--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iedb_api.py	Mon Feb 17 16:04:07 2020 -0500
@@ -0,0 +1,142 @@
+#!/usr/bin/env python
+"""
+"""
+import sys
+import os.path
+import re
+import optparse
+import urllib
+import urllib2
+from optparse import OptionParser
+
+mhci_methods = ['recommended','consensus','netmhcpan','ann','smmpmbec','smm','comblib_sidney2008','netmhccons','pickpocket']
+mhcii_methods = ['recommended','consensus3','NetMHCIIpan','nn_align','smm_align','comblib','tepitope']
+processing_methods = ['recommended','consensus','netmhcpan','ann','smmpmbec','smm','comblib_sidney2008']
+mhcnp_methods = ['mhcnp']
+bcell_methods = ['Bepipred','Chou-FasmanEmini','Karplus-Schulz','Kolaskar-Tongaonkar','Parker']
+prediction_methods = {'mhci':mhci_methods,'mhcii':mhcii_methods,'processing':processing_methods,'mhcnp':mhcnp_methods,'bcell':bcell_methods}
+
+def warn_err(msg,exit_code=1):
+  sys.stderr.write(msg)
+  if exit_code:
+    sys.exit(exit_code)
+
+
+def __main__():
+  #Parse Command Line
+  parser = optparse.OptionParser()
+  parser.add_option( '-p', '--prediction', dest='prediction', default='mhci', choices=['mhci','mhcii','processing','mhcnp','bcell'], help='IEDB API prediction service' )
+  parser.add_option( '-s', '--sequence', dest='sequence', action="append", default=None, help='Peptide Sequence' )
+  parser.add_option( '-m', '--method', dest='method', default='recommended', choices=['recommended','consensus','netmhcpan','ann','smmpmbec','smm','comblib_sidney2008','netmhccons','pickpocket' ], help='prediction method' )
+  parser.add_option( '-a', '--allele', dest='allele', action="append", default=[], help='Alleles for which to make predictions' )
+  parser.add_option( '-l', '--length', dest='length', action="append", default=[], choices=['8', '9', '10', '11', '12', '13', '14', '15'], help='lengths for which to make predictions, 1 per allele' )
+  parser.add_option( '-i', '--input', dest='input', default=None, help='Input file for peptide sequences (fasta or tabular)' )
+  parser.add_option( '-c', '--column', dest='column', default=None, help='Peptide Column in a tabular input file' )
+  parser.add_option( '-C', '--id_column', dest='id_column', default=None, help='ID Column in a tabular input file' )
+  parser.add_option( '-o', '--output', dest='output', default=None, help='Output file for query results' )
+  parser.add_option( '-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr'  )
+  (options, args) = parser.parse_args()
+
+  aapat = '^[ABCDEFGHIKLMNPQRSTVWY]+$'          
+
+  if not options.allele and options.prediction != 'bcell':
+    warn_err('-a allele required\n', exit_code=1)
+
+  if not (options.sequence or options.input): 
+    warn_err('NO Sequences given: either -s sequence or -i input_file is required\n', exit_code=1)
+
+  if options.output != None:
+    try:
+      outputPath = os.path.abspath(options.output)
+      outputFile = open(outputPath, 'w')
+    except Exception, e:
+      warn_err("Unable to open output file: %s\n" % e, exit_code=1)
+  else:
+    outputFile = sys.stdout
+
+  url = 'http://tools-api.iedb.org/tools_api/%s/' % options.prediction
+
+  #TODO parse alleles from the options.alleles file
+  alleles = ','.join(options.allele)
+  lengths = ','.join(options.length)
+  method = options.method
+
+  results = []
+  global header
+  header = None
+
+  sequence_text = []
+  def add_seq(seqid,seq):
+    sequence_text.append(">%s\n%s" % (seqid if seqid else "peptide%d" % len(sequence_text),seq))
+
+  def query(url,seq,allele,length,seqid=None,method='recommended'):
+    global header
+    params = dict()
+    if method:
+      params['method'] = method
+    params['sequence_text'] = seq
+    params['allele'] = allele
+    params['length'] = length
+    data = urllib.urlencode(params)
+    request = urllib2.Request(url, data)
+    if options.debug:
+      print >> sys.stderr, "url %s %s %s" % (request.get_full_url(), seqid if seqid else "None", seq)
+    response = None
+    response = urllib2.urlopen(request)
+    if response and response.getcode() == 200:
+      resp_data = response.readlines()
+      for line in resp_data:
+        if line.find('eptide') > 0:
+          header = "#%s%s" % ("ID\t" if seqid else "", line)
+          continue
+        if seqid:
+          results.append("%s\t%s" % (seqid,line))
+        else:
+          results.append(line)
+    elif not response:
+      warn_err("NO response from IEDB server\n",  exit_code=3)
+    else:
+      warn_err("Error connecting to IEDB server\n",  exit_code=response.getcode())
+
+  if options.sequence:
+    for i,seq in enumerate(options.sequence):
+      query(url,seq,alleles,lengths,seqid=None,method=method)
+  if options.input:
+    try:
+      fh = open(options.input,'r')
+      if options.column: ## tabular
+        col = int(options.column)
+        idcol = int(options.id_column) if options.id_column else None
+        for i,line in enumerate(fh):
+          fields = line.split('\t')
+          if len(fields) > col:
+            seq = re.sub('[_*]','',fields[col])
+            if re.match(aapat,seq):
+              seqid = fields[idcol] if idcol != None and idcol < len(fields) else None
+              query(url,seq,alleles,lengths,seqid=seqid,method=method)
+            else:
+              warn_err('Line %d, Not a peptide: %s\n' % (i,seq),exit_code=None)
+      else:  ## fasta
+        seqid = None
+        seq = ''
+        for i,line in enumerate(fh):
+          if line.startswith('>'):
+            if seqid and len(seq) > 0:
+              query(url,seq,alleles,lengths,seqid=seqid,method=method)
+            seqid = line[1:].strip()
+            seq = ''
+          else:
+            seq += line.strip()
+        if seqid and len(seq) > 0:
+          query(url,seq,alleles,lengths,seqid=seqid,method=method)
+      fh.close()
+    except Exception, e:
+      warn_err("Unable to open input file: %s\n" % e, exit_code=1)
+
+  if header:
+    outputFile.write(header)  
+  for line in results:
+    outputFile.write(line)  
+
+if __name__ == "__main__": __main__()
+