# HG changeset patch
# User saketkc
# Date 1397517371 14400
# Node ID b9de63c7255939162d16c5fe514a55195131f739
# Parent  8aceb7fc57f5a9cad5e5de4958f0887ec35c9ad8
Uploaded

diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/README.rst	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,34 @@
+Galaxy wrapper for the CHASM webservice 
+===================================================
+
+This tool is copyright 2014 by Saket Choudhary<saketkc@gmail.com>, Indian Institute of Technology Bombay
+All rights reserved. MIT licensed.
+
+Licence (MIT)
+=============
+
+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.
+
+Citations
+===========
+
+
+If you use this Galaxy tool in work leading to a scientific publication please cite:
+
+Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R (2013). CRAVAT: Cancer-Related Analysis of VAriants Toolkit Bioinformatics, 29(5):647-648.
diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/chasm_webservice.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/chasm_webservice.py	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,279 @@
+#!/usr/bin/python
+"""
+The MIT License (MIT)
+
+Copyright (c) 2014 Saket Choudhary, <saketkc@gmail.com>
+
+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.
+
+"""
+import sys
+import requests
+import argparse
+import time
+from functools import wraps
+import simplejson as json
+import zipfile
+import tempfile
+import ntpath
+import shutil
+import xlrd
+import csv
+import os
+sheet_map = {0: 'Variant_Analysis.csv',
+             1: 'Amino_Acid_Level_Analysis.csv', 2: 'Gene_Level_Analysis.csv'}
+
+
+def retry(ExceptionToCheck, tries=4, delay=3, backoff=2, logger=None):
+    '''Retry calling the decorated function using an exponential backoff.
+
+    http://www.saltycrane.com/blog/2009/11/trying-out-retry-decorator-python/
+    original from: http://wiki.python.org/moin/PythonDecoratorLibrary#Retry
+
+    :param ExceptionToCheck: the exception to check. may be a tuple of
+        exceptions to check
+    :type ExceptionToCheck: Exception or tuple
+    :param tries: number of times to try (not retry) before giving up
+    :type tries: int
+    :param delay: initial delay between retries in seconds
+    :type delay: int
+    :param backoff: backoff multiplier e.g. value of 2 will double the delay
+        each retry
+    :type backoff: int
+    :param logger: logger to use. If None, print
+    :type logger: logging.Logger instance
+    '''
+    def deco_retry(f):
+
+        @wraps(f)
+        def f_retry(*args, **kwargs):
+            mtries, mdelay = tries, delay
+            while mtries > 1:
+                try:
+                    return f(*args, **kwargs)
+                except ExceptionToCheck, e:
+                    #msg = '%s, Retrying in %d seconds...' % (str(e), mdelay)
+                    msg = 'Retrying in %d seconds...' % (mdelay)
+                    if logger:
+                        logger.warning(msg)
+                    else:
+                        print msg
+                    time.sleep(mdelay)
+                    mtries -= 1
+                    mdelay *= backoff
+            return f(*args, **kwargs)
+
+        return f_retry  # true decorator
+
+    return deco_retry
+CANCERTYPES = ['Bladder', 'Blood-Lymphocyte', 'Blood-Myeloid',
+               'Brain-Cerebellum', 'Brain-Glioblastoma_Multiforme',
+               'Brain-Lower_Grade_Glioma', 'Breast', 'Cervix',
+               'Colon', 'Head_and_Neck', 'Kidney-Chromophobe',
+               'Kidney-Clear_Cell', 'Kidney-Papiallary_Cell',
+               'Liver-Nonviral', 'Liver-Viral', 'Lung-Adenocarcinoma',
+               'Lung-Squamous_Cell', 'Melanoma', 'Other', 'Ovary',
+               'Pancreas', 'Prostate-Adenocarcinoma', 'Rectum',
+               'Skin', 'Stomach', 'Thyroid', 'Uterus']
+
+__URL__ = 'http://www.cravat.us/rest/service/submit'
+
+
+def stop_err(msg):
+    sys.stderr.write('%s\n' % msg)
+    sys.exit()
+
+
+class CHASMWeb:
+
+    def __init__(self,
+                 mutationbox=None, filepath=None,
+                 is_hg_18=None, analysis_type=None,
+                 analysis_program=None, chosendb=None,
+                 cancer_type=None, email=None,
+                 annotate_genes=None, text_reports=None,
+                 mupit_out=None):
+        self.mutationbox = mutationbox
+        self.filepath = filepath
+        self.is_hg_18 = is_hg_18
+        self.analysis_type = analysis_type
+        self.analysis_program = analysis_program
+        self.chosendb = chosendb
+        self.email = email
+        self.annotate_genes = annotate_genes
+        self.cancer_type = cancer_type
+        self.email = email
+        self.annotate_genes = annotate_genes
+        self.text_reports = text_reports
+        self.mupit_input = mupit_out
+
+    def make_request(self):
+        data = {
+            'mutations  ': self.mutationbox,
+            'hg18': self.is_hg_18,
+            'analysistype': self.analysis_type,
+            'analysisitem': self.analysis_program,
+            'chasmclassifier': self.cancer_type,
+            'geneannotation': self.annotate_genes,
+            'email': self.email,
+            'tsvreport': 'on',  # self.text_reports,
+            'mupitinput': self.mupit_input,
+        }
+        stripped_data = {}
+
+        for key, value in data.iteritems():
+            if value is True:
+                value = 'on'
+            if value is not None and value is not False:
+                stripped_data[key] = value
+
+        if not self.mutationbox:
+            file_payload = {'inputfile': open(self.filepath)}
+            request = requests.post(
+                __URL__, data=stripped_data, files=file_payload)
+        else:
+            request = requests.post(
+                __URL__, data=stripped_data, files=dict(foo='bar'))
+        job_id = json.loads(request.text)['jobid']
+        return job_id
+
+    @retry(requests.exceptions.HTTPError)
+    def zip_exists(self, job_id):
+        url = 'http://www.cravat.us/results/%s/%s.zip' % (job_id, job_id)
+        zip_download_request = requests.request('GET', url)
+        if zip_download_request.status_code == 404:
+            raise requests.HTTPError()
+        else:
+            return url
+
+    def download_zip(self, url, job_id):
+        self.tmp_dir = tempfile.mkdtemp()
+        r = requests.get(url, stream=True)
+        if r.status_code == 200:
+            self.path = os.path.join(self.tmp_dir, job_id + '.zip')
+            with open(self.path, 'wb') as f:
+                for chunk in r.iter_content(128):
+                    f.write(chunk)
+        else:
+            self.path = None
+        return self.path
+
+    def move_files(self, file_map):
+        fh = open(self.path, 'rb')
+        zip_files = zipfile.ZipFile(fh)
+        for name in zip_files.namelist():
+            filename = ntpath.basename(name)
+            extension = ntpath.splitext(filename)[-1]
+            source_file = zip_files.open(name)
+            if extension == '.txt':
+                target_file = open(file_map['error.txt'], 'wb')
+            elif filename != 'SnvGet Feature Description.xls' and extension != '.xls':
+                target_file = open(file_map[filename], 'wbb')
+            else:
+                target_file = None
+            if target_file:
+                with source_file, target_file:
+                    shutil.copyfileobj(source_file, target_file)
+            if filename == 'SnvGet Feature Description.xls':
+                with xlrd.open_workbook(source_file) as wb:
+                    sheet_names = wb.sheet_names()
+                    for name in sheet_names:
+                        sh = wb.sheet_by_name(name)
+                        name_shortened = name.replace(' ').strip() + '.csv'
+                        with open(name_shortened, 'wb') as f:
+                            c = csv.writer(f)
+                            for r in range(sh.nrows):
+                                c.writerow(sh.row_values(r))
+        shutil.rmtree(self.tmp_dir)
+        fh.close()
+
+
+def main(params):
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-i', '--input',
+                        type=str, dest='mutationbox',
+                        help='Input variants')
+    parser.add_argument('--path', type=str,
+                        dest='input_file_location',
+                        help='Input file location')
+    parser.add_argument('--hg18', dest='hg18',
+                        action='store_true')
+    parser.add_argument('--analysis_type', dest='analysis_type',
+                        type=str,
+                        choices=['driver', 'functional',
+                                 'geneannotationonly'],
+                        default='driver')
+    parser.add_argument('--chosendb', dest='chosendb',
+                        type=str, nargs='*',
+                        choices=['CHASM', 'SnvGet'],
+                        default='CHASM')
+    parser.add_argument('--cancertype', dest='cancer_type',
+                        type=str, choices=CANCERTYPES,
+                        required=True)
+    parser.add_argument('--email', dest='email',
+                        required=True, type=str)
+    parser.add_argument('--annotate', dest='annotate',
+                        action='store_true', default=None)
+    parser.add_argument('--tsv_report', dest='tsv_report',
+                        action='store_true', default=None)
+    parser.add_argument('--mupit_out', dest='mupit_out',
+                        action='store_true', default=None)
+    parser.add_argument('--gene_analysis_out', dest='gene_analysis_out',
+                        type=str, required=True)
+    parser.add_argument('--variant_analysis_out',
+                        dest='variant_analysis_out',
+                        type=str, required=True)
+    parser.add_argument('--amino_acid_level_analysis_out',
+                        dest='amino_acid_level_analysis_out',
+                        type=str, required=True,)
+    parser.add_argument('--error_file', dest='error_file_out',
+                        type=str, required=True)
+    parser.add_argument('--snv_box_out', dest='snv_box_out',
+                        type=str, required=False)
+    parser.add_argument('--snv_features', dest='snv_features_out',
+                        type=str, required=False)
+    args = parser.parse_args(params)
+    chasm_web = CHASMWeb(mutationbox=args.mutationbox,
+                         filepath=args.input_file_location,
+                         is_hg_18=args.hg18,
+                         analysis_type=args.analysis_type,
+                         chosendb=args.chosendb,
+                         cancer_type=args.cancer_type,
+                         email=args.email,
+                         annotate_genes=args.annotate,
+                         text_reports=args.tsv_report,
+                         mupit_out=args.mupit_out)
+    job_id = chasm_web.make_request()
+    file_map = {'Amino_Acid_Level_Analysis.Result.tsv': args.amino_acid_level_analysis_out,
+                'SNVBox.tsv': args.snv_box_out,
+                'Variant_Analysis.Result.tsv': args.variant_analysis_out,
+                'Gene_Level_Analysis.Result.tsv': args.gene_analysis_out,
+                'SnvGet Feature Description.xls': args.snv_features_out,
+                'error.txt': args.error_file_out
+                }
+    url = chasm_web.zip_exists(job_id)
+    download = chasm_web.download_zip(url, job_id)
+    if download:
+        chasm_web.move_files(file_map=file_map)
+    else:
+        stop_err('Unable to download from the server')
+
+if __name__ == '__main__':
+    main(sys.argv[1:])
diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/chasm_webservice.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/chasm_webservice.xml	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,288 @@
+<tool id="chasm_webservice" name="CHASM Webservice" version="1.0.0" hidden="false">
+    <requirements>
+        <requirement type="package" version="2.2.1">requests</requirement>
+        <requirement type="python-module">requests</requirement>
+    </requirements>
+    <description>CHASM score using CRAVAT webservice</description>
+    <command interpreter="python">
+        chasm_webservice.py --path $input
+                            --analysis_type $analysis_type
+                            --cancertype $tissue_type
+                            --email $__user_email__
+                            --gene_analysis_out $gene_analysis_out
+                            --variant_analysis_out $variant_analysis_out
+                            --amino_acid_level_analysis_out $amino_acid_level_analysis_out
+                            --error_file $error_file
+    </command>
+    <inputs>
+        <param format="txt" name="input" type="data" label="Variants File" />
+        <param name="analysis_type" type="select" label="Choose analysis type" help="
+                                                                        Cancer driver analysis predicts whether\
+                                                                        the submitted variants are cancer drivers.\
+                                                                        Functional effect analysis predicts whether\
+                                                                        the submitted variants will have any\
+                                                                        functional effect on their translated proteins.\
+                                                                        Annotation only provides\
+                                                                        GeneCard and PubMed information on\
+                                                                        the genes containing the submitted variants.">
+            <option value="driver">Cancer driver analysis</option>
+            <option value="functional">Functional effect analysis</option>
+            <option value="geneannotationonly">Annotation only</option>
+        </param>
+
+        <param name="gene_annotation" type="select" label="Include Gene annotation">
+            <option value="no">No</option>
+            <option value="yes">Yes</option>
+        </param>
+
+        <param name="tissue_type" type="select" label="Tissue Type">
+            <option value="Bladder">Bladder</option>
+            <option value="Blood-Lymphocyte">Blood-Lymphocyte</option>
+            <option value="Blood-Myeloid">Blood-Myeloid</option>
+            <option value="Brain-Cerebellum">Brain-Cerebellum</option>
+            <option value="Brain-Glioblastoma_Multiforme">Brain-Glioblastoma_Multiforme</option>
+            <option value="Brain-Lower_Grade_Glioma">Brain-Lower_Grade_Glioma</option>
+            <option value="Breast">Breast</option>
+            <option value="Cervix">Cervix</option>
+            <option value="Colon">Colon</option>
+            <option value="Head_and_Neck">Head_and_Neck</option>
+            <option value="Kidney-Chromophobe">Kidney-Chromophobe</option>
+            <option value="Kidney-Clear_Cell">Kidney-Clear_Cell</option>
+            <option value="Kidney-Papiallary_Cell">Kidney-Papiallary_Cell</option>
+            <option value="Liver-Nonviral">Liver-Nonviral</option>
+            <option value="Liver-Viral">Liver-Viral</option>
+            <option value="Lung-Adenocarcinoma">Lung-Adenocarcinoma</option>
+            <option value="Lung-Squamous_Cell">Lung-Squamous_Cell</option>
+            <option value="Melanoma">Melanoma</option>
+            <option value="Other">Other</option>
+            <option value="Ovary">Ovary</option>
+            <option value="Pancreas">Pancreas</option>
+            <option value="Prostate-Adenocarcinoma">Prostate-Adenocarcinoma</option>
+            <option value="Rectum">Rectum</option>
+            <option value="Skin">Skin</option>
+            <option value="Stomach">Stomach</option>
+            <option value="Thyroid">Thyroid</option>
+            <option value="Uterus">Uterus</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="gene_analysis_out" label="${tool.name} on ${on_string}: genes" />
+        <data format="tabular" name="variant_analysis_out" label="${tool.name} on ${on_string}: variant" />
+        <data format="tabular" name="amino_acid_level_analysis_out" label="${tool.name} on ${on_string}: aminoacid" />
+        <data format="tabular" name="error_file" label="${tool.name} on ${on_string}: error" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="chasm_input.txt"/>
+            <param name="gene_annotation" value="yes"/>
+            <param name="analysis_type" value="driver"/>
+            <param name="tissue_type" value="Other"/>
+            <output name="gene_analysis_out" file="chasm_output_genes.txt"/>
+            <output name="variant_analysis_out" file="chasm_output_variants.txt"/>
+            <output name="amino_acid_level_analysis_out" file="chasm_output_aminoacids.txt"/>
+            <output name="error_file" file="chasm_output_error.txt"/>
+        </test>
+    </tests>
+
+    <help>
+        **What it does**
+
+
+        CRAVAT: Cancer-Related Analysis of VAriants Toolkit is a web server with simple interface where cancer-related analysis of variants are performed. To cite CRAVAT, please use this article.
+
+        CRAVAT currently employs three analysis tools, CHASM, SNVGet, and VEST
+
+        **Input**
+
+        -Comment lines start with ">", "#", or "!".
+
+
+        -Data fields are separated by a tab or a space.
+
+
+        -The following two formats can be used for input data, but all the data rows should be in the same format:
+
+        .. class:: infomark
+
+        Genomic-coordinate format (separated by a tab or a space):
+
+
+        # UID / Chr. / Position / Strand / Ref. base / Alt. base / Sample ID (optional)
+        TR1	chr17	7577506	-	G	T	TCGA-02-0231
+
+
+        TR2	chr10	123279680	-	G	A	TCGA-02-3512
+
+
+        TR3	chr13	49033967	+	C	A	TCGA-02-3532
+
+
+        TR4	chr7	116417505	+	G	T	TCGA-02-1523
+
+
+        TR5	chr7	140453136	-	T	A	TCGA-02-0023
+
+
+        TR6	chr17	37880998	+	G	T	TCGA-02-0252
+
+
+        Ins1 chr17	37880998	+	G	GT	TCGA-02-0252
+
+
+        Del1 chr17	37880998	+	GA	G	TCGA-02-0252
+
+
+        CSub1 chr2	39871235	+	ATGCT	GA	TCGA-02-0252
+
+
+
+        Position is a 1-based open coordinate. For insertions and deletions, use the base before the insertion or the
+        first base of the deletion as the reference base. If you do not have strand information from your sequencing results,
+        it is likely that they are all reported on the + strand.
+        Make sure that your reported reference base matches the base in the reported position in the
+        hg19 reference sequence (or hg18 if you checked hg18 checkbox).
+
+        .. class:: infomark
+
+        Amino-acid residue substitution format (separated by a tab or a space):
+
+
+        # UID / Transcript / AA change / Sample ID (optional)
+
+
+        TR1	NM_001126116.1	D127Y	TCGA-02-0231
+
+
+        TR2	NM_001144919.1	R162Q	TCGA-02-3512
+
+
+        TR3	NM_000321.2	Q702K	TCGA-02-3532
+
+
+        TR4	NM_000245.2	A1108S	TCGA-02-1523
+
+
+        TR5	NM_004333.4	V600E	TCGA-02-0023
+
+
+        TR6	NM_001005862.1	G746V	TCGA-02-0252
+
+
+        trascript identifier can be from either NCBI Refseq, CCDS, or Ensembl.
+        Refseq and CCDS accessions can be specified without version numbers.
+        The format of "AA change" column is (reference AA)(AA position)(alternate AA), without "(" and ")".
+        Reference and alternate AAs should be from the 20 essential amino acids and each of them should be one amino acid-long.
+
+
+        **Analysis**
+
+
+        .. class:: infomark
+
+
+        Analysis Type:
+
+
+        -*Cancer driver analysis*: This analysis predicts whether the submitted variants are cancer drivers or not.
+
+
+        -*Functional effect analysis*: This analysis predicts whether the submitted variants will have any functional effect on their translated proteins or not.
+
+
+        -*Gene annotation only*: This analysis provides GeneCard and PubMed information on the genes containing the submitted variants.
+
+
+        Currently, the following tissue types can be chosen at CRAVAT.
+
+
+        Name	Full name	Source	Date
+
+
+        Bladder	Bladder Urothelial Carcinoma	BLCA (TCGA)	Jun 2013
+
+
+        Blood-Lymphocyte	Chronic Lymphocytic Leukemia	CLL (ICGC)	Mar 2013
+
+
+        Blood-Myeloid	Acute Myeloid Leukemia	LAML (TCGA)	Jun 2013
+
+
+        Brain-Cerebellum	Medulloblastoma	MB (mixed source)	Dec 2010
+
+
+        Brain-Glioblastoma-Multiforme	Glioblastoma Multiforme	GBM (TCGA)	Jun 2013
+
+
+        Brain-Lower-Grade-Glioma	Brain Lower Grade Glioma	LGG (TCGA)	Jun 2013
+
+
+        Breast	Breast Invasive Carcinoma	BRCA (TCGA)	Jun 12012
+
+
+        Cervix	Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma	CESC (TCGA)	Jun 2013
+
+
+        Colon	Colon Adenocarcinoma	COAD (TCGA)	Jun 2013
+
+
+        Head and Neck	Head and Neck Squamous Cell Carcinoma	HNSC (TCGA)	Jun 2013
+
+
+        Kidney-Chromophobe	Kidney Chromophobe	KICH (TCGA)	Jun 2013
+
+
+        Kidney-Clear-Cell	Kidney Renal Clear Cell Carcinoma	KIRC (TCGA)	Jun 2013
+
+
+        Kidney-Papillary-Cell	Kidney Renal Papillary Cell Carcinoma	KIRP (TCGA)	Jun 2013
+
+
+        Liver-Nonviral	Hepatocellular Carcinoma (Secondary to Alcohol and Adiposity)	HCCA (ICGC)	Mar 2013
+
+
+        Liver-Viral	Hepatocellular Carcinoma (Viral)	HCCV (ICGC)	Mar 2013
+
+
+        Lung-Adenocarcinoma	Lung Adenocarcinoma	LUAD (TCGA)	Jun 2013
+
+
+        Lung-Squamous Cell	Lung Squamous Cell Carcinoma	LUSC (TCGA)	Jun 2013
+
+
+        Melanoma	Melanoma	ML (Yardena Samuels lab)	Dec 2011
+
+
+        Other	General purpose	OV (TCGA)	Jun 2013
+
+
+        Ovary	Ovarian Serous Cystadenocarcinoma	OV (TCGA)	Jun 2013
+
+
+        Pancreas	Pancreatic Cancer	PNCC (ICGC))	Mar 2013
+
+
+        Prostate-Adenocarcinoma	Prostate Adenocarcinoma	PRAD (TCGA)	Jun 2013
+
+
+        Rectum	Rectum Adenocarcinoma	READ (TCGA)	Jun 2013
+
+
+        Skin	Skin Cutaneous Melanoma	SKCM (TCGA)	Jun 2013
+
+
+        Stomach	Stomach Adenocarcinoma	STAD (TCGA)	Jun 2013
+
+
+        Thyroid	Thyroid Carcinoma	THCA (TCGA)	Jun 2013
+
+
+        Uterus	Uterine Corpus Endometriod Carcinoma	UCEC (TCGA)	Jun 2013
+
+        **Citation**
+
+        If  you use this tool please cite:
+
+        Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R (2013). CRAVAT: Cancer-Related Analysis of VAriants Toolkit Bioinformatics, 29(5):647-648.
+
+    </help>
+</tool>
diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/test-data/chasm_input.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/test-data/chasm_input.txt	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,5 @@
+TR1 chr22 30421786 + A T
+TR2 chr22 29446079 + A G
+TR3 chr22 29446079 + A G
+TR4 chr22 40814500 - A G
+TR5 chr22 40815256 + C T
diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/test-data/chasm_output_aminoacids.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/test-data/chasm_output_aminoacids.txt	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,13 @@
+#Amino Acid Level Analysis Report
+#2014-04-14 18:52:00.963260
+#Analysis done at http://www.cravat.us.
+#Input file: dataset_34.dat
+#This report shows analysis results at amino acid level.
+#Input coordinate was hg19 genomic.
+#For more information on CRAVAT, visit http://www.cravat.us.
+#
+Transcript	Amino acid position	Sequence Ontology	Reference amino acid(s)	Alternate amino acid(s)	HUGO symbol	Other transcripts	Occurrences in study [amino acid change]	Transcript by COSMIC	AA change by COSMIC	Occurrences in COSMIC [amino acid change]	Occurrences in COSMIC by primary sites [amino acid change]
+NM_021090.3	1198	MS	N	I	MTMR3	NM_153051.2:aAc>aTc:N1161I, NM_153050.2:aAc>aTc:N1170I, ENST00000323630:aAc>aTc:N1062I, ENST00000351488:aAc>aTc:N1161I, ENST00000333027:aAc>aTc:N1170I, ENST00000406629:aAc>aTc:N1170I, ENST00000401950:aAc>aTc:N1198I	1			0	
+NM_001206998.1	637	MS	H	R	ZNRF3	NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R	2			0	
+NM_020831.3	648	MS	S	G	MKL1	ENST00000396617:Agc>Ggc:S648G, ENST00000402042:Agc>Ggc:S598G, ENST00000407029:Agc>Ggc:S648G, ENST00000355630:Agc>Ggc:S648G	1	ENST00000355630	p.S648G (stomach 1)	1	stomach(1
)
+NM_020831.3	396	MS	A	T	MKL1	ENST00000396617:Gcc>Acc:A396T, ENST00000402042:Gcc>Acc:A346T, ENST00000407029:Gcc>Acc:A396T, ENST00000355630:Gcc>Acc:A396T	1			0	
diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/test-data/chasm_output_error.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/test-data/chasm_output_error.txt	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,1 @@
+# End of input format error output. If nothing is above this line, there was no format error in the input.
\ No newline at end of file
diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/test-data/chasm_output_genes.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/test-data/chasm_output_genes.txt	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,14 @@
+#Gene Level Analysis Report
+#2014-04-14 18:52:00.963904
+#Analysis done at http://www.cravat.us.
+#Input file: dataset_34.dat
+#This report shows analysis results at gene level.
+#The composite p-value (Stouffer's combined p-value) and composite FDR of a gene show how probable it is to get the same p-value distribution for the gene as that obtained from the input variants by chance.
+#Input coordinate was hg19 genomic.
+#Tissue type for CHASM analysis: Other
+#For more information on CRAVAT, visit http://www.cravat.us.
+#
+HUGO symbol	Best driver score from representative transcripts	Composite p value	Composite FDR	Occurrences in study [gene mutated]	Occurrences in COSMIC [gene mutated]	Occurrences in COSMIC by primary sites [gene mutated]
+MTMR3	0.6	0.3364	0.55	1	102	upper_aerodigestive_tract(2);large_intestine(24);haematopoietic_and_lymphoid_tissue(5);endometrium(12);urinary_tract(4);oesophagus(1);liver(3);skin(17);lung(17);ovary(5);prostate(2);kidney(4);breast(6
)
+ZNRF3	0.514	0.171	0.55	2	73	upper_aerodigestive_tract(2);large_intestine(19);autonomic_ganglia(1);haematopoietic_and_lymphoid_tissue(2);endometrium(12);urinary_tract(2);lung(16);liver(5);skin(1);oesophagus(3);ovary(2);NS(1);prostate(2);kidney(3);breast(2
)
+MKL1	0.728	0.793956248886469	1	2	68	large_intestine(15);stomach(2);central_nervous_system(1);haematopoietic_and_lymphoid_tissue(3);endometrium(13);urinary_tract(1);lung(19);breast(3);skin(1);ovary(5);kidney(4);liver(1
)
diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/test-data/chasm_output_variants.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/test-data/chasm_output_variants.txt	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,15 @@
+#Variant Level Analysis Report
+#2014-04-14 18:52:00.964521
+#Analysis done at http://www.cravat.us.
+#Input file: dataset_34.dat
+#This report shows analysis results at variant level.
+#Input coordinate was hg19 genomic.
+#Tissue type for CHASM analysis: Other
+#For more information on CRAVAT, visit http://www.cravat.us.
+#
+ID	Chromosome	Position	Strand	Reference base	Alternate base	Sample ID	HUGO symbol	Transcript	Transcript strand	Codon change	Amino acid position	Sequence Ontology	Reference amino acid(s)	Alternate amino acid(s)	Other transcripts	Mappability Warning	Driver score of representative transcript (driver mutations close to 0)	Empirical p-value	FDR (Benjamini-Hochberg) (not available with less than 10 unique mutations)	Best driver score and transcript	All transcripts and driver scores	dbSNP	1000 Genomes allele frequency	ESP6500 allele frequency (European American)	ESP6500 allele frequency (African American)	Occurrences in study [exact nucleotide change]	Transcript by COSMIC	AA change by COSMIC	Occurrences in COSMIC [exact nucleotide change]	Occurrences in COSMIC by primary sites [exact nucleotide change]
+TR1	CHR22	30421786	+	A	T	No_sample_ID	MTMR3	NM_021090.3	+	aAc>aTc	1198	MS	N	I	NM_153051.2:aAc>aTc:N1161I, NM_153050.2:aAc>aTc:N1170I, ENST00000323630:aAc>aTc:N1062I, ENST00000351488:aAc>aTc:N1161I, ENST00000333027:aAc>aTc:N1170I, ENST00000406629:aAc>aTc:N1170I, ENST00000401950:aAc>aTc:N1198I		0.6(NM_021090.3:N1198I)	0.3364	0.60	0.572(ENST00000323630:N1062I)	ENST00000323630:N1062I(0.572),ENST00000406629:N1170I(0.602),ENST00000401950:N1198I(0.6),ENST00000351488:N1161I(0.572),NM_153050.2:N1170I(0.572),ENST00000333027:N1170I(0.572),NM_021090.3:N1198I(0.6),NM_153051.2:N1161I(0.572)	rs75623810	0.00778388278388	0	0.0226963	1				
+TR2	CHR22	29446079	+	A	G	No_sample_ID	ZNRF3	NM_001206998.1	+	cAc>cGc	637	MS	H	R	NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R		0.514(NM_001206998.1:H637R)	0.1710	0.60	0.442(ENST00000544604:H637R)	ENST00000544604:H637R(0.442),NM_032173.3:H537R(0.514),ENST00000402174:H537R(0.514),ENST00000406323:H537R(0.514),NM_001206998.1:H637R(0.514),ENST00000332811:H537R(0.514)	rs62641746	0	0.00569767	0.000907853	2				
+TR3	CHR22	29446079	+	A	G	No_sample_ID	ZNRF3	NM_001206998.1	+	cAc>cGc	637	MS	H	R	NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R		0.514(NM_001206998.1:H637R)	0.1710	0.60	0.442(ENST00000544604:H637R)	ENST00000544604:H637R(0.442),NM_032173.3:H537R(0.514),ENST00000402174:H537R(0.514),ENST00000406323:H537R(0.514),NM_001206998.1:H637R(0.514),ENST00000332811:H537R(0.514)	rs62641746	0	0.00569767	0.000907853	2				
+TR4	CHR22	40814500	-	A	G	No_sample_ID	MKL1	NM_020831.3	-	Agc>Ggc	648	MS	S	G	ENST00000396617:Agc>Ggc:S648G, ENST00000402042:Agc>Ggc:S598G, ENST00000407029:Agc>Ggc:S648G, ENST00000355630:Agc>Ggc:S648G		0.728(NM_020831.3:S648G)	0.6890	0.80	0.708(ENST00000402042:S598G)	ENST00000407029:S648G(0.728),NM_020831.3:S648G(0.728),ENST00000396617:S648G(0.728),ENST00000355630:S648G(0.728),ENST00000402042:S598G(0.708)	rs878756	0.419871794872	0.396977	0.860645	1	ENST00000355630	p.S648G (stomach 1)	1	stomach(1)
+TR5	CHR22	40815256	+	C	T	No_sample_ID	MKL1	NM_020831.3	-	Gcc>Acc	396	MS	A	T	ENST00000396617:Gcc>Acc:A396T, ENST00000402042:Gcc>Acc:A346T, ENST00000407029:Gcc>Acc:A396T, ENST00000355630:Gcc>Acc:A396T		0.748(NM_020831.3:A396T)	0.7476	0.80	0.748(ENST00000407029:A396T)	ENST00000407029:A396T(0.748),NM_020831.3:A396T(0.748),ENST00000396617:A396T(0.748),ENST00000355630:A396T(0.748),ENST00000402042:A346T(0.754)	rs34736200	0.0201465201465	0.00127907	0.0832955	1				
diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/test-data/ma_nucleotide_output.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/test-data/ma_nucleotide_output.csv	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,4 @@
+"","Mutation","AA variant","Gene","MSA","PDB","Func. Impact","FI score","Uniprot","Refseq","MSA height","Codon start position","Func. region","Protein bind.site","DNA/RNA bind.site","small.mol bind.site"
+"1","hg19,13,32912555,G,T","D1355Y","BRCA2","http://getma.org/?cm=msa&ty=f&p=BRCA2_HUMAN&rb=1247&re=1420&var=D1355Y","","low","1.24","BRCA2_HUMAN","NP_000050","14","chr13:32912555","","","",""
+"2","hg19,7,55178574,G,A","","","","","","","","","0","","","","",""
+"3","hg19,7,55178574,G,A","","","","","","","","","0","","","","",""
diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/test-data/ma_proper_nucleotide.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/test-data/ma_proper_nucleotide.csv	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,3 @@
+13,32912555,G,T   BRCA2
+7,55178574,G,A   GBM
+7,55178574,G,A   GBM
diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/test-data/ma_proper_protein.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/test-data/ma_proper_protein.csv	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,6 @@
+EGFR_HUMAN,R521K
+EGFR_HUMAN,R98Q,Polymorphism
+EGFR_HUMAN,G719D,disease
+NP_000537,G356A
+NP_000537,G360A,dbSNP:rs35993958
+NP_000537,S46A,Abolishes,phosphorylation
diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/test-data/ma_proper_protein.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/test-data/ma_proper_protein.tsv	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,6 @@
+EGFR_HUMAN R521K 
+EGFR_HUMAN R98Q Polymorphism 
+EGFR_HUMAN G719D disease 
+NP_000537 G356A 
+NP_000537 G360A dbSNP:rs35993958 
+NP_000537 S46A Abolishes phosphorylation 
diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/test-data/ma_protein_output.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/test-data/ma_protein_output.csv	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,7 @@
+"","Mutation","AA variant","Gene","MSA","PDB","Func. Impact","FI score","Uniprot","Refseq","MSA height","Codon start position","Func. region","Protein bind.site","DNA/RNA bind.site","small.mol bind.site"
+"1","EGFR_HUMAN R521K","R521K","EGFR","http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=482&re=681&var=R521K","http://getma.org/pdb.php?prot=EGFR_HUMAN&from=482&to=681&var=R521K","neutral","0.405","EGFR_HUMAN","NP_005219","399","chr7:55196748","1","1","",""
+"2","EGFR_HUMAN R98Q","R98Q","EGFR","http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=57&re=168&var=R98Q","http://getma.org/pdb.php?prot=EGFR_HUMAN&from=57&to=168&var=R98Q","neutral","0.6","EGFR_HUMAN","NP_005219","181","chr7:55178543","","","",""
+"3","EGFR_HUMAN G719D","G719D","EGFR","http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=G719D","http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=G719D","medium","3.115","EGFR_HUMAN","NP_005219","700","chr7:55209201","1","1","","0UN IRE FMM ANP CY7 HYZ 03P ITI DKI 685 T95 T74 ZZY M97 6XP 0K0 KRW 0JJ 0K1 P17 112 1N1 JIN STI P5C 585 S19 P16 VX6 P3Y SX7 ACK B90 AMP ZD6 STU 7PY BI9 BII ATP ADP 4ST VG8 YAM P1E 7X4 7X5 7X6 7X8 349 3JZ"
+"4","NP_000537 G356A","G356A","TP53","http://getma.org/?cm=msa&ty=f&p=P53_HUMAN&rb=318&re=359&var=G356A","http://getma.org/pdb.php?prot=P53_HUMAN&from=318&to=359&var=G356A","neutral","-0.895","P53_HUMAN","NP_000537","45","chr17:7514684","","1","",""
+"5","NP_000537 G360A","G360A","TP53","http://getma.org/?cm=msa&ty=f&p=P53_HUMAN&rb=360&re=393&var=G360A","","medium","2.25","P53_HUMAN","NP_000537","15","chr17:7514672","","","",""
+"6","NP_000537 S46A","S46A","TP53","http://getma.org/?cm=msa&ty=f&p=P53_HUMAN&rb=30&re=94&var=S46A","http://getma.org/pdb.php?prot=P53_HUMAN&from=30&to=94&var=S46A","neutral","0.55","P53_HUMAN","NP_000537","5","chr17:7520274","1","1","",""
diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/test-data/polyphen2_full.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/test-data/polyphen2_full.txt	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,23 @@
+#o_acc               	 o_pos	o_aa1	o_aa2	rsid      	acc       	   pos	aa1	aa2	nt1	nt2	        prediction	            based_on	    effect	        pph2_class	 pph2_prob	  pph2_FPR	  pph2_TPR	  pph2_FDR	    site	  region	    PHAT	dScore	Score1	Score2	MSAv	  Nobs	 Nstruct	 Nfilt	PDB_id	PDB_pos	PDB_ch	 ident	length	NormASA	SecStr	MapReg	  dVol	 dProp	B-fact	 H-bonds	 AveNHet	 MinDHet	 AveNInt	 MinDInt	 AveNSit	 MinDSit	Transv	CodPos	CpG	 MinDJxn	     PfamHit	  IdPmax	  IdPSNP	  IdQmin
+Q13615-2            	  1170	    N	    I	         ?	Q13615-2  	  1170	  N	  I	  A	  T	 probably damaging	           alignment	         ?	       deleterious	     0.998	    0.0112	     0.273	    0.0274	       ?	       ?	       ?	+2.214	-1.705	-3.919	   2	    37	       ?	     ?	     ?	      ?	     ?	     ?	     ?	      ?	     ?	     ?	     ?	     ?	     ?	       ?	       ?	       ?	       ?	       ?	       ?	       ?	     1	     1	  0	   -2313	           ?	   1.268	       ?	   47.09	# chr22:30421786|AT|uc003agu.3+|MTMR3|NP_694690
+Q13615              	  1198	    N	    I	         ?	Q13615    	  1198	  N	  I	  A	  T	 probably damaging	           alignment	         ?	       deleterious	     0.998	    0.0112	     0.273	    0.0274	      NO	      NO	       ?	+2.296	-1.580	-3.876	   2	    38	       ?	     ?	     ?	      ?	     ?	     ?	     ?	      ?	     ?	     ?	     ?	     ?	     ?	       ?	       ?	       ?	       ?	       ?	       ?	       ?	     1	     1	  0	   -3099	          NO	   1.010	       ?	   45.58	# chr22:30421786|AT|uc003agv.3+|MTMR3|NP_066576
+Q13615-3            	  1161	    N	    I	         ?	Q13615-3  	  1161	  N	  I	  A	  T	 probably damaging	           alignment	         ?	       deleterious	     0.998	    0.0112	     0.273	    0.0274	       ?	       ?	       ?	+2.214	-1.705	-3.919	   2	    37	       ?	     ?	     ?	      ?	     ?	     ?	     ?	      ?	     ?	     ?	     ?	     ?	     ?	       ?	       ?	       ?	       ?	       ?	       ?	       ?	     1	     1	  0	   -3099	           ?	   1.275	       ?	   47.37	# chr22:30421786|AT|uc003agw.3+|MTMR3|NP_694691
+Q9ULT6              	   637	    H	    R	         ?	Q9ULT6    	   637	  H	  R	  A	  G	            benign	           alignment	         ?	           neutral	     0.002	     0.704	     0.987	     0.452	      NO	      NO	       ?	+0.398	-2.258	-2.656	   2	    47	       ?	     ?	     ?	      ?	     ?	     ?	     ?	      ?	     ?	     ?	     ?	     ?	     ?	       ?	       ?	       ?	       ?	       ?	       ?	       ?	     0	     1	  2	    +858	          NO	  20.363	  20.363	   77.46	# chr22:29446079|AG|uc003aeg.2+|ZNRF3|NP_115549
+Q9ULT6              	   637	    H	    R	         ?	Q9ULT6    	   637	  H	  R	  A	  G	            benign	           alignment	         ?	           neutral	     0.002	     0.704	     0.987	     0.452	      NO	      NO	       ?	+0.398	-2.258	-2.656	   2	    47	       ?	     ?	     ?	      ?	     ?	     ?	     ?	      ?	     ?	     ?	     ?	     ?	     ?	       ?	       ?	       ?	       ?	       ?	       ?	       ?	     0	     1	  2	   -1599	          NO	  20.363	  20.363	   77.46	# chr22:29446079|AG|uc003aeh.1+|ZNRF3|NP_115549
+Q969V6              	   648	    S	    C	         ?	Q969V6    	   648	  S	  C	  A	  T	 possibly damaging	           alignment	         ?	       deleterious	      0.89	    0.0639	     0.821	    0.0953	      NO	COMPBIAS	       ?	+2.837	-1.909	-4.746	   2	    32	       ?	     ?	     ?	      ?	     ?	     ?	     ?	      ?	     ?	     ?	     ?	     ?	     ?	       ?	       ?	       ?	       ?	       ?	       ?	       ?	     1	     0	  0	    +123	          NO	   1.320	       ?	   90.33	# chr22:40814500|TA|uc003ayv.1-|MKL1|NP_065882
+Q969V6              	   648	    S	    R	         ?	Q969V6    	   648	  S	  R	  A	  C	            benign	           alignment	         ?	           neutral	     0.167	     0.131	      0.92	     0.162	      NO	COMPBIAS	       ?	+1.814	-1.909	-3.723	   2	    32	       ?	     ?	     ?	      ?	     ?	     ?	     ?	      ?	     ?	     ?	     ?	     ?	     ?	       ?	       ?	       ?	       ?	       ?	       ?	       ?	     1	     0	  2	    +123	          NO	   2.525	       ?	   90.33	# chr22:40814500|TG|uc003ayv.1-|MKL1|NP_065882
+Q969V6              	   648	    S	    C	         ?	Q969V6    	   648	  S	  C	  A	  T	 possibly damaging	           alignment	         ?	       deleterious	      0.89	    0.0639	     0.821	    0.0953	      NO	COMPBIAS	       ?	+2.837	-1.909	-4.746	   2	    32	       ?	     ?	     ?	      ?	     ?	     ?	     ?	      ?	     ?	     ?	     ?	     ?	     ?	       ?	       ?	       ?	       ?	       ?	       ?	       ?	     1	     0	  0	    +123	          NO	   1.320	       ?	   90.33	# chr22:40814500|TA|uc003ayw.1-|MKL1|NP_065882
+Q969V6              	   648	    S	    R	         ?	Q969V6    	   648	  S	  R	  A	  C	            benign	           alignment	         ?	           neutral	     0.167	     0.131	      0.92	     0.162	      NO	COMPBIAS	       ?	+1.814	-1.909	-3.723	   2	    32	       ?	     ?	     ?	      ?	     ?	     ?	     ?	      ?	     ?	     ?	     ?	     ?	     ?	       ?	       ?	       ?	       ?	       ?	       ?	       ?	     1	     0	  2	    +123	          NO	   2.525	       ?	   90.33	# chr22:40814500|TG|uc003ayw.1-|MKL1|NP_065882
+E7ER32              	   648	    S	    C	         ?	E7ER32    	   648	  S	  C	  A	  T	 possibly damaging	           alignment	         ?	       deleterious	     0.953	    0.0514	     0.788	    0.0812	      NO	      NO	       ?	+2.837	-1.909	-4.746	   2	    33	       ?	     ?	     ?	      ?	     ?	     ?	     ?	      ?	     ?	     ?	     ?	     ?	     ?	       ?	       ?	       ?	       ?	       ?	       ?	       ?	     1	     0	  0	    +123	          NO	   1.255	       ?	   87.22	# chr22:40814500|TA|uc010gye.1-|MKL1|
+E7ER32              	   648	    S	    R	         ?	E7ER32    	   648	  S	  R	  A	  C	            benign	           alignment	         ?	           neutral	     0.337	     0.111	     0.901	     0.142	      NO	      NO	       ?	+1.814	-1.909	-3.723	   2	    33	       ?	     ?	     ?	      ?	     ?	     ?	     ?	      ?	     ?	     ?	     ?	     ?	     ?	       ?	       ?	       ?	       ?	       ?	       ?	       ?	     1	     0	  2	    +123	          NO	   2.402	       ?	   87.22	# chr22:40814500|TG|uc010gye.1-|MKL1|
+B0QY83              	   598	    S	    C	         ?	B0QY83    	   598	  S	  C	  A	  T	 possibly damaging	        alignment_mz	         ?	       deleterious	     0.726	    0.0797	     0.856	     0.112	      NO	      NO	       ?	+2.847	-1.931	-4.778	   3	    31	       ?	     ?	     ?	      ?	     ?	     ?	     ?	      ?	     ?	     ?	     ?	     ?	     ?	       ?	       ?	       ?	       ?	       ?	       ?	       ?	     1	     0	  0	    +123	          NO	   1.615	       ?	   91.49	# chr22:40814500|TA|uc010gyf.1-|MKL1|NP_065882
+B0QY83              	   598	    S	    R	         ?	B0QY83    	   598	  S	  R	  A	  C	            benign	        alignment_mz	         ?	           neutral	     0.047	     0.168	     0.942	     0.195	      NO	      NO	       ?	+1.674	-1.931	-3.605	   3	    31	       ?	     ?	     ?	      ?	     ?	     ?	     ?	      ?	     ?	     ?	     ?	     ?	     ?	       ?	       ?	       ?	       ?	       ?	       ?	       ?	     1	     0	  2	    +123	          NO	   5.560	       ?	   91.49	# chr22:40814500|TG|uc010gyf.1-|MKL1|NP_065882
+Q969V6              	   396	    A	    T	         ?	Q969V6    	   396	  A	  T	  G	  A	            benign	           alignment	         ?	           neutral	     0.009	     0.233	     0.961	     0.247	      NO	      NO	       ?	+0.097	-1.540	-1.637	   2	    39	       ?	     ?	     ?	      ?	     ?	     ?	     ?	      ?	     ?	     ?	     ?	     ?	     ?	       ?	       ?	       ?	       ?	       ?	       ?	       ?	     0	     0	  1	    +879	          NO	  21.659	  21.659	   88.08	# chr22:40815256|CT|uc003ayv.1-|MKL1|NP_065882
+Q969V6              	   396	    A	    T	         ?	Q969V6    	   396	  A	  T	  G	  A	            benign	           alignment	         ?	           neutral	     0.009	     0.233	     0.961	     0.247	      NO	      NO	       ?	+0.097	-1.540	-1.637	   2	    39	       ?	     ?	     ?	      ?	     ?	     ?	     ?	      ?	     ?	     ?	     ?	     ?	     ?	       ?	       ?	       ?	       ?	       ?	       ?	       ?	     0	     0	  1	    +879	          NO	  21.659	  21.659	   88.08	# chr22:40815256|CT|uc003ayw.1-|MKL1|NP_065882
+E7ER32              	   396	    A	    T	         ?	E7ER32    	   396	  A	  T	  G	  A	            benign	           alignment	         ?	           neutral	     0.009	     0.233	     0.961	     0.247	      NO	      NO	       ?	+0.097	-1.540	-1.637	   2	    39	       ?	     ?	     ?	      ?	     ?	     ?	     ?	      ?	     ?	     ?	     ?	     ?	     ?	       ?	       ?	       ?	       ?	       ?	       ?	       ?	     0	     0	  1	    +879	          NO	  20.554	  20.554	   83.58	# chr22:40815256|CT|uc010gye.1-|MKL1|
+B0QY83              	   346	    A	    T	         ?	B0QY83    	   346	  A	  T	  G	  A	            benign	        alignment_mz	         ?	           neutral	     0.008	     0.239	     0.963	     0.252	      NO	      NO	       ?	+0.456	-1.547	-2.003	   3	    32	       ?	     ?	     ?	      ?	     ?	     ?	     ?	      ?	     ?	     ?	     ?	     ?	     ?	       ?	       ?	       ?	       ?	       ?	       ?	       ?	     0	     0	  1	    +879	          NO	  21.940	  21.940	   89.22	# chr22:40815256|CT|uc010gyf.1-|MKL1|NP_065882
+## Sources:
+##   Predictions: PolyPhen-2 v2.2.2r398
+##   Sequences:   UniProtKB/UniRef100 Release 2011_12 (14-Dec-2011)
+##   Structures:  PDB/DSSP Snapshot 03-Jan-2012 (78304 Structures)
+##   Genes:       UCSC MultiZ46Way GRCh37/hg19 (08-Oct-2009)
diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/test-data/polyphen2_input.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/test-data/polyphen2_input.txt	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,5 @@
+chr22:30421786 A/T
+chr22:29446079 A/G
+chr22:40814500 A/G
+chr22:40815256 C/T
+
diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/test-data/polyphen2_log.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/test-data/polyphen2_log.txt	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,38 @@
+===========================
+Stage 1/7: Validating input
+===========================
+No errors
+
+===============================
+Stage 2/7: Mapping genomic SNPs
+===============================
+WARNING: (chr22:40814500 - uc003ayv.1) None of the input alleles (A/G) matches reference allele (T)
+WARNING: (chr22:40814500 - uc003ayw.1) None of the input alleles (A/G) matches reference allele (T)
+WARNING: (chr22:40814500 - uc010gye.1) None of the input alleles (A/G) matches reference allele (T)
+WARNING: (chr22:40814500 - uc010gyf.1) None of the input alleles (A/G) matches reference allele (T)
+Total errors/warnings: 4
+
+============================
+Stage 3/7: Collecting output
+============================
+No errors
+
+===============================================
+Stage 4/7: Building MSA and annotating proteins
+===============================================
+No errors
+
+============================
+Stage 5/7: Collecting output
+============================
+No errors
+
+=====================
+Stage 6/7: Predicting
+=====================
+No errors
+
+=============================
+Stage 7/7: Generating reports
+=============================
+No errors
diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/test-data/polyphen2_short.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/test-data/polyphen2_short.txt	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,23 @@
+#o_acc               	 o_pos	o_aa1	o_aa2	rsid      	acc       	   pos	aa1	aa2	        prediction	 pph2_prob	  pph2_FPR	  pph2_TPR
+Q13615-2            	  1170	    N	    I	         ?	Q13615-2  	  1170	  N	  I	 probably damaging	     0.998	    0.0112	     0.273	# chr22:30421786|AT|uc003agu.3+|MTMR3|NP_694690
+Q13615              	  1198	    N	    I	         ?	Q13615    	  1198	  N	  I	 probably damaging	     0.998	    0.0112	     0.273	# chr22:30421786|AT|uc003agv.3+|MTMR3|NP_066576
+Q13615-3            	  1161	    N	    I	         ?	Q13615-3  	  1161	  N	  I	 probably damaging	     0.998	    0.0112	     0.273	# chr22:30421786|AT|uc003agw.3+|MTMR3|NP_694691
+Q9ULT6              	   637	    H	    R	         ?	Q9ULT6    	   637	  H	  R	            benign	     0.002	     0.704	     0.987	# chr22:29446079|AG|uc003aeg.2+|ZNRF3|NP_115549
+Q9ULT6              	   637	    H	    R	         ?	Q9ULT6    	   637	  H	  R	            benign	     0.002	     0.704	     0.987	# chr22:29446079|AG|uc003aeh.1+|ZNRF3|NP_115549
+Q969V6              	   648	    S	    C	         ?	Q969V6    	   648	  S	  C	 possibly damaging	      0.89	    0.0639	     0.821	# chr22:40814500|TA|uc003ayv.1-|MKL1|NP_065882
+Q969V6              	   648	    S	    R	         ?	Q969V6    	   648	  S	  R	            benign	     0.167	     0.131	      0.92	# chr22:40814500|TG|uc003ayv.1-|MKL1|NP_065882
+Q969V6              	   648	    S	    C	         ?	Q969V6    	   648	  S	  C	 possibly damaging	      0.89	    0.0639	     0.821	# chr22:40814500|TA|uc003ayw.1-|MKL1|NP_065882
+Q969V6              	   648	    S	    R	         ?	Q969V6    	   648	  S	  R	            benign	     0.167	     0.131	      0.92	# chr22:40814500|TG|uc003ayw.1-|MKL1|NP_065882
+E7ER32              	   648	    S	    C	         ?	E7ER32    	   648	  S	  C	 possibly damaging	     0.953	    0.0514	     0.788	# chr22:40814500|TA|uc010gye.1-|MKL1|
+E7ER32              	   648	    S	    R	         ?	E7ER32    	   648	  S	  R	            benign	     0.337	     0.111	     0.901	# chr22:40814500|TG|uc010gye.1-|MKL1|
+B0QY83              	   598	    S	    C	         ?	B0QY83    	   598	  S	  C	 possibly damaging	     0.726	    0.0797	     0.856	# chr22:40814500|TA|uc010gyf.1-|MKL1|NP_065882
+B0QY83              	   598	    S	    R	         ?	B0QY83    	   598	  S	  R	            benign	     0.047	     0.168	     0.942	# chr22:40814500|TG|uc010gyf.1-|MKL1|NP_065882
+Q969V6              	   396	    A	    T	         ?	Q969V6    	   396	  A	  T	            benign	     0.009	     0.233	     0.961	# chr22:40815256|CT|uc003ayv.1-|MKL1|NP_065882
+Q969V6              	   396	    A	    T	         ?	Q969V6    	   396	  A	  T	            benign	     0.009	     0.233	     0.961	# chr22:40815256|CT|uc003ayw.1-|MKL1|NP_065882
+E7ER32              	   396	    A	    T	         ?	E7ER32    	   396	  A	  T	            benign	     0.009	     0.233	     0.961	# chr22:40815256|CT|uc010gye.1-|MKL1|
+B0QY83              	   346	    A	    T	         ?	B0QY83    	   346	  A	  T	            benign	     0.008	     0.239	     0.963	# chr22:40815256|CT|uc010gyf.1-|MKL1|NP_065882
+## Sources:
+##   Predictions: PolyPhen-2 v2.2.2r398
+##   Sequences:   UniProtKB/UniRef100 Release 2011_12 (14-Dec-2011)
+##   Structures:  PDB/DSSP Snapshot 03-Jan-2012 (78304 Structures)
+##   Genes:       UCSC MultiZ46Way GRCh37/hg19 (08-Oct-2009)
diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/test-data/polyphen2_snp.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/test-data/polyphen2_snp.txt	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,28 @@
+#snp_pos         	str	        gene	  transcript	 ccid	        ccds	cciden	refa	        type	   ntpos	nt1	nt2	flanks	trv	cpg	  jxdon	  jxacc	   exon	  cexon	jxc	dgn	  cdnpos	frame	cdn1	cdn2	aa1	aa2	   aapos	spmap	     spacc	      spname	    refs_acc	    dbrsid	dbobsrvd	   dbavHet	 dbavHetSE	dbRmPaPt	comments
+chr22:30421786  	  +	       MTMR3	  uc003agu.3	    ?	 CCDS13871.1	     1	 A/T	    missense	  142629	  A	  T	    AC	  1	  0	  -2313	   -168	  20/20	  18/18	  ?	  0	    1170	    1	 AAC	 ATC	  N	  I	    1170	    1	  Q13615-2	 MTMR3_HUMAN	   NP_694690	rs75623810	     A/T	  0.016564	  0.089485	   A>A>A
+chr22:30421786  	  +	       MTMR3	  uc003agv.3	16552	 CCDS13870.1	     1	 A/T	    missense	  142629	  A	  T	    AC	  1	  0	  -3099	   -168	  20/20	  18/18	  ?	  0	    1198	    1	 AAC	 ATC	  N	  I	    1198	    1	    Q13615	 MTMR3_HUMAN	   NP_066576	rs75623810	     A/T	  0.016564	  0.089485	   A>A>A
+chr22:30421786  	  +	       MTMR3	  uc003agw.3	    ?	 CCDS46682.1	     1	 A/T	    missense	  142629	  A	  T	    AC	  1	  0	  -3099	   -168	  19/19	  17/17	  ?	  0	    1161	    1	 AAC	 ATC	  N	  I	    1161	    1	  Q13615-3	 MTMR3_HUMAN	   NP_694691	rs75623810	     A/T	  0.016564	  0.089485	   A>A>A
+chr22:29446079  	  +	       ZNRF3	  uc003aeg.2	16531	 CCDS42999.1	     1	 A/G	    missense	  166190	  A	  G	    CC	  0	  2	   +858	   -895	    8/9	    7/8	  ?	  0	     537	    1	 CAC	 CGC	  H	  R	     637	    1	    Q9ULT6	 ZNRF3_HUMAN	   NP_115549	rs62641746	     A/G	  0.030762	  0.120144	   A>A>A
+chr22:29446079  	  +	       ZNRF3	  uc003aeh.1	    ?	 CCDS42999.1	 0.982	 A/G	    missense	   63040	  A	  G	    CC	  0	  2	  -1599	   -895	    7/7	    7/7	  ?	  0	     537	    1	 CAC	 CGC	  H	  R	     637	    1	    Q9ULT6	 ZNRF3_HUMAN	   NP_115549	rs62641746	     A/G	  0.030762	  0.120144	   A>A>A
+chr22:40814500  	  -	        MKL1	  uc003ayv.1	    ?	 CCDS14003.1	     1	 T/A	    missense	   44939	  A	  T	    CG	  1	  0	   +123	   -889	   9/12	   9/12	  ?	  0	     648	    0	 AGC	 TGC	  S	  C	     648	    1	    Q969V6	  MKL1_HUMAN	   NP_065882	         ?	       ?	         ?	         ?	       ?
+chr22:40814500  	  -	        MKL1	  uc003ayv.1	    ?	 CCDS14003.1	     1	 T/G	    missense	   44939	  A	  C	    CG	  1	  2	   +123	   -889	   9/12	   9/12	  ?	  0	     648	    0	 AGC	 CGC	  S	  R	     648	    1	    Q969V6	  MKL1_HUMAN	   NP_065882	         ?	       ?	         ?	         ?	       ?
+chr22:40814500  	  -	        MKL1	  uc003ayw.1	16752	 CCDS14003.1	     1	 T/A	    missense	  218191	  A	  T	    CG	  1	  0	   +123	   -889	  12/15	   9/12	  ?	  0	     648	    0	 AGC	 TGC	  S	  C	     648	    1	    Q969V6	  MKL1_HUMAN	   NP_065882	         ?	       ?	         ?	         ?	       ?
+chr22:40814500  	  -	        MKL1	  uc003ayw.1	16752	 CCDS14003.1	     1	 T/G	    missense	  218191	  A	  C	    CG	  1	  2	   +123	   -889	  12/15	   9/12	  ?	  0	     648	    0	 AGC	 CGC	  S	  R	     648	    1	    Q969V6	  MKL1_HUMAN	   NP_065882	         ?	       ?	         ?	         ?	       ?
+chr22:40814500  	  -	        MKL1	  uc010gye.1	    ?	           ?	     ?	 T/A	    missense	  218191	  A	  T	    CG	  1	  0	   +123	   -889	  12/15	   9/12	  ?	  0	     648	    0	 AGC	 TGC	  S	  C	     648	    1	    E7ER32	E7ER32_HUMAN	           ?	         ?	       ?	         ?	         ?	       ?
+chr22:40814500  	  -	        MKL1	  uc010gye.1	    ?	           ?	     ?	 T/G	    missense	  218191	  A	  C	    CG	  1	  2	   +123	   -889	  12/15	   9/12	  ?	  0	     648	    0	 AGC	 CGC	  S	  R	     648	    1	    E7ER32	E7ER32_HUMAN	           ?	         ?	       ?	         ?	         ?	       ?
+chr22:40814500  	  -	        MKL1	  uc010gyf.1	    ?	           ?	     ?	 T/A	    missense	  218191	  A	  T	    CG	  1	  0	   +123	   -889	  11/14	   8/11	  ?	  0	     598	    0	 AGC	 TGC	  S	  C	     598	    1	    B0QY83	B0QY83_HUMAN	   NP_065882	         ?	       ?	         ?	         ?	       ?
+chr22:40814500  	  -	        MKL1	  uc010gyf.1	    ?	           ?	     ?	 T/G	    missense	  218191	  A	  C	    CG	  1	  2	   +123	   -889	  11/14	   8/11	  ?	  0	     598	    0	 AGC	 CGC	  S	  R	     598	    1	    B0QY83	B0QY83_HUMAN	   NP_065882	         ?	       ?	         ?	         ?	       ?
+chr22:40815256  	  -	        MKL1	  uc003ayv.1	    ?	 CCDS14003.1	     1	 C/T	    missense	   44183	  G	  A	    CC	  0	  1	   +879	   -133	   9/12	   9/12	  ?	  0	     396	    0	 GCC	 ACC	  A	  T	     396	    1	    Q969V6	  MKL1_HUMAN	   NP_065882	rs34736200	     G/A	  0.047299	   0.14633	   A>A>A
+chr22:40815256  	  -	        MKL1	  uc003ayw.1	16752	 CCDS14003.1	     1	 C/T	    missense	  217435	  G	  A	    CC	  0	  1	   +879	   -133	  12/15	   9/12	  ?	  0	     396	    0	 GCC	 ACC	  A	  T	     396	    1	    Q969V6	  MKL1_HUMAN	   NP_065882	rs34736200	     G/A	  0.047299	   0.14633	   A>A>A
+chr22:40815256  	  -	        MKL1	  uc010gye.1	    ?	           ?	     ?	 C/T	    missense	  217435	  G	  A	    CC	  0	  1	   +879	   -133	  12/15	   9/12	  ?	  0	     396	    0	 GCC	 ACC	  A	  T	     396	    1	    E7ER32	E7ER32_HUMAN	           ?	rs34736200	     G/A	  0.047299	   0.14633	   A>A>A
+chr22:40815256  	  -	        MKL1	  uc010gyf.1	    ?	           ?	     ?	 C/T	    missense	  217435	  G	  A	    CC	  0	  1	   +879	   -133	  11/14	   8/11	  ?	  0	     346	    0	 GCC	 ACC	  A	  T	     346	    1	    B0QY83	B0QY83_HUMAN	   NP_065882	rs34736200	     G/A	  0.047299	   0.14633	   A>A>A
+## Totals:
+##   lines input               4
+##   lines skipped             0
+##   alleles annotated        17
+##     missense               17
+##     nonsense                0
+##     coding-synon            0
+##     intron                  0
+##     utr-3                   0
+##     utr-5                   0
diff -r 8aceb7fc57f5 -r b9de63c72559 chasm_webservice/tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chasm_webservice/tool_dependencies.xml	Mon Apr 14 19:16:11 2014 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="requests" version="2.2.1">
+        <repository changeset_revision="570c2648d96d" name="package_requests_2_2_1" owner="saketkc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>
diff -r 8aceb7fc57f5 -r b9de63c72559 tools/chasm/README.rst
--- a/tools/chasm/README.rst	Fri Nov 01 06:01:52 2013 +0530
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-Galaxy wrapper for the CHASM webservice at CRAVAT(v2.0)
-===================================================
-
-This tool is copyright 2013 by Saket Choudhary, Indian Institute of Technology Bombay
-All rights reserved. MIT licensed.
-
-Licence (MIT)
-=============
-
-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.
-
-Citations
-===========
-
-
-If you use this Galaxy tool in work leading to a scientific publication please cite:
-
-Carter, Hannah, et al. "Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations."
-Cancer research 69.16 (2009): 6660-6667.
-
-Wong, Wing Chung, et al. "CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer."
-Bioinformatics 27.15 (2011): 2147-2148.
diff -r 8aceb7fc57f5 -r b9de63c72559 tools/chasm/chasm_web.py
--- a/tools/chasm/chasm_web.py	Fri Nov 01 06:01:52 2013 +0530
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,222 +0,0 @@
-#!/usr/bin/python
-"""
-The MIT License (MIT)
-
-Copyright (c) 2013 Saket Choudhary, <saketkc@gmail.com>
-
-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.
-
-"""
-import requests
-import argparse
-import sys
-import time
-from functools import wraps
-import simplejson as json
-import zipfile
-import tempfile, ntpath, shutil
-import xlrd
-import csv
-import os
-sheet_map = {0:"Variant_Analysis.csv",1:"Amino_Acid_Level_Analysis.csv",2:"Gene_Level_Analysis.csv"}
-def retry(ExceptionToCheck, tries=4, delay=3, backoff=2, logger=None):
-    """Retry calling the decorated function using an exponential backoff.
-
-    http://www.saltycrane.com/blog/2009/11/trying-out-retry-decorator-python/
-    original from: http://wiki.python.org/moin/PythonDecoratorLibrary#Retry
-
-    :param ExceptionToCheck: the exception to check. may be a tuple of
-        exceptions to check
-    :type ExceptionToCheck: Exception or tuple
-    :param tries: number of times to try (not retry) before giving up
-    :type tries: int
-    :param delay: initial delay between retries in seconds
-    :type delay: int
-    :param backoff: backoff multiplier e.g. value of 2 will double the delay
-        each retry
-    :type backoff: int
-    :param logger: logger to use. If None, print
-    :type logger: logging.Logger instance
-    """
-    def deco_retry(f):
-
-        @wraps(f)
-        def f_retry(*args, **kwargs):
-            mtries, mdelay = tries, delay
-            while mtries > 1:
-                try:
-                    return f(*args, **kwargs)
-                except ExceptionToCheck, e:
-                    #msg = "%s, Retrying in %d seconds..." % (str(e), mdelay)
-                    msg = "Retrying in %d seconds..." %  (mdelay)
-                    if logger:
-                        logger.warning(msg)
-                    else:
-                        print msg
-                    time.sleep(mdelay)
-                    mtries -= 1
-                    mdelay *= backoff
-            return f(*args, **kwargs)
-
-        return f_retry  # true decorator
-
-    return deco_retry
-CANCERTYPES =["Bladder","Blood-Lymphocyte","Blood-Myeloid","Brain-Cerebellum","Brain-Glioblastoma_Multiforme","Brain-Lower_Grade_Glioma","Breast","Cervix","Colon","Head_and_Neck","Kidney-Chromophobe","Kidney-Clear_Cell","Kidney-Papiallary_Cell","Liver-Nonviral","Liver-Viral","Lung-Adenocarcinoma","Lung-Squamous_Cell","Melanoma","Other","Ovary","Pancreas","Prostate-Adenocarcinoma","Rectum","Skin","Stomach","Thyroid","Uterus"]
-URL="http://www.cravat.us/ClassifierSelect1"
-def stop_err( msg ):
-    sys.stderr.write( '%s\n' % msg )
-    sys.exit()
-
-class CHASMWeb:
-    def __init__( self, mutationbox=None, filepath=None,is_hg_18=None, analysis_type=None, analysis_program=None, chosendb=None, cancer_type=None, email=None, annotate_genes=None, text_reports=None, mupit_out=None ):
-        self.mutationbox = mutationbox
-        self.filepath = filepath
-        self.is_hg_18 = is_hg_18
-        self.analysis_type = analysis_type
-        self.analysis_program = analysis_program
-        self.chosendb = chosendb
-        self.email = email
-        self.annotate_genes = annotate_genes
-        self.cancer_type = cancer_type
-        self.email = email
-        self.annotate_genes = annotate_genes
-        self.text_reports=text_reports
-        self.mupit_input= mupit_out
-    def make_request( self ):
-        data = {
-                "mutationbox":self.mutationbox,
-                "hg18": self.is_hg_18,
-                "analysistype": self.analysis_type,
-                "chosendb": self.analysis_program,
-                "cancertype": self.cancer_type,
-                "geneannotcheckbox": self.annotate_genes,
-                "emailbox": self.email,
-                "tsvreport": self.text_reports,
-                "mupitinput": self.mupit_input,
-                }
-        stripped_data = {}
-
-        for key,value in data.iteritems():
-            if value==True:
-                value="on"
-            if value!=None and value!=False:
-                stripped_data[key]=value
-        #print stripped_data
-        if not self.mutationbox:
-            file_payload={"inputfile":open(self.filepath)}
-            request = requests.post(URL, data=stripped_data, files=file_payload)
-        else:
-            request = requests.post(URL, data=stripped_data, files=dict(foo='bar'))
-        job_id = json.loads(request.text)["jobId"]
-        return job_id
-    @retry(requests.exceptions.HTTPError)
-    def zip_exists(self,job_id ):
-        url="http://www.cravat.us/results/%s/%s.zip" %(job_id,job_id)
-        zip_download_request = requests.request("GET", url)
-        if zip_download_request.status_code==404:
-            raise requests.HTTPError()
-        else:
-            return url
-    def download_zip( self, url, job_id):
-        self.tmp_dir = tempfile.mkdtemp()
-        r = requests.get( url, stream=True )
-        if r.status_code == 200:
-            self.path = os.path.join( self.tmp_dir,job_id+".zip" )
-            with open(self.path, 'wb') as f:
-                for chunk in r.iter_content(128):
-                    f.write(chunk)
-        else:
-            self.path = None
-        return self.path
-
-    def move_files( self, file_map ):
-        fh = open(self.path,"rb")
-        zip_files = zipfile.ZipFile(fh)
-        for name in zip_files.namelist():
-            filename = ntpath.basename(name)
-            extension = ntpath.splitext(filename)[-1]
-            source_file = zip_files.open(name)
-            if extension==".txt":
-                target_file = open(file_map["error.txt"],"wb")
-            elif filename!="SnvGet Feature Description.xls" and extension!=".xls":
-                target_file = open(file_map[filename],"wbb")#file(os.path.join(output_dir,filename),"wb")
-            else:
-                target_file=None
-            if target_file:
-                with source_file,target_file:
-                    shutil.copyfileobj(source_file,target_file)
-            if filename=="SnvGet Feature Description.xls":
-                with xlrd.open_workbook(source_file) as wb:
-                    sheet_names = wb.sheet_names()
-                    for name  in sheet_names:
-                        sh=wb.sheet_by_name(name)
-                        name_shortened= name.replace(" ").strip()+".csv"
-                        with open(name_shortened,'wb') as f:
-                            c = csv.writer(f)
-                            for r in range(sh.nrows):
-                                c.writerow(sh.row_values(r))
-        shutil.rmtree(self.tmp_dir)
-        fh.close()
-def main(params):
-
-    parser = argparse.ArgumentParser()
-    parser.add_argument("-i","--input", type=str, dest="mutationbox", help="Input variants")
-    parser.add_argument("--path",type=str,dest="input_file_location", help="Input file location")
-    parser.add_argument("--hg18", dest="hg18", action="store_true")
-    parser.add_argument("--analysis_type",dest="analysis_type",type=str,choices=["driver","functional","geneannotationonly"], default="driver")
-    parser.add_argument("--chosendb",dest="chosendb",type=str,nargs="*",choices=["CHASM","SnvGet"], default="CHASM")
-    parser.add_argument("--cancertype", dest="cancer_type", type=str, choices=CANCERTYPES, required=True)
-    parser.add_argument("--email", dest="email", required=True, type=str)
-    parser.add_argument("--annotate", dest="annotate", action="store_true", default=None )
-    parser.add_argument("--tsv_report", dest="tsv_report", action="store_true", default=None )
-    parser.add_argument("--mupit_out", dest="mupit_out", action="store_true", default=None )
-    parser.add_argument("--gene_analysis_out", dest="gene_analysis_out", type=str, required=True)
-    parser.add_argument("--variant_analysis_out", dest="variant_analysis_out", type=str, required=True)
-    parser.add_argument("--amino_acid_level_analysis_out", dest="amino_acid_level_analysis_out", type=str, required=True,)
-    parser.add_argument("--error_file", dest="error_file_out", type=str, required=True)
-    parser.add_argument("--snv_box_out", dest="snv_box_out", type=str, required=False)
-    parser.add_argument("--snv_features", dest="snv_features_out", type=str, required=False)
-    args = (parser.parse_args(params))
-    chasm_web = CHASMWeb(mutationbox=args.mutationbox,
-                         filepath=args.input_file_location,
-                         is_hg_18 = args.hg18,
-                         analysis_type=args.analysis_type,
-                         chosendb = args.chosendb,
-                         cancer_type = args.cancer_type,
-                         email=args.email,
-                         annotate_genes=args.annotate,
-                         text_reports=args.tsv_report,
-                         mupit_out=args.mupit_out)
-    job_id=chasm_web.make_request()
-    file_map = {"Amino_Acid_Level_Analysis.tsv":args.amino_acid_level_analysis_out,
-                "SNVBox.tsv":args.snv_box_out,
-                "Variant_Analysis.tsv":args.variant_analysis_out,
-                "Gene_Level_Analysis.tsv":args.gene_analysis_out,
-                "SnvGet Feature Description.xls":args.snv_features_out,
-                "error.txt":args.error_file_out
-                }
-    url = chasm_web.zip_exists(job_id)
-    download = chasm_web.download_zip(url,job_id)
-    if download:
-        move = chasm_web.move_files(file_map=file_map)
-    else:
-        stop_err("Unable to download from the server")
-
-if __name__=="__main__":
-    main(sys.argv[1:])
diff -r 8aceb7fc57f5 -r b9de63c72559 tools/chasm/chasm_web.xml
--- a/tools/chasm/chasm_web.xml	Fri Nov 01 06:01:52 2013 +0530
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,94 +0,0 @@
-<tool id="chasm_webservice" name="CHASM Webservice" version="1.0.0" hidden="false">
-    <requirements>
-            <requirement type="package" version="2.0.1">requests</requirement>
-    </requirements>
-    <description>CHASM score using CRAVAT webservice</description>
-    <command interpreter="python">
-        chasm_web.py --path $input --analysis_type $analysis_type --cancertype $tissue_type --email $__user_email__ --gene_analysis_out $gene_analysis_out  --variant_analysis_out $variant_analysis_out --amino_acid_level_analysis_out $amino_acid_level_analysis_out  --error_file $error_file
-    </command>
-    <inputs>
-        <param format="txt" name="input" type="data" label="Variants File" />
-        <param name="analysis_type" type="select" label="Choose analysis type" help="
-                                                                        Cancer driver analysis predicts whether\
-                                                                        the submitted variants are cancer drivers.\
-                                                                        Functional effect analysis predicts whether\
-                                                                        the submitted variants will have any\
-                                                                        functional effect on their translated proteins.\
-                                                                        Annotation only provides\
-                                                                        GeneCard and PubMed information on\
-                                                                        the genes containing the submitted variants.">
-            <option value="driver">Cancer driver analysis</option>
-            <option value="functional">Functional effect analysis</option>
-            <option value="geneannotationonly">Annotation only</option>
-        </param>
-
-        <param name="gene_annotation" type="select" label="Include Gene annotation">
-            <option value="no">No</option>
-            <option value="yes">Yes</option>
-        </param>
-
-        <param name="tissue_type" type="select" label="Tissue Type">
-            <option value="Bladder">Bladder</option>
-            <option value="Blood-Lymphocyte">Blood-Lymphocyte</option>
-            <option value="Blood-Myeloid">Blood-Myeloid</option>
-            <option value="Brain-Cerebellum">Brain-Cerebellum</option>
-            <option value="Brain-Glioblastoma_Multiforme">Brain-Glioblastoma_Multiforme</option>
-            <option value="Brain-Lower_Grade_Glioma">Brain-Lower_Grade_Glioma</option>
-            <option value="Breast">Breast</option>
-            <option value="Cervix">Cervix</option>
-            <option value="Colon">Colon</option>
-            <option value="Head_and_Neck">Head_and_Neck</option>
-            <option value="Kidney-Chromophobe">Kidney-Chromophobe</option>
-            <option value="Kidney-Clear_Cell">Kidney-Clear_Cell</option>
-            <option value="Kidney-Papiallary_Cell">Kidney-Papiallary_Cell</option>
-            <option value="Liver-Nonviral">Liver-Nonviral</option>
-            <option value="Liver-Viral">Liver-Viral</option>
-            <option value="Lung-Adenocarcinoma">Lung-Adenocarcinoma</option>
-            <option value="Lung-Squamous_Cell">Lung-Squamous_Cell</option>
-            <option value="Melanoma">Melanoma</option>
-            <option value="Other">Other</option>
-            <option value="Ovary">Ovary</option>
-            <option value="Pancreas">Pancreas</option>
-            <option value="Prostate-Adenocarcinoma">Prostate-Adenocarcinoma</option>
-            <option value="Rectum">Rectum</option>
-            <option value="Skin">Skin</option>
-            <option value="Stomach">Stomach</option>
-            <option value="Thyroid">Thyroid</option>
-            <option value="Uterus">Uterus</option>
-        </param>
-    </inputs>
-    <outputs>
-        <data format="tabular" name="gene_analysis_out"/>
-        <data format="tabular" name="variant_analysis_out" />
-        <data format="tabular" name="amino_acid_level_analysis_out" />
-        <data format="tabular" name="error_file"/>
-    </outputs>
-    <help>
-        **What it does**
-        * CHASM (Cancer-specific High-throughput Annotation of Somatic Mutations) is a method that predicts the functional significance of somatic missense variants
-        observed in the genomes of cancer cells, allowing variants to be prioritized in subsequent functional studies, based on the probability that they confer
-        increased fitness to a cancer cell. CHASM uses a machine learning method called Random Forest to distinguish between driver and passenger somatic missense variation.
-        The Random Forest is trained on a positive class of drivers curated from the COSMIC database and a negative class of passengers, generated in silico,
-        according to passenger base substitution frequencies estimated for a specific tumor type. Each variant is represented by a list of features,
-        including amino acid substitution properties, alignment-based estimates of conservation at the variant position, predicted local structure and annotations from
-        the UniProt Knowledgebase. Only missense mutations are analyzed by CHASM.  For more information on CHASM, please visit http://wiki.chasmsoftware.org
-
-        * SNVGet retrieves selected predictive features for a variant. Features can be broadly categorized into 3 types:
-            - Amino Acid Substitution features
-            - Protein-based position-specific features
-            - Exon-specific features
-            Only missense mutations are analyzed by SNVGet. For more information on SNVBox (database made with SNVGet), please visit http://wiki.chasmsoftware.org
-        * VEST is a method that predicts the functional effect of a variant.
-
-
-
-        **Citation**
-        If you use this Galaxy tool in work leading to a scientific publication please cite:
-
-        Carter, Hannah, et al. "Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations."
-        Cancer research 69.16 (2009): 6660-6667.
-
-        Wong, Wing Chung, et al. "CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer."
-        Bioinformatics 27.15 (2011): 2147-2148.
-    </help>
-</tool>
diff -r 8aceb7fc57f5 -r b9de63c72559 tools/chasm/tool_dependencies.xml
--- a/tools/chasm/tool_dependencies.xml	Fri Nov 01 06:01:52 2013 +0530
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<tool_dependency>
-     <package name="requests" version="2.0.1">
-         <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_requests_2_0" owner="saketkc"/>
-    </package>
-</tool_dependency>
-