release 0.9

seanlaidlaw · Apr 7, 2019 · 27fc0e7 · 27fc0e7
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diff --git a/README.md b/README.md
@@ -1,17 +1,14 @@
-[![Known Vulnerabilities](https://snyk.io/test/github/SL-LAIDLAW/Metallaxis/badge.svg?targetFile=requirements.txt)](https://snyk.io/test/github/SL-LAIDLAW/Metallaxis?targetFile=requirements.txt)
 [![Maintainability](https://api.codeclimate.com/v1/badges/636053f63e1587622300/maintainability)](https://codeclimate.com/github/SL-LAIDLAW/Metallaxis/maintainability)
-[![Documentation Status](https://readthedocs.org/projects/metallaxis/badge/?version=latest)](https://metallaxis.readthedocs.io/en/latest/?badge=latest)
-[![PyPI version](https://badge.fury.io/py/Metallaxis.svg)](https://badge.fury.io/py/Metallaxis)
-
+[![PyPI version](https://badge.fury.io/py/Metallaxis.svg)](https://badge.fury.io/py/Metallaxis) 
 [![Python 3.6](https://img.shields.io/badge/python-3.6-blue.svg)](https://www.python.org/downloads/release/python-360/)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
 # Metallaxis
 
 Metallaxis is a Python graphical interface for viewing and annotating VCF
-files. On loading a VCF file or compressed variant (vcf.gz,vcf.xz) it will make
-an API call to EMSEMBL's [VEP](https://www.ensembl.org/vep) with the IDs of the
-VCF.
+files. On loading a VCF file or compressed variant (vcf.gz,vcf.xz) it will generate statistics, graphs, and open a table view where the variants can be sorted, filtered, and their position visualised compared to the location of genes, based on data retrieved from API requests to ENSEMBL.
+
+Additionally, there is the option to annotate the VCF, whereby the dbSNP and clinVar databases are downloaded and SnpEff is used to annotate the VCF, to view the impact of the variant.
 
 On the interface basic statistics and graphs are displayed in the
 statistics pane, and a Table pane is also avaliable on which variants can be
@@ -20,12 +17,12 @@ filtered by data from VCF, from annotation, or parsed form the INFO column.
 ## Features
 - INFO column splitting into columns that can be sorted
 - Filtering of all VCF columns
-- Automatic annotation from VEP (provided VCF is human)
+- Automatic annotation from dbSNP, ClinVar, and ENSEMBL (provided VCF is human)
 - Automatically generated statistics and graphs
-- Savable analysis as a HDF5 data store
+- Savable analysis as a portable sqlite database
 
 ## Authors
-Sean Laidlaw & Qiqi He
+Sean Laidlaw
 
 ## Requirements:
 Python:
@@ -35,10 +32,10 @@ Libraries
 - python-magic : 0.4.15
 - pandas : 0.23.4
 - numpy : 1.15.4
-- tables : 3.4.4
 - PyQt5 : 5.11.2
 - requests : 2.20.1
 - matplotlib : 3.0.2
+- wget : 3.2
 
 
 ## Installation
@@ -76,38 +73,34 @@ python3 -m metallaxis ../samples/1000_genomes_extract.vcf.gz
 Or to load a previously saved Metallaxis session, by using the saved HDF5 as
 argument:
 ```bash
-python3 -m metallaxis ../saves/big_saved_analysis.h5
+python3 -m metallaxis ../saves/big_saved_analysis.sqlite
 ```
 
 
 ## Screenshots
 
-Changing the Species to "Human" in the Settings window allows you to check "Annotate Variants", meaning that the next loaded file will have its IDs sent to be annotated from the VEP API. 
-
-![settings_annot_off](img/interface_settings_annotation_off.png)
-![settings_annot_on](img/interface_settings_annotation_on.png)
-
-Example variant data displaying statistics of variants by chromosome, types of variants, and averages. As well as number of variants by position for each chromosome.
+Example variant data displaying statistics of variants by chromosome, as well as number of variants by position for each chromosome.
 ![window_statistics](img/interface_window_statistics.png)
 ![window_statistics_pos](img/interface_window_statistics_pos.png)
 
-Example variant data with VEP annotation listing consequence terms, biotype, gene id, impact, etc. for some of our variants.
+Example variant data with annotation listing consequence terms, biotype, gene id, impact, etc. for some of our variants.
 
 ![window_annotation](img/interface_window_annotation.png)
 
 Example data showing off filtering ability of _Metallaxis_, not just limited to normal VCF columns but works equally well on recently obtained annotation columns:
 
 ![window_filter](img/interface_window_filter.png)
 
+Visualising variant position compared to nearby genes is also easy, with a customisable window, allowing zooming in or out.
 
+![gene_view](img/interface_window_gene_view.png)
+![gene_view](img/interface_window_gene_view_zoom.png)
 
 
 ## TODO
-1. Rewrite API request to retry in case of server error
 1. Generate statistics off of annotation data
 1. Write documentation to be generated by Sphinx
 1. Split \_\_main__ into separate files for easy importing and readability
-1. Optimise writing annotation data to HDF5 to reduce performance bottleneck
 1. Add secondary annotation to get ontology and phenotype information
 
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -26,7 +26,7 @@
 # The short X.Y version
 version = ''
 # The full version, including alpha/beta/rc tags
-release = '0.8'
+release = '0.9'
 
 
 # -- General configuration ---------------------------------------------------
@@ -176,4 +176,4 @@
 epub_exclude_files = ['search.html']
 
 
-# -- Extension configuration -------------------------------------------------
+# -- Extension configuration -------------------------------------------------
diff --git a/img/interface_settings_annotation_off.png b/img/interface_settings_annotation_off.png
diff --git a/img/interface_settings_annotation_on.png b/img/interface_settings_annotation_on.png
diff --git a/img/interface_window_gene_view.png b/img/interface_window_gene_view.png
diff --git a/img/interface_window_gene_view_zoom.png b/img/interface_window_gene_view_zoom.png
diff --git a/img/interface_window_statistics.png b/img/interface_window_statistics.png
diff --git a/metallaxis/MetallaxisGui.ui b/metallaxis/MetallaxisGui.ui
@@ -30,7 +30,7 @@
        <enum>Qt::LeftToRight</enum>
       </property>
       <property name="currentIndex">
-          <number>2</number>
+          <number>1</number>
       </property>
       <property name="usesScrollButtons">
        <bool>false</bool>
@@ -245,14 +245,21 @@
                <number>0</number>
               </property>
               <item>
-               <widget class="QLabel" name="label_3">
+                  <widget class="QLabel" name="chrom_selection_label">
+                      <property name="enabled">
+                          <bool>false</bool>
+                      </property>
                 <property name="text">
                  <string>Choose a chromosome to view variants by position:</string>
                 </property>
                </widget>
               </item>
               <item>
-               <widget class="QComboBox" name="chrom_selection_stat_comboBox"/>
+                  <widget class="QComboBox" name="chrom_selection_stat_comboBox">
+                      <property name="enabled">
+                          <bool>false</bool>
+                      </property>
+                  </widget>
               </item>
              </layout>
             </item>

diff --git a/metallaxis/SVGClasses.py b/metallaxis/SVGClasses.py
@@ -1,4 +1,5 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
 """\
 SVG.py - Construct/display SVG scenes.
 

diff --git a/metallaxis/__main__.py b/metallaxis/__main__.py
@@ -35,7 +35,7 @@
 from PyQt5.QtSvg import QSvgWidget
 
 # Import SVG Drawing Classes
-import SVGClasses
+from metallaxis import SVGClasses
 
 # for plotting graphs
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
@@ -565,9 +565,13 @@ def database_encode(decompressed_file, variant_stats, metadata_dict):
 	(metadata_dict). Then encodes them as tables into a database.
 	Returns filename of created sqlite database.
 	"""
-	os.remove(sqlite_output_name)
 	sqlite_output = sqlite3.connect(sqlite_output_name)
-	# conn = sqlite_connection.cursor()
+	cursor = sqlite_connection.cursor()
+	cursor.execute("DROP TABLE IF EXISTS df;")
+	cursor.execute("DROP TABLE IF EXISTS stats;")
+	cursor.execute("DROP TABLE IF EXISTS metadata;")
+	cursor.execute("DROP TABLE IF EXISTS chrom_genes;")
+	sqlite_output.commit()
 
 	# write each entry from metadata_dict to a new "metadata" table in database
 	for metadata_line_nb in metadata_dict:
@@ -754,14 +758,15 @@ def __init__(self):
 		self.setWindowTitle("Metallaxis")
 		# initialise progress bar
 		self.MetallaxisProgress = MetallaxisProgress()
-		self.MetallaxisProgress.show()
+
+		# Setup inital GUI
+		self.graphicsView.setMaximumHeight(0)
 
 		# Center GUI on screen
 		qt_rectangle = self.frameGeometry()
 		center_point = QDesktopWidget().availableGeometry().center()
 		qt_rectangle.moveCenter(center_point)
 
-		self.progress_bar(1, "setting up gui")
 		# buttons on interface
 		self.open_vcf_button.clicked.connect(self.select_and_parse)
 		# menus on interface
@@ -851,6 +856,7 @@ def select_and_parse(self, cli_arg=False):
 		of the database file directly. Accepts no arguments, and returns nothing. This function exists solely to call other
 		functions, as menu items in PyQt can only call one function.
 		"""
+		self.MetallaxisProgress.show()
 
 		if not cli_arg:
 			selected_file = self.select_file()
@@ -1154,7 +1160,8 @@ def write_database_to_interface(self, loaded_database):
 		self.filter_lineedit.setEnabled(True)
 		self.filter_box.setEnabled(True)
 		self.view_variant_btn.setEnabled(True)
-		self.graphicsView.setMaximumHeight(0)
+		self.chrom_selection_stat_comboBox.setEnabled(True)
+		self.chrom_selection_label.setEnabled(True)
 
 		# get column numbers for ID, POS, etc.
 		self.progress_bar(47, "Extracting column data")
@@ -1194,12 +1201,10 @@ def write_database_to_interface(self, loaded_database):
 			var_counts_value = stats_sql_result['Result'][i]
 			var_counts[var_counts_key] = var_counts_value
 
-		if "ALT_Types" in var_counts:
-			ALT_Types = eval(var_counts["ALT_Types"])
-
 		self.progress_bar(49, "Plotting Statistics")
 
 		if "ALT_Types" in var_counts:
+			ALT_Types = eval(var_counts["ALT_Types"])
 			# plot piechart of proportions of types of ALT
 			# get the value for each ALT_Types key in order, per type of Alt so it can be graphed
 			alt_values_to_plot = []
@@ -1244,8 +1249,8 @@ def write_database_to_interface(self, loaded_database):
 				plt.ylabel('Number of Variants')
 				total_figure.tight_layout()
 				self.stat_plot_layout.addWidget(FigureCanvas(total_figure))
+				self.chrom_selection_stat_comboBox.addItems(graph_df.index)
 
-		self.chrom_selection_stat_comboBox.addItems(graph_df.index)
 		# setup variants by position graph for first chromosome in list
 		if list_chromosomes[0]:
 			self.changed_chrom_stat_combobox(list_chromosomes[0])

diff --git a/requirements.txt b/requirements.txt
@@ -1,7 +1,6 @@
 python-magic==0.4.15
 pandas==0.23.4
 numpy==1.15.4
-tables==3.4.4
 PyQt5==5.11.2
 requests==2.20.1
 matplotlib==3.0.2

diff --git a/setup.py b/setup.py
@@ -8,22 +8,22 @@
 
 setup(
 	name="Metallaxis",
-	version="0.8",
+	version="0.9",
 	license='GPLv3',
 	author="Sean Laidlaw",
 	author_email="seanlaidlaw95@gmail.com",
 	url='https://github.com/SL-LAIDLAW/Metallaxis',
-	description="A graphical python-based VCF viewer with optional VEP annotation",
+	description="A graphical python-based VCF viewer with optional annotation",
 	packages=['metallaxis'],
-	package_data={'':['*.ui']},
+	package_data={'': ['*.ui', 'annotation/*']},
 	include_package_data=True,
 	install_requires=[
 		'python-magic',
 		'pandas',
 		'numpy',
-		'tables',
 		'PyQt5',
 		'requests',
+		'wget',
 		'matplotlib'
 	],
 	classifiers=[