variable + # Calculate soft threshold if the user specified the + # SoftThreshold variable if requestform.get('SoftThresholds') is not None: powers = [int(threshold.strip()) for threshold in requestform['SoftThresholds'].rstrip().split(",")] rpow = r_unlist(r_c(powers)) - print(("SoftThresholds: {} == {}".format(powers, rpow))) + print("SoftThresholds: {} == {}".format(powers, rpow)) self.sft = self.r_pickSoftThreshold( rM, powerVector=rpow, verbose=5) - print(("PowerEstimate: {}".format(self.sft[0]))) + print("PowerEstimate: {}".format(self.sft[0])) self.results['PowerEstimate'] = self.sft[0] if self.sft[0][0] is ri.NA_Integer: - print("No power is suitable for the analysis, just use 1") + print "No power is suitable for the analysis, just use 1" # No power could be estimated self.results['Power'] = 1 else: @@ -141,7 +145,11 @@ class WGCNA(object): # Create the block wise modules using WGCNA network = self.r_blockwiseModules( - rM, power=self.results['Power'], TOMType=requestform['TOMtype'], minModuleSize=requestform['MinModuleSize'], verbose=3) + rM, + power=self.results['Power'], + TOMType=requestform['TOMtype'], + minModuleSize=requestform['MinModuleSize'], + verbose=3) # Save the network for the GUI self.results['network'] = network @@ -155,8 +163,9 @@ class WGCNA(object): self.results['imgloc'] = GENERATED_IMAGE_DIR + self.results['imgurl'] r_png(self.results['imgloc'], width=1000, height=600, type='cairo-png') mergedColors = self.r_labels2colors(network[1]) - self.r_plotDendroAndColors(network[5][0], mergedColors, "Module colors", - dendroLabels=False, hang=0.03, addGuide=True, guideHang=0.05) + self.r_plotDendroAndColors(network[5][0], mergedColors, + "Module colors", dendroLabels=False, + hang=0.03, addGuide=True, guideHang=0.05) r_dev_off() sys.stdout.flush() @@ -177,6 +186,4 @@ class WGCNA(object): template_vars["results"] = self.results self.render_image(results) sys.stdout.flush() - # r_sink(type = "message") # This restores R output to the stdout/stderr - # r_sink() # We should end the Rpy session more or less return(dict(template_vars)) |