├── CHANGES.txt ├── LICENSE.txt ├── README.md ├── examples ├── example1_bismark.txt ├── example2_bismark.txt ├── example_amplicons.txt ├── example_methpat.tsv ├── example_methpat_vis.png └── methpat.html ├── methpat ├── __init__.py ├── data │ ├── bootstrap.min.css │ ├── bootstrap.min.js │ ├── d3.v3.min.js │ ├── jquery-ui.min.js │ ├── jquery.min.js │ └── saveSvgAsPng.js ├── doc_template.py ├── methpat.py ├── version.py └── visualise.py └── setup.py /CHANGES.txt: -------------------------------------------------------------------------------- 1 | v1.0.0, Dec 8 2013, -- Initial release. 2 | -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- 1 | methpat License 2 | -------------------------------------------------------------------- 3 | Copyright (c) 2013 4 | Bernard J Pope, Darren Korbie, Nicholas C Wong 5 | 6 | All rights reserved. 7 | 8 | Redistribution and use in source and binary forms, with or without 9 | modification, are permitted provided that the following conditions 10 | are met: 11 | 1. Redistributions of source code must retain the above copyright 12 | notice, this list of conditions and the following disclaimer. 13 | 2. Redistributions in binary form must reproduce the above copyright 14 | notice, this list of conditions and the following disclaimer in the 15 | documentation and/or other materials provided with the distribution. 16 | 3. The name of the author may not be used to endorse or promote products 17 | derived from this software without specific prior written permission. 18 | 19 | THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR 20 | IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES 21 | OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 22 | IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, 23 | INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 24 | NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, 25 | DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY 26 | THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 27 | (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF 28 | THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 29 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | Introduction 2 | ============ 3 | 4 | This program summarises the resultant DNA methylation pattern data from the output of [Bismark](http://www.bioinformatics.babraham.ac.uk/projects/bismark/) bismark_methylation_extractor. Information of the DNA methylation positions for each amplicon, DNA methylation patterns observed within each amplicon and their abundance counts are summarised into a tab delimited text file amenable for further downstream statistical analysis. Methpat also outputs a HTML file containing visualisations of the methylation pattern data. 5 | 6 | Homepage 7 | -------- 8 | 9 | The [homepage for methpat](http://bjpop.github.io/methpat/) contains additional information about the program. 10 | 11 | 12 | License 13 | ------- 14 | 15 | Methpat is released as open source software under the terms of the 3 clause BSD License. See the file LICENCE.txt in the [source code repository of methpat](https://github.com/bjpop/methpat). 16 | 17 | Installation 18 | ------------ 19 | 20 | Methpat currently requires version 2.7 of Python. 21 | 22 | The best way to install Methpat is to use the following command: 23 | 24 | pip install git+https://github.com/bjpop/methpat.git 25 | 26 | This will automatically download and install the dependencies of methpat. 27 | 28 | Usage 29 | ----- 30 | 31 | ``` 32 | usage: methpat [-h] [--version] [--count_thresh THRESH] --amplicons 33 | AMPLICONS_FILE [--logfile FILENAME] [--html FILENAME] 34 | [--webassets {package,local,online}] [--title TITLE] 35 | [--filterpartial] [--min_cpg_percent PERCENT] 36 | BISMARK_FILE 37 | 38 | Summarise methylation patterns in bismark output, and generate visualisation. 39 | 40 | positional arguments: 41 | BISMARK_FILE input bismark file 42 | 43 | optional arguments: 44 | -h, --help show this help message and exit 45 | --version show program's version number and exit 46 | --count_thresh THRESH 47 | only display methylation patterns with at least THRESH 48 | number of matching reads, defaults to "0" 49 | --amplicons AMPLICONS_FILE 50 | file containing amplicon information in TSV format 51 | --logfile FILENAME log progress in FILENAME, defaults to "methpat.log" 52 | --html FILENAME save visualisation in html FILENAME defaults to 53 | "methpat.html" 54 | --webassets {package,local,online} 55 | location of assets used by output visualisation web 56 | page, defaults to "package" 57 | --title TITLE title of the output visualisation page, defaults to 58 | "Methylation Patterns" 59 | --filterpartial Ignore reads which contain (at least one) unknown 60 | methylation status 61 | --min_cpg_percent PERCENT 62 | only consider CPG sites which occur at least PERCENT 63 | of reads for an amplicon 64 | 65 | ``` 66 | -------------------------------------------------------------------------------- /examples/example_amplicons.txt: -------------------------------------------------------------------------------- 1 | chr5 112073439 112073576 APC_138 137 21 23 2 | chr17 41277353 41277474 BRCA1_122 121 26 21 3 | chr16 68771221 68771344 CDH1_3'_124 123 24 25 4 | chr16 68770947 68771087 CDH1_SNP_141 140 21 19 5 | chr9 21974948 21975096 CDKN2A_149 148 25 20 6 | chr9 90112780 90112885 DAPK1_p1_106 105 26 19 7 | chr9 90112992 90113146 DAPK1_p2_155 154 19 23 8 | chr9 90113565 90113688 DAPK1_i1_124 123 23 22 9 | chr11 67351061 67351211 GSTP1_151 150 23 23 10 | chr10 131265509 131265538 MGMT_110 29 24 22 11 | chr10 131265469 131265623 MGMT_merged 154 22 20 12 | chr3 25469832 25469955 RARB_124 123 23 29 13 | chr3 50378193 50378345 RASSF1A_153 152 23 25 14 | chr1 25256058 25256152 RUNX3_95 94 28 28 15 | chr3 37034629 37034740 MLH1 111 21 28 16 | -------------------------------------------------------------------------------- /examples/example_methpat_vis.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bjpop/methpat/afe2b72addcae631b89bed041c31f8b6f6b13cd1/examples/example_methpat_vis.png -------------------------------------------------------------------------------- /methpat/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bjpop/methpat/afe2b72addcae631b89bed041c31f8b6f6b13cd1/methpat/__init__.py -------------------------------------------------------------------------------- /methpat/data/bootstrap.min.js: -------------------------------------------------------------------------------- 1 | /*! 2 | * Bootstrap v3.3.1 (http://getbootstrap.com) 3 | * Copyright 2011-2014 Twitter, Inc. 4 | * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) 5 | */ 6 | if("undefined"==typeof jQuery)throw new Error("Bootstrap's JavaScript requires jQuery");+function(a){var 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