ChronQC 1.0.2 version changes

HISTORY.rst

@@ -2,8 +2,13 @@
 
 History
 -------
+1.0.2: Changes
 
-Features
+* Added stacked bar plot and bar and line plot
+* Bug fixes
+* Error handling
+
+1.0.1: Features
 
 * Designed for quality control based on historical data
 * Generates interactive time-series plots for various metrics, allowing comparison of the current run to historical runs

README.rst

@@ -1,4 +1,4 @@
-.. image:: https://github.com/nilesh-tawari/ChronQC/blob/master/docs/_static/ChronQC_logo.png
+.. image:: https://github.com/nilesh-tawari/test/blob/master/docs/_static/ChronQC_logo.png
 	:target: https://github.com/nilesh-tawari/ChronQC
 
 .. image:: https://img.shields.io/pypi/v/chronqc.svg
@@ -7,37 +7,37 @@
 .. image:: https://readthedocs.org/projects/chronqc/badge/?version=latest
         :target: http://chronqc.readthedocs.io/en/latest/?badge=latest
 
-An Open-source Quality Control Monitoring System for Clinical NGS
-=================================================================
+A Quality Control Monitoring System for Clinical Next Generation Sequencing
+===========================================================================
 
 * Free software: MIT license
 * Documentation: http://chronqc.readthedocs.io/en/latest/.
 
+ChronQC is a quality control (QC) tracking system for clinical implementation of next-generation sequencing (NGS). ChronQC generates time series plots for various QC metrics, which allows comparison of the current run to historical runs. ChronQC has multiple features for tracking QC data including Westgard rules for clinical validity, laboratory-defined thresholds, and historical observations within a specified period. Users can record their notes and corrective actions directly onto the plots for long-term recordkeeping.
+
 Features
 --------
 
-* Designed for quality control based on historical data
-* Generates interactive time-series plots for various metrics, allowing comparison of the current run to historical runs
-* Record users' notes and corrective actions directly onto the graphs for long-term record-keeping
-* Provides highly customizable different chart types
-* Supports customized database for plotting
-* Works with output of MultiQC
-
-
-ChronQC is an open-source, interactive, record-keeping QC system. ChronQC captures QC data from `MultiQC <https://github.com/ewels/MultiQC>`__ output and stores the metrics in a database. ChronQC then automatically generates interactive time-series plots for various metrics, allowing comparison of the current run to historical runs. In QC meetings, users can record their notes and corrective actions directly onto the graphs for long-term record-keeping.
+* Suited for different assays in a clinical laboratory
+* Generates interactive time series plots for various metrics
+* Records users' notes and corrective actions onto the graphs to facilitate long-term recordkeeping
+* Provides high level of customization: works with local databases and generates different chart types
+* Leverages existing standard tools such as `MultiQC <https://github.com/ewels/MultiQC>`__
 
-Live report:
-=============
+Example live ChronQC report
+===========================
 `https://nilesh-tawari.github.io/chronqc <https://nilesh-tawari.github.io/chronqc>`_
 
 
 ChronQC workflow
 ================
-.. image::  https://github.com/nilesh-tawari/ChronQC/blob/master/docs/_static/ChronQC_workflow.png
+ChronQC has two components: a command line interface compatible with NGS sequencing machines and a graphical user interface compatible with the clinical environment. HTML plots display metrics for each run or sample. Annotations are displayed on the right side of the plot and are stored in the chronqc.annotations.sqlite database for long-term recordkeeping.
+
+.. image::  https://github.com/nilesh-tawari/test/blob/master/docs/_static/ChronQC_workflow.png
 	:target: https://github.com/nilesh-tawari/ChronQC
 
-Examples:
-=========
+Examples
+========
 
 ChronQC plots can be generated from,
 
@@ -54,7 +54,7 @@ For details of chart types see the `documentation. <http://chronqc.readthedocs.i
 
 Requirement
 ===========
-Generating database and creating interactive charts is performed with code written for Python.
+ChronQC is implemented in Python (tested with v2.7 / v3.5 / v3.6) and runs on all common operating systems (Windows, Linux and Mac OS X).
 
 Installation
 ============
@@ -93,9 +93,11 @@ If you would like the development version instead, the command is::
 Citation
 ========
 
-An Open-source Quality Control Monitoring System for Clinical NGS (Manuscript under construction)
+ChronQC: A Quality Control Monitoring System for Clinical Next Generation Sequencing
+ Nilesh R. Tawari, Justine Jia Wen Seow, Dharuman Perumal, Jack L. Ow, Shimin Ang, Arun G. Devasia, Pauline C. Ng
+ (Manuscript under construction)
 
 License
 =======
 
-This project is licensed under the MIT License - see the `LICENSE.md <https://github.com/nilesh-tawari/ChronQC/blob/master/LICENSE>`_ file for details
+This project is licensed under the MIT License - see the `LICENSE.md <https://github.com/nilesh-tawari/test/blob/master/LICENSE>`_ file for details

README_pypi.rst

@@ -0,0 +1,79 @@
+.. image:: https://img.shields.io/pypi/v/chronqc.svg
+        :target: https://pypi.python.org/pypi/chronqc
+
+.. image:: https://readthedocs.org/projects/chronqc/badge/?version=latest
+        :target: http://chronqc.readthedocs.io/en/latest/?badge=latest
+
+ChronQC: A Quality Control Monitoring System for Clinical Next Generation Sequencing
+====================================================================================
+
+* Free software: MIT license
+* Documentation: http://chronqc.readthedocs.io/en/latest/.
+
+ChronQC is a quality control (QC) tracking system for clinical implementation of next-generation sequencing (NGS). ChronQC generates time series plots for various QC metrics, which allows comparison of the current run to historical runs. ChronQC has multiple features for tracking QC data including Westgard rules for clinical validity, laboratory-defined thresholds, and historical observations within a specified period. Users can record their notes and corrective actions directly onto the plots for long-term recordkeeping.
+
+Features
+--------
+
+* Suited for different assays in a clinical laboratory
+* Generates interactive time series plots for various metrics
+* Records users' notes and corrective actions onto the graphs to facilitate long-term recordkeeping
+* Provides high level of customization: works with local databases and generates different chart types
+* Leverages existing standard tools such as `MultiQC <https://github.com/ewels/MultiQC>`__
+
+Example live ChronQC report
+===========================
+`https://nilesh-tawari.github.io/chronqc <https://nilesh-tawari.github.io/chronqc>`_
+
+
+Examples
+========
+
+ChronQC plots can be generated from,
+
+1. A custom SQLite database. 
+	* For example see, `examples/custom_db_example <https://github.com/nilesh-tawari/ChronQC/tree/master/examples/custom_db_example>`_.
+
+2. The output of `MultiQC <https://github.com/ewels/MultiQC>`__. 
+	* For example on creating the ChronQC database and plots see, `examples/multiqc_example_1 <https://github.com/nilesh-tawari/ChronQC/tree/master/examples/multiqc_example_1>`_.
+	* For example on creating, updating the ChronQC database and plots see, `examples/multiqc_example_2 <https://github.com/nilesh-tawari/ChronQC/tree/master/examples/multiqc_example_2>`_.
+
+For complete command line reference see the `documentation. <http://chronqc.readthedocs.io/en/latest/>`__
+
+For details of chart types see the `documentation. <http://chronqc.readthedocs.io/en/latest/>`__
+
+Requirement
+===========
+ChronQC is implemented in Python (tested with v2.7 / v3.5 / v3.6) and runs on all common operating systems (Windows, Linux and Mac OS X).
+
+Installation
+============
+
+You can install ChronQC from PyPI using pip as follows::
+
+	pip install chronqc
+
+Alternatively, you can install from GitHub::
+
+	git clone https://github.com/nilesh-tawari/ChronQC.git
+	cd ChronQC
+	pip install -r requirements.txt
+	pip install --editable .
+
+
+If you would like the development version instead, the command is::
+
+	pip install --upgrade --force-reinstall git+https://github.com/nilesh-tawari/ChronQC.git
+
+
+Citation
+========
+
+ChronQC: A Quality Control Monitoring System for Clinical Next Generation Sequencing
+ Nilesh R. Tawari, Justine Jia Wen Seow, Dharuman Perumal, Jack L. Ow, Shimin Ang, Arun G. Devasia, Pauline C. Ng
+ (Manuscript under construction)
+
+License
+=======
+
+This project is licensed under the MIT License - see the `LICENSE.md <https://github.com/nilesh-tawari/ChronQC/blob/master/LICENSE>`_ file for details

chronqc/chronqc.py

@@ -1,11 +1,14 @@
 from __future__ import absolute_import, division, print_function, with_statement, unicode_literals
-import click
-from . import chronqc_db
-from . import chronqc_plot
 import argparse
 import sys
-from . import chronqc_annotation
-
+try:
+    from . import chronqc_db
+    from . import chronqc_plot
+    from . import chronqc_annotation
+except (ValueError, SystemError):
+    import chronqc_db
+    import chronqc_plot
+    import chronqc_annotation
 
 def run_plot(args):
     """
@@ -29,7 +32,7 @@ def run_annotation(args):
     """
     runs main function from chronqc_annotation.py
     """
-    print("running chronqc_annotation")
+    #print("running chronqc_annotation")
     chronqc_annotation.main()
 
 # @click.command()

chronqc/chronqc_db.py

@@ -5,7 +5,6 @@
 @author: tawarinr
 """
 from __future__ import absolute_import, division, print_function, with_statement, unicode_literals
-from . import utils
 import os
 import os.path as op
 import sys
@@ -14,6 +13,11 @@
 import numpy as np
 import pandas as pd
 import sqlite3
+try:
+    from . import utils
+except (ValueError, SystemError):
+    import utils
+
 try:
     import configparser
     Config = configparser.ConfigParser()  # ver. < 3.0
@@ -49,7 +53,7 @@ def creation_date(path_to_file):
     try:
         file_time = op.getmtime(path_to_file)
         return time.strftime("%m/%d/%Y", time.localtime(file_time))
-    except FileNotFoundError:
+    except:
         return np.nan
 
 
@@ -62,11 +66,11 @@ def main(args):
     takes number of arguments and produces ChronQC SQLite database
     """
     if args.mode == 'update' and not args.db:
-        parser.error("can't update database {} without a -db argument".format(args.mode))
+        print("can't update database {} without a -db argument".format(args.mode))
     elif args.mode == 'update' and args.prefix:
         print("can't use prefix in update mode so ignoring it")
     elif args.mode == 'create' and not args.output:
-        parser.error("provide output directory --output argument for creating db".format(args.mode))
+        print("provide output directory --output argument for creating db".format(args.mode))
 
 # output dir and file
     # Get output directory 1. user defined 2. db dir 3. multiqc_stats dir
@@ -189,6 +193,13 @@ def main(args):
     # remove blank spaces in column names
     df.columns = [x.strip().replace(' ', '_') for x in df.columns]
     logger.info("Kept {0} records after merging run, date and stats for ChronQC SQLite db".format(len(df)))
+# convert boolean types This method will not work for obect type column
+#    booleandf = df.select_dtypes(include=[bool])
+#    booleanDictionary = {True: 'TRUE', False: 'FALSE'}
+#    for column in booleandf:
+#        df[column] = df[column].map(booleanDictionary)        
+    df.replace(to_replace=True, value='TRUE', inplace=True)
+    df.replace(to_replace=False, value='FALSE', inplace=True)
 # write db
     cnx = sqlite3.connect(out_file)
     if args.mode == 'create':