Mercurial > repos > saketkc > polyphen2
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/README.rst Mon Apr 14 17:27:06 2014 -0400 @@ -0,0 +1,35 @@ +Galaxy wrapper for the Polyphen2 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: + +Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. Nat Methods 7(4):248-249 (2010). +"A method and server for predicting damaging missense mutations."
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/polyphen2_web.py Mon Apr 14 17:27:06 2014 -0400 @@ -0,0 +1,208 @@ +#!/usr/bin/python +from bs4 import BeautifulSoup +import argparse +import sys +import time +import os +import tempfile +import requests +import shutil +import csv +submission_url = 'http://genetics.bwh.harvard.edu/cgi-bin/ggi/ggi2.cgi' +result_url = 'http://genetics.bwh.harvard.edu' + +refresh_interval = 30 +TIMEOUT = 60 * 60 +TIME_DELAY = 7 +MAX_TRIES = 30 + +# Genome assembly version used for chromosome +# coordinates of the SNPs in user input +UCSCDB = ['hg19', 'hg18'] +# Classifier model used for predictions. +MODELNAME = ['HumDiv', 'HumVar'] + +# Set of transcripts on which genomic SNPs will be mapped +SNPFILTER = { + 'All': 0, + 'Canonical': 1, + 'CCDS': 3, +} +# Functional SNP categories to include in genomic SNPs annotation report +SNPFUNCTION = ['c', 'm', ''] + + +def stop_err(msg, err=1): + sys.stderr.write('%s\n' % msg) + sys.exit(err) + + +class Polyphen2Web: + + def __init__(self, ucscdb=None, model_name=None, snp_filter=None, + snp_function=None, file_location=None, email=None): + self.ucscdb = ucscdb + self.model_name = model_name + self.snp_filter = snp_filter + self.snp_function = snp_function + self.file_location = file_location + self.notify_me = email + + def soupify(self, string): + return BeautifulSoup(string) + + def make_request(self): + in_txt = csv.reader(open(self.file_location, 'rb'), delimiter='\t') + tmp_dir = tempfile.mkdtemp() + path = os.path.join(tmp_dir, 'csv_file') + with open(path, 'wb') as fh: + a = csv.writer(fh) + a.writerows(in_txt) + contents = open(self.file_location, 'r').read().replace( + '\t', ' ').replace('::::::::::::::', '') + if self.snp_function == 'All': + self.snp_function = '' + payload = { + '_ggi_project': 'PPHWeb2', + '_ggi_origin': 'query', + '_ggi_batch': contents, + '_ggi_target_pipeline': '1', + 'MODELNAME': self.model_name, + 'UCSCDB': self.ucscdb, + 'SNPFILTER': SNPFILTER[self.snp_filter], + 'SNPFUNC': self.snp_function, + 'NOTIFYME': '', + + } + if self.notify_me: + payload['NOTIFYME'] = self.notify_me + request = requests.post(submission_url, data=payload) + content = request.content + soup = self.soupify(content) + sid_soup = soup.find('input', {'name': 'sid'}) + try: + sid = sid_soup['value'] + except: + sid = None + shutil.rmtree(tmp_dir) + return sid + + def poll_for_files(self, sid, + max_tries=MAX_TRIES, + time_delay=TIME_DELAY, + timeout=TIMEOUT): + payload = { + '_ggi_project': 'PPHWeb2', + '_ggi_origin': 'manage', + '_ggi_target_manage': 'Refresh', + 'sid': sid, + } + content = None + tries = 0 + url_dict = None + while True: + tries += 1 + if tries > max_tries: + stop_err('Number of tries exceeded!') + request = requests.post(submission_url, data=payload) + content = request.content + soup = self.soupify(content) + all_tables = soup.findAll('table') + if all_tables: + try: + running_jobs_table = all_tables[-2] + except: + running_jobs_table = None + if running_jobs_table: + rows = running_jobs_table.findAll('tr') + if len(rows) == 1: + row = rows[0] + hrefs = row.findAll('a') + # print hrefs + if len(hrefs) >= 3: + short_txt = hrefs[0]['href'] + # print short_txt + path = short_txt.split('-')[0] + full_txt = result_url + path + '-full.txt' + log_txt = result_url + path + '-log.txt' + snps_txt = result_url + path + '-snps.txt' + short_txt = result_url + path + \ + '-short.txt' # short_txt + url_dict = { + 'full_file': full_txt, + 'snps_file': snps_txt, + 'log_file': log_txt, + 'short_file': short_txt, + } + return url_dict + time.sleep(time_delay) + return url_dict + + def save_to_files(self, url_dict, args): + tmp_dir = tempfile.mkdtemp() + for key, value in url_dict.iteritems(): + r = requests.get(value, stream=True) + if r.status_code == 200: + path = os.path.join(tmp_dir, key) + with open(path, 'wb') as f: + for chunk in r.iter_content(128): + f.write(chunk) + shutil.move(path, args[key]) + if os.path.exists(tmp_dir): + shutil.rmtree(tmp_dir) + return True + + +def main(args): + parser = argparse.ArgumentParser() + parser.add_argument('-u', + '--ucscdb', + dest='ucscdb', + choices=UCSCDB, + required=True, type=str) + parser.add_argument('-m', '--model', + dest='modelname', choices=MODELNAME, + required=True, type=str) + parser.add_argument('-fl', '--filter', + '--snpfilter', dest='snpfilter', + choices=SNPFILTER.keys(), + required=True, type=str) + parser.add_argument('-i', '--input', + dest='input', nargs='?', + required=True, type=str, + default=sys.stdin) + parser.add_argument('-e', '--email', + dest='email', + required=False, default=None) + parser.add_argument('--log', dest='log_file', + required=True, default=None, type=str) + parser.add_argument('--short', dest='short_file', + required=True, default=None, type=str) + parser.add_argument('--full', dest='full_file', + required=True, default=None, type=str) + parser.add_argument('--snp', dest='snps_file', + required=True, default=None, type=str) + parser.add_argument('--function', dest='snpfunction', + required=True, type=str) + args_s = vars(parser.parse_args(args)) + polyphen2_web = Polyphen2Web(ucscdb=args_s['ucscdb'], + model_name=args_s['modelname'], + snp_filter=args_s['snpfilter'], + snp_function=args_s['snpfunction'], + file_location=args_s['input'], + email=args_s['email']) + sid = polyphen2_web.make_request() + if not sid: + stop_err( + 'Something went wrong! The tracking id could not be retrieved.') + url_dict = polyphen2_web.poll_for_files(sid) + locations = {} + if not url_dict: + stop_err('There was error downloading the output files!') + for key in url_dict.keys(): + locations[key] = args_s[key] + polyphen2_web.save_to_files(url_dict, locations) + return True + +if __name__ == '__main__': + main(sys.argv[1:])
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/polyphen2_web.xml Mon Apr 14 17:27:06 2014 -0400 @@ -0,0 +1,104 @@ +<tool id="polyphen2_web" name="PolyPhen-2 Webservice"> + <description>Compute functional impact of SNVs </description> + <requirements> + <requirement type="package" version="4.1.0">beautifulsoup4</requirement> + <requirement type="python-module">bs4</requirement> + </requirements> + <command interpreter="python"> + polyphen2_web.py --ucscdb $ucscdb + --model $model + --filter $filter + --function $function + --input $input + --log $log_file + --full $full_file + --short $short_file + --snp $snp_file + </command> + <inputs> + <param format="txt" name="input" type="data" label="Variants File" /> + <param name="ucscdb" type="select" label="Genome Assembly"> + <option value="hg19">GRCh37/hg19</option> + <option value="hg18">NCBI36/hg18</option> + </param> + <param name="model" type="select" label="Classifier Model"> + <option value="HumDiv">HumDiv</option> + <option value="HumVar">HumVar</option> + </param> + <param name="filter" type="select" label="Transcripts"> + <option value="All">All</option> + <option value="Canonical">Canonical</option> + <option value="CCDS">CCDS</option> + </param> + <param name="function" type="select" label="Annotations"> + <option value="c">Canonical</option> + <option value="m">CCDS</option> + <option value="All">All</option> + </param> + </inputs> + <outputs> + <data format="tabular" name="log_file" label="${tool.name} on ${on_string}: log" /> + <data format="tabular" name="full_file" label="${tool.name} on ${on_string}: full"/> + <data format="tabular" name="short_file" label="${tool.name} on ${on_string}: short"/> + <data format="tabular" name="snp_file" label="${tool.name} on ${on_string}: snp"/> + </outputs> + + <tests> + <test> + <param name="input" value="polyphen2_input.txt"/> + <param name="ucscdb" value="hg19"/> + <param name="model" value="HumDiv"/> + <param name="filter" value="All"/> + <param name="function" value="All"/> + <output name="log_file" file="polyphen2_log.txt"/> + <output name="full_file" file="polyphen2_full.txt"/> + <output name="short_file" file="polyphen2_short.txt"/> + <output name="snp_file" file="polyphen2_snp.txt"/> + </test> + </tests> + <help> + **What it does** + This tool interacts with the Web Version of Polyphen2 hosted at http://genetics.bwh.harvard.edu/pph2/ + + PolyPhen-2 (Polymorphism Phenotyping v2) is a software tool which predicts possible impact of amino acid substitutions + on the structure and function of human proteins using straightforward physical and evolutionary comparative considerations. + + .. class:: infomark + + * HumDiv model uses 5% / 10% FPR thresholds for “probably damaging” / “possibly damaging” predictions + + .. class:: infomark + + * HumVar model uses 10% / 20% FPR thresholds for “probably damaging” / “possibly damaging” predictions + + .. class:: infomark + + + '''Input format''': + + + chr22:30421786 A/T + + chr22:29446079 A/G + + chr22:40814500 A/G + + chr22:40815256 C/T + + + **Citations** + + If you use this tool please cite: + + Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. Nat Methods 7(4):248-249 (2010). + "A method and server for predicting damaging missense mutations." + + </help> +</tool> + + + + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/test-data/chasm_input.txt Mon Apr 14 17:27:06 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/test-data/ma_nucleotide_output.csv Mon Apr 14 17:27:06 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","","","","",""
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/test-data/ma_proper_nucleotide.csv Mon Apr 14 17:27:06 2014 -0400 @@ -0,0 +1,3 @@ +13,32912555,G,T BRCA2 +7,55178574,G,A GBM +7,55178574,G,A GBM
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/test-data/ma_proper_protein.csv Mon Apr 14 17:27:06 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/test-data/ma_proper_protein.tsv Mon Apr 14 17:27:06 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/test-data/ma_protein_output.csv Mon Apr 14 17:27:06 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","",""
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/test-data/polyphen2_full.txt Mon Apr 14 17:27:06 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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/test-data/polyphen2_input.txt Mon Apr 14 17:27:06 2014 -0400 @@ -0,0 +1,5 @@ +chr22:30421786 A/T +chr22:29446079 A/G +chr22:40814500 A/G +chr22:40815256 C/T +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/test-data/polyphen2_log.txt Mon Apr 14 17:27:06 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/test-data/polyphen2_short.txt Mon Apr 14 17:27:06 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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/test-data/polyphen2_snp.txt Mon Apr 14 17:27:06 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