diff polyphen2_web/polyphen2_web.py @ 0:b319f980c9e6 draft

Uploaded

--- /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:])