# HG changeset patch # User saket-choudhary # Date 1412725229 14400 # Node ID e51722489ddb4e791ddc0ed01b2eaf9adf8c343c Uploaded diff -r 000000000000 -r e51722489ddb mutationassesor_web/README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mutationassesor_web/README.rst Tue Oct 07 19:40:29 2014 -0400 @@ -0,0 +1,36 @@ +Galaxy wrapper for the Mutation Assessor webservice +=================================================== + +This tool is copyright 2014 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: + +Reva B, Antipin Y, Sander C. Nucleic Acids Research (2011) "Predicting the Functional Impact of Protein Mutations: Application to Cancer Genomics" + +Reva, B.A., Antipin, Y.A. and Sander, C. (2007) Genome Biol, 8, R232. "Determinants of protein function revealed by combinatorial entropy optimization" diff -r 000000000000 -r e51722489ddb mutationassesor_web/mutation_assesor.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mutationassesor_web/mutation_assesor.py Tue Oct 07 19:40:29 2014 -0400 @@ -0,0 +1,66 @@ +#!/usr/bin/env python +import sys +import requests +import os +import argparse +import re +import csv +import StringIO +__url__ = 'http://mutationassessor.org/' + + +def stop_err(msg, err=1): + sys.stderr.write('%s\n' % msg) + sys.exit(err) + + +def main_web(args): + assert os.path.exists(args.input) + with open(args.input) as f: + contents = f.read().strip() + if args.hg19 is True and args.protein is True: + stop_err('--hg19 option conflicts with --protein') + if args.protein is False: + ## Replace tabs/space with commas + re.sub('[\t\s]+', ',', contents) + if args.hg19: + ## Append hg19 to each line + lines = contents.split('\n') + contents = ('\n').join( + map((lambda x: 'hg19,' + x), + lines)) + + payload = {'vars': contents, 'tableQ': 1} + request = requests.post(__url__, data=payload) + response = request.text + if request.status_code != requests.codes.ok: + stop_err("""Error retrieving response from server. + Server returned %s . + Output: %s + """ % (request.status_code, response)) + r = StringIO.StringIO(response) + reader = csv.reader(r, delimiter=",") + csv.writer(open(args.output, "wb"), delimiter='\t').writerows(reader) + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description="Process input output paths") + parser.add_argument('--input', + type=str, + required=True, + help='Input file location') + parser.add_argument('--output', + type=str, + required=True, + help='Output file locatio') + parser.add_argument('--log', + type=str, + required=False) + parser.add_argument('--hg19', + action='store_true', + help="""Use hg19 build. + Appends 'hg19' to each input line""") + parser.add_argument('--protein', + action='store_true', + help='Inputs are in protein space') + args = parser.parse_args() + main_web(args) diff -r 000000000000 -r e51722489ddb mutationassesor_web/mutation_assesor.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mutationassesor_web/mutation_assesor.xml Tue Oct 07 19:40:29 2014 -0400 @@ -0,0 +1,107 @@ + + MutationAssesor web service + + requests + requests + + mutation_assesor.py --input $input --output $output + #if $options.protein == "yes" + --protein + #else + $options.hg19 + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + **What it does** + + This script calls MutationAssesor(http://mutationassessor.org/) Web API to fetch + Mutation Assesor scores and associated output. + + Input is a tab separated or comma separated varaibles file. MutationAssesor + server accepts list of variants, one variant per line, plus optional text thrown in + which might be a description of the variants in genomic coordinates. The + variants are assumed to be coming from '+' strand: + <genome build>,<chromosome>,<position>,<reference allele>,<substituted allele> + + + Genome build is optional. By default 'hg18' build is used. + Input needs to be formatted in the following format: + + 1. Nucleotide space: + + 13,32912555,G,T BRCA2 + + 7,55178574,G,A GBM + + 7,55178574,G,A GBM + + Note that the tool takes care of prepending 'hg19' while running the tool, if you + select 'yes' under 'hg19' label + + 2. Protein Space + <protein ID> <variant> <text>, where <protein ID> can be : + + 1. Uniprot protein accession (i.e. EGFR_HUMAN) + 2. NCBI Refseq protein ID (i.e. NP_005219) + + EGFR_HUMAN R521K + EGFR_HUMAN R98Q Polymorphism + EGFR_HUMAN G719D disease + NP_000537 G356A + NP_000537 G360A dbSNP:rs35993958 + NP_000537 S46A Abolishes phosphorylation + + + + **Citations** + + If you use this tool in Galaxy, please cite : + Reva B, Antipin Y, Sander C. Nucleic Acids Research (2011) + "Predicting the Functional Impact of Protein Mutations: Application to Cancer Genomics" + + Reva, B.A., Antipin, Y.A. and Sander, C. (2007) Genome Biol, 8, R232. + "Determinants of protein function revealed by combinatorial entropy optimization" + + + + + + diff -r 000000000000 -r e51722489ddb mutationassesor_web/test-data/ma_nucleotide_output.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mutationassesor_web/test-data/ma_nucleotide_output.csv Tue Oct 07 19:40:29 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 000000000000 -r e51722489ddb mutationassesor_web/test-data/ma_proper_nucleotide.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mutationassesor_web/test-data/ma_proper_nucleotide.csv Tue Oct 07 19:40:29 2014 -0400 @@ -0,0 +1,3 @@ +13,32912555,G,T BRCA2 +7,55178574,G,A GBM +7,55178574,G,A GBM diff -r 000000000000 -r e51722489ddb mutationassesor_web/test-data/ma_proper_protein.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mutationassesor_web/test-data/ma_proper_protein.csv Tue Oct 07 19:40:29 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 000000000000 -r e51722489ddb mutationassesor_web/test-data/ma_protein_output.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mutationassesor_web/test-data/ma_protein_output.csv Tue Oct 07 19:40:29 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 EGFR_HUMAN,R521K 0 +2 EGFR_HUMAN,R98Q,POLYMORPHISM EGFR_HUMAN,R98Q,POLYMORPHISM 0 +3 EGFR_HUMAN,G719D,DISEASE EGFR_HUMAN,G719D,DISEASE 0 +4 NP_000537,G356A NP_000537,G356A 0 +5 NP_000537,G360A,DBSNP:RS35993958 NP_000537,G360A,DBSNP:RS35993958 0 +6 NP_000537,S46A,ABOLISHES,PHOSPHORYLATION NP_000537,S46A,ABOLISHES,PHOSPHORYLATION 0 diff -r 000000000000 -r e51722489ddb mutationassesor_web/test-data/mutationassessor_input.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mutationassesor_web/test-data/mutationassessor_input.txt Tue Oct 07 19:40:29 2014 -0400 @@ -0,0 +1,13 @@ +EGFR_HUMAN G719S +EGFR_HUMAN G724S +EGFR_HUMAN E734K +EGFR_HUMAN L747F +EGFR_HUMAN R748P +EGFR_HUMAN Q787R +EGFR_HUMAN T790M +EGFR_HUMAN L833V +EGFR_HUMAN V834L +EGFR_HUMAN L858R +EGFR_HUMAN L861Q +EGFR_HUMAN G873E +EGFR_HUMAN R962G diff -r 000000000000 -r e51722489ddb mutationassesor_web/test-data/mutationassessor_output.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mutationassesor_web/test-data/mutationassessor_output.tsv Tue Oct 07 19:40:29 2014 -0400 @@ -0,0 +1,14 @@ + 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 G719S G719S EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=G719S http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=G719S high 3.88 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 +2 EGFR_HUMAN G724S G724S EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=G724S http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=G724S medium 2.7 EGFR_HUMAN NP_005219 700 chr7:55209216 1 ANP 112 ATP AMP 057 +3 EGFR_HUMAN E734K E734K EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=E734K http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=E734K neutral -0.08 EGFR_HUMAN NP_005219 700 chr7:55209924 +4 EGFR_HUMAN L747F L747F EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=L747F http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=L747F low 1.9 EGFR_HUMAN NP_005219 700 chr7:55209963 1 +5 EGFR_HUMAN R748P R748P EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=R748P http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=R748P low 1.155 EGFR_HUMAN NP_005219 700 chr7:55209966 1 VX6 STU S19 +6 EGFR_HUMAN Q787R Q787R EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=Q787R http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=Q787R neutral 0.225 EGFR_HUMAN NP_005219 700 chr7:55216555 +7 EGFR_HUMAN T790M T790M EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=T790M http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=T790M low 1.17 EGFR_HUMAN NP_005219 700 chr7:55216564 1 1 AQ4 AEE CY0 DJK IRE FMM ANP CY7 HYZ ITI POX 03P 03Q GW7 DKI 477 685 0JE T95 T74 ZZY PFY M97 6XP 0K0 VGH KRW 0JJ 0K1 PRC STI P17 112 1N1 7MP GIN JIN B91 919 9DP DB8 4ST 627 0JK P5C S19 P16 406 VX6 P3Y NIL SX7 0LI XY3 ACK PP1 X2M B90 AMP ZD6 X2K X2L ACP DBQ STU 057 7PY BII ATP ADP YAM P1E 7X4 7X5 7X6 7X8 349 3JZ 4JZ +8 EGFR_HUMAN L833V L833V EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=L833V http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=L833V neutral -1.13 EGFR_HUMAN NP_005219 700 chr7:55226933 1 STI GIN B91 919 406 NIL 0LI +9 EGFR_HUMAN V834L V834L EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=V834L http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=V834L low 1.87 EGFR_HUMAN NP_005219 700 chr7:55226936 1 STI GIN 406 0LI XY3 PTR +10 EGFR_HUMAN L858R L858R EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=L858R http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=L858R medium 3.32 EGFR_HUMAN NP_005219 700 chr7:55227008 1 FMM CY7 HYZ ITI POX 03P GW7 BI9 ATP VG8 YAM +11 EGFR_HUMAN L861Q L861Q EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=L861Q http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=L861Q neutral 0.735 EGFR_HUMAN NP_005219 700 chr7:55227017 1 GIN PTR +12 EGFR_HUMAN G873E G873E EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=G873E http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=G873E neutral 0.775 EGFR_HUMAN NP_005219 700 chr7:55227053 1 +13 EGFR_HUMAN R962G R962G EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=R962G http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=R962G low 0.805 EGFR_HUMAN NP_005219 700 chr7:55235538 1 diff -r 000000000000 -r e51722489ddb mutationassesor_web/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mutationassesor_web/tool_dependencies.xml Tue Oct 07 19:40:29 2014 -0400 @@ -0,0 +1,6 @@ + + + + + +