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1 #!/usr/bin/python
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2 """
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3 The MIT License (MIT)
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4
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5 Copyright (c) 2013 Saket Choudhary, <saketkc@gmail.com>
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6
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7 Permission is hereby granted, free of charge, to any person obtaining a copy
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8 of this software and associated documentation files (the "Software"), to deal
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9 in the Software without restriction, including without limitation the rights
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10 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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11 copies of the Software, and to permit persons to whom the Software is
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12 furnished to do so, subject to the following conditions:
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13
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14 The above copyright notice and this permission notice shall be included in
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15 all copies or substantial portions of the Software.
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16
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17 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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18 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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19 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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20 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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21 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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22 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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23 THE SOFTWARE.
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24
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25 """
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26 import requests
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27 import argparse
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28 import sys
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29 import time
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30 from functools import wraps
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31 import simplejson as json
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32 import zipfile
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33 import tempfile, ntpath, shutil
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34 import xlrd
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35 import csv
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36 import os
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37 sheet_map = {0:"Variant_Analysis.csv",1:"Amino_Acid_Level_Analysis.csv",2:"Gene_Level_Analysis.csv"}
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38 def retry(ExceptionToCheck, tries=4, delay=3, backoff=2, logger=None):
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39 """Retry calling the decorated function using an exponential backoff.
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40
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41 http://www.saltycrane.com/blog/2009/11/trying-out-retry-decorator-python/
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42 original from: http://wiki.python.org/moin/PythonDecoratorLibrary#Retry
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43
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44 :param ExceptionToCheck: the exception to check. may be a tuple of
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45 exceptions to check
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46 :type ExceptionToCheck: Exception or tuple
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47 :param tries: number of times to try (not retry) before giving up
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48 :type tries: int
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49 :param delay: initial delay between retries in seconds
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50 :type delay: int
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51 :param backoff: backoff multiplier e.g. value of 2 will double the delay
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52 each retry
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53 :type backoff: int
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54 :param logger: logger to use. If None, print
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55 :type logger: logging.Logger instance
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56 """
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57 def deco_retry(f):
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58
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59 @wraps(f)
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60 def f_retry(*args, **kwargs):
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61 mtries, mdelay = tries, delay
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62 while mtries > 1:
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63 try:
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64 return f(*args, **kwargs)
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65 except ExceptionToCheck, e:
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66 #msg = "%s, Retrying in %d seconds..." % (str(e), mdelay)
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67 msg = "Retrying in %d seconds..." % (mdelay)
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68 if logger:
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69 logger.warning(msg)
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70 else:
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71 print msg
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72 time.sleep(mdelay)
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73 mtries -= 1
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74 mdelay *= backoff
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75 return f(*args, **kwargs)
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76
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77 return f_retry # true decorator
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78
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79 return deco_retry
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80 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"]
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81 URL="http://www.cravat.us/ClassifierSelect1"
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82 def stop_err( msg ):
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83 sys.stderr.write( '%s\n' % msg )
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84 sys.exit()
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85
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86 class CHASMWeb:
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87 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 ):
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88 self.mutationbox = mutationbox
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89 self.filepath = filepath
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90 self.is_hg_18 = is_hg_18
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91 self.analysis_type = analysis_type
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92 self.analysis_program = analysis_program
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93 self.chosendb = chosendb
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94 self.email = email
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95 self.annotate_genes = annotate_genes
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96 self.cancer_type = cancer_type
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97 self.email = email
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98 self.annotate_genes = annotate_genes
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99 self.text_reports=text_reports
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100 self.mupit_input= mupit_out
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101 def make_request( self ):
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102 data = {
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103 "mutationbox":self.mutationbox,
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104 "hg18": self.is_hg_18,
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105 "analysistype": self.analysis_type,
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106 "chosendb": self.analysis_program,
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107 "cancertype": self.cancer_type,
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108 "geneannotcheckbox": self.annotate_genes,
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109 "emailbox": self.email,
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110 "tsvreport": self.text_reports,
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111 "mupitinput": self.mupit_input,
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112 }
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113 stripped_data = {}
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114
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115 for key,value in data.iteritems():
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116 if value==True:
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117 value="on"
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118 if value!=None and value!=False:
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119 stripped_data[key]=value
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120 #print stripped_data
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121 if not self.mutationbox:
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122 file_payload={"inputfile":open(self.filepath)}
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123 request = requests.post(URL, data=stripped_data, files=file_payload)
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124 else:
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125 request = requests.post(URL, data=stripped_data, files=dict(foo='bar'))
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126 job_id = json.loads(request.text)["jobId"]
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127 return job_id
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128 @retry(requests.exceptions.HTTPError)
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129 def zip_exists(self,job_id ):
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130 url="http://www.cravat.us/results/%s/%s.zip" %(job_id,job_id)
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131 zip_download_request = requests.request("GET", url)
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132 if zip_download_request.status_code==404:
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133 raise requests.HTTPError()
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134 else:
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135 return url
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136 def download_zip( self, url, job_id):
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137 self.tmp_dir = tempfile.mkdtemp()
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138 r = requests.get( url, stream=True )
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139 if r.status_code == 200:
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140 self.path = os.path.join( self.tmp_dir,job_id+".zip" )
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141 with open(self.path, 'wb') as f:
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142 for chunk in r.iter_content(128):
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143 f.write(chunk)
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144 else:
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145 self.path = None
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146 return self.path
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147
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148 def move_files( self, file_map ):
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149 fh = open(self.path,"rb")
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150 zip_files = zipfile.ZipFile(fh)
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151 for name in zip_files.namelist():
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152 filename = ntpath.basename(name)
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153 extension = ntpath.splitext(filename)[-1]
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154 source_file = zip_files.open(name)
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155 if extension==".txt":
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156 target_file = open(file_map["error.txt"],"wb")
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157 elif filename!="SnvGet Feature Description.xls" and extension!=".xls":
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158 target_file = open(file_map[filename],"wbb")#file(os.path.join(output_dir,filename),"wb")
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159 else:
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160 target_file=None
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161 if target_file:
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162 with source_file,target_file:
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163 shutil.copyfileobj(source_file,target_file)
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164 if filename=="SnvGet Feature Description.xls":
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165 with xlrd.open_workbook(source_file) as wb:
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166 sheet_names = wb.sheet_names()
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167 for name in sheet_names:
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168 sh=wb.sheet_by_name(name)
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169 name_shortened= name.replace(" ").strip()+".csv"
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170 with open(name_shortened,'wb') as f:
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171 c = csv.writer(f)
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172 for r in range(sh.nrows):
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173 c.writerow(sh.row_values(r))
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174 shutil.rmtree(self.tmp_dir)
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175 fh.close()
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176 def main(params):
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177
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178 parser = argparse.ArgumentParser()
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179 parser.add_argument("-i","--input", type=str, dest="mutationbox", help="Input variants")
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180 parser.add_argument("--path",type=str,dest="input_file_location", help="Input file location")
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181 parser.add_argument("--hg18", dest="hg18", action="store_true")
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182 parser.add_argument("--analysis_type",dest="analysis_type",type=str,choices=["driver","functional","geneannotationonly"], default="driver")
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183 parser.add_argument("--chosendb",dest="chosendb",type=str,nargs="*",choices=["CHASM","SnvGet"], default="CHASM")
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184 parser.add_argument("--cancertype", dest="cancer_type", type=str, choices=CANCERTYPES, required=True)
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185 parser.add_argument("--email", dest="email", required=True, type=str)
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186 parser.add_argument("--annotate", dest="annotate", action="store_true", default=None )
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187 parser.add_argument("--tsv_report", dest="tsv_report", action="store_true", default=None )
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188 parser.add_argument("--mupit_out", dest="mupit_out", action="store_true", default=None )
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189 parser.add_argument("--gene_analysis_out", dest="gene_analysis_out", type=str, required=True)
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190 parser.add_argument("--variant_analysis_out", dest="variant_analysis_out", type=str, required=True)
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191 parser.add_argument("--amino_acid_level_analysis_out", dest="amino_acid_level_analysis_out", type=str, required=True,)
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192 parser.add_argument("--error_file", dest="error_file_out", type=str, required=True)
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193 parser.add_argument("--snv_box_out", dest="snv_box_out", type=str, required=False)
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194 parser.add_argument("--snv_features", dest="snv_features_out", type=str, required=False)
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195 args = (parser.parse_args(params))
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196 chasm_web = CHASMWeb(mutationbox=args.mutationbox,
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197 filepath=args.input_file_location,
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198 is_hg_18 = args.hg18,
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199 analysis_type=args.analysis_type,
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200 chosendb = args.chosendb,
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201 cancer_type = args.cancer_type,
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202 email=args.email,
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203 annotate_genes=args.annotate,
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204 text_reports=args.tsv_report,
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205 mupit_out=args.mupit_out)
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206 job_id=chasm_web.make_request()
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207 file_map = {"Amino_Acid_Level_Analysis.tsv":args.amino_acid_level_analysis_out,
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208 "SNVBox.tsv":args.snv_box_out,
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209 "Variant_Analysis.tsv":args.variant_analysis_out,
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210 "Gene_Level_Analysis.tsv":args.gene_analysis_out,
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211 "SnvGet Feature Description.xls":args.snv_features_out,
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212 "error.txt":args.error_file_out
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213 }
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214 url = chasm_web.zip_exists(job_id)
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215 download = chasm_web.download_zip(url,job_id)
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216 if download:
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217 move = chasm_web.move_files(file_map=file_map)
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218 else:
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219 stop_err("Unable to download from the server")
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220
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221 if __name__=="__main__":
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222 main(sys.argv[1:])
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