Mercurial > repos > sanbi-uwc > data_manager_shapeit2_reference
changeset 0:4f7004475124 draft default tip
planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
author | sanbi-uwc |
---|---|
date | Tue, 18 Sep 2018 00:54:49 -0400 |
parents | |
children | |
files | LICENSE bioblend/.ipynb_checkpoints/Untitled-checkpoint.ipynb bioblend/.nbgrader.log bioblend/Untitled.ipynb data_manager/shapeit_ref.py data_manager/shapeit_ref.xml data_manager_conf.xml test-data/sample.out tool-data/shapeit2_ref.loc.sample tool_data_table_conf.xml.sample |
diffstat | 10 files changed, 374 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Tue Sep 18 00:54:49 2018 -0400 @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2018 pvanheus + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bioblend/.ipynb_checkpoints/Untitled-checkpoint.ipynb Tue Sep 18 00:54:49 2018 -0400 @@ -0,0 +1,6 @@ +{ + "cells": [], + "metadata": {}, + "nbformat": 4, + "nbformat_minor": 2 +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bioblend/.nbgrader.log Tue Sep 18 00:54:49 2018 -0400 @@ -0,0 +1,26 @@ +[NotebookApp | WARNING] No nbgrader_config.py file found (rerun with --debug to see where nbgrader is looking) +[NotebookApp | INFO] Loading the validate_assignment nbgrader serverextension +[NotebookApp | INFO] ✓ nbpresent HTML export ENABLED +[NotebookApp | WARNING] ✗ nbpresent PDF export DISABLED: No module named 'nbbrowserpdf' +[NotebookApp | INFO] Serving notebooks from local directory: /home/pvh/Documents/code/SANBI/CPGR/data_managers/data_manager_shapeit_ref/bioblend +[NotebookApp | INFO] 0 active kernels +[NotebookApp | INFO] The Jupyter Notebook is running at: +[NotebookApp | INFO] http://localhost:8888/?token=61e63c3509f8ac0317fda9361f366d62624139ff97fe34b1 +[NotebookApp | INFO] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation). +[NotebookApp | CRITICAL] + + Copy/paste this URL into your browser when you connect for the first time, + to login with a token: + http://localhost:8888/?token=61e63c3509f8ac0317fda9361f366d62624139ff97fe34b1 +[NotebookApp | INFO] Accepting one-time-token-authenticated connection from 127.0.0.1 +[NotebookApp | INFO] Creating new notebook in +[NotebookApp | INFO] Kernel started: 80389481-149c-4b52-9ae8-fa1b81e1ca1b +[NotebookApp | INFO] Adapting to protocol v5.1 for kernel 80389481-149c-4b52-9ae8-fa1b81e1ca1b +[NotebookApp | INFO] Saving file at /Untitled.ipynb +[NotebookApp | INFO] Saving file at /Untitled.ipynb +[NotebookApp | INFO] Saving file at /Untitled.ipynb +[NotebookApp | INFO] Saving file at /Untitled.ipynb +[NotebookApp | INFO] Saving file at /Untitled.ipynb +[NotebookApp | INFO] Saving file at /Untitled.ipynb +[NotebookApp | INFO] Saving file at /Untitled.ipynb +[NotebookApp | INFO] Starting buffering for 80389481-149c-4b52-9ae8-fa1b81e1ca1b:8df5e156c9b94abc8d2818315546f1cf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bioblend/Untitled.ipynb Tue Sep 18 00:54:49 2018 -0400 @@ -0,0 +1,196 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "from bioblend import toolshed" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "ts = toolshed.ToolShedInstance(url='https://testtoolshed.g2.bx.psu.edu', key='49ad6deed569af1c011647e3911b9ea7')\n", + "all_repos = ts.repositories.get_repositories()" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[{'category_ids': ['83f763caf629aa54'],\n", + " 'deleted': False,\n", + " 'deprecated': False,\n", + " 'description': 'Add path for SHAPEIT reference data to shapeit_ref table',\n", + " 'homepage_url': '',\n", + " 'id': '59c15cd8db07b838',\n", + " 'model_class': 'Repository',\n", + " 'name': 'data_manager_shapeit_reference',\n", + " 'owner': 'sanbi-uwc',\n", + " 'private': False,\n", + " 'remote_repository_url': 'https://github.com/pvanheus/data_manager_shapeit_reference',\n", + " 'times_downloaded': 22,\n", + " 'type': 'unrestricted',\n", + " 'user_id': '25a703560f0040ae'}]" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "[ repo for repo in all_repos if repo['owner'] == 'sanbi-uwc' and repo['name'] == 'data_manager_shapeit_reference' ]" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [], + "source": [ + "all_revisions = ts.repositories.repository_revisions() " + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[{'changeset_revision': '6b54dcb42cd5',\n", + " 'downloadable': False,\n", + " 'has_repository_dependencies': False,\n", + " 'id': 'c85f89a2a97b5743',\n", + " 'includes_datatypes': 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/shapeit_ref.py Tue Sep 18 00:54:49 2018 -0400 @@ -0,0 +1,62 @@ +#!/usr/bin/env python3 + +from __future__ import division, print_function +import argparse +import json +import os +import os.path + + +def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry): + data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {}) + data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, []) + data_manager_dict['data_tables'][data_table_name].append(data_table_entry) + return data_manager_dict + + +_add_data_table_entry.__annotations__ = {'data_manager': dict, 'data_table_name': str, 'data_table_entry': dict, 'return': dict} + + +def assert_prefix_exists(prefix, path, prefix_type): + prefix_exists = False + for filename in os.listdir(path): + if filename.startswith(prefix): + prefix_exists = True + break + else: + if not prefix_exists: + exit("Unable to find a file with {} prefix {} in {}".format(prefix_type, prefix, path)) + + +assert_prefix_exists.__annotations__ = {'prefix': str, 'path': str, 'prefix_type': str, 'return': None} + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='Generate a data manager output for SHAPEIT reference data') + parser.add_argument('key', help='Short key to identify this reference set (no spaces)') + parser.add_argument('name', help='Description of reference set') + parser.add_argument('path', help='Filesystem path to directory containing this reference set') + parser.add_argument('reference_prefix', help='Filename prefix for the reference (.hap / .legend / .sample) files') + parser.add_argument('map_prefix', help='Filename prefix for map files in this reference set') + parser.add_argument('sample_prefix', help='Filename prefix for sample file in this reference set') + parser.add_argument('output_file', type=argparse.FileType('w'), help='JSON file used to write data manager values to') + args = parser.parse_args() + + if not os.path.exists(args.path): + exit("Unable to find specified path {}".format(args.path)) + + assert_prefix_exists(args.reference_prefix, args.path, 'reference') + assert_prefix_exists(args.map_prefix, args.path, 'map') + assert_prefix_exists(args.sample_prefix, args.path, 'sample') + + for column in ('key', 'name', 'path', 'reference_prefix', 'map_prefix', 'sample_prefix'): + value = getattr(args, column) + if '\t' in value: + exit("TAB character found in {} argument".format(column)) + + data_manager_dict = {} + data_table_entry = dict(value=args.key, name=args.name, path=args.path, + reference_prefix=args.reference_prefix, map_prefix=args.map_prefix, + sample_prefix=args.sample_prefix) + _add_data_table_entry(data_manager_dict, 'shapeit2_ref', data_table_entry) + + args.output_file.write(json.dumps(data_manager_dict, sort_keys=True) + '\n')
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/shapeit_ref.xml Tue Sep 18 00:54:49 2018 -0400 @@ -0,0 +1,34 @@ +<tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.8"> + <command detect_errors="exit_code"><![CDATA[ + python $__tool_directory__/shapeit_ref.py + '${value}' + '${name}' + '${path}' + '${reference_prefix}' + '${map_prefix}' + '${sample_prefix}' + '${output_file}' + ]]></command>> + <inputs> + <param name="value" type="text" label="Short key to identify this reference set (no spaces)" /> + <param name="name" type="text" label="Description of the reference data" /> + <param name="path" type="text" label="Filesystem path to directory containing this reference set" /> + <param name="reference_prefix" type="text" label="Filename prefix for the reference (.hap / .legend / .sample) files" /> + <param name="map_prefix" type="text" label="Filename prefix for map files in this reference set" /> + <param name="sample_prefix" type="text" label="Filename prefix for sample file for this reference set"> + </inputs> + <outputs> + <data name="output_file" format="data_manager_json" /> + </outputs> + <help><![CDATA[ + This data manager updates the *shapeit_ref* table with information about locally-maintained reference data + used by the SHAPEIT_ haplotype estimation (i.e. phasing) package. An example for the 1000 Genomes + dataset is available here_. + + .. _SHAPEIT: http://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html + .. _here: https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html + ]]></help> + <citations> + <citation type="doi">10.1038/nmeth.1785</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Tue Sep 18 00:54:49 2018 -0400 @@ -0,0 +1,15 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/shapeit_ref.xml" id="data_manager_shapeit2_reference"> + <data_table name="shapeit2_ref"> + <output> + <column name="value" /> + <column name="name" /> + <column name="path" /> + <column name="reference_prefix" /> + <column name="map_prefix" /> + <column name="sample_prefix" /> + </output> + </data_table> + </data_manager> +</data_managers>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample.out Tue Sep 18 00:54:49 2018 -0400 @@ -0,0 +1,1 @@ +{"data_tables": {"shapeit2_ref": [{"name": "1000 Genomes Project (phase 3) haplotypes (http://mathgen.stats.ox.ac.uk/impute/1000GPX20Phase3.html)", "value": "1000GP_Phase3", "map_prefix": "genetic_map_chr", "path": "/tools/databases/1000G/1000GP_Phase3", "reference_prefix": "1000GP_Phase3_chr", "sample_prefix": "1000GP_Phase3"}]}}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/shapeit2_ref.loc.sample Tue Sep 18 00:54:49 2018 -0400 @@ -0,0 +1,7 @@ +#This file lists the locations of SHAPEIT reference data connections +# +#<value> <name> <path> <reference_file_prefix> <map_file_prefix> <sample_file_prefix> +# +#For example +# +#1000G_Phase3 1000 Genomes project haplotypes /path/to/shapeit_ref/1000G 1000GP_Phase3_chr genetic_map_chr 1000GP_Phase3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Sep 18 00:54:49 2018 -0400 @@ -0,0 +1,6 @@ +<tables> + <table name="shapeit2_ref" comment_char="#"> + <columns>value, name, path, reference_prefix, map_prefix, sample_prefix</columns> + <file path="tool-data/shapeit2_ref.loc" /> + </table> +</tables>