def loadMotifs(args,sigLvl,filterMotifs):
"""load and store motifs from XML files giving each a unique ID and culling out the ones we want."""
# --- load motifs ---
motifDict = {}
ID = 0
for path in args:
tmpDict = parseScopeXML(path)
# --- Give Each Motif its ID ---
while tmpDict:
k,v = tmpDict.popitem()
# --- add the unique ID to the tuple key and the motif obj---
# -- key --
k = list(k)
k.insert(2,ID)
k = tuple(k)
# -- obj --
v.motifID = ID
# --- add motif to motifDict --
motifDict[k] = v
ID+=1
# --- Cull Out The Ones We Want ---
culledDict = {}
while motifDict:
k,v = motifDict.popitem()
if float(v.sigvalue) < sigLvl:
continue
elif v.consensus in filterMotifs:
culledDict[k] = v
# --- Return Results ---
for m in culledDict:
print culledDict[m].consensus
return culledDict
return False
usage = '\n\npython %s outDir "geneName geneName ..." scopeOut.xml [scopeOut.xml]' % (sys.argv[0].split('/')[-1])
if len(sys.argv) < 3:
print usage
exit(0)
# 1. Open all files into own scopeOut dicts
inDict = {}
for path in sys.argv[4:]:
inDict[path] = parseScopeXML(path)
# Parse GeneNames
geneNames = sys.argv[2].split()
# Print list of motifs and File names that hit genes listed:
hits = {}
for f in inDict:
tmp = {}
for motif in inDict[f]:
if testForGenes(geneNames,motif):
hits[(f,motif)] = inDict[f][motif]
hitKeys = hits.keys()
hitKeys.sort(key=lambda x: (x[0],x[1]))
#!/usr/bin/env python
import optparse
import sys
from gusPyCode.defs.parseSCOPE import parseScopeXML,toXMSfile
if __name__ == "__main__":
#+++++++++++ Hard Code Figure Settings For Now +++++++++++
print '\n\n\n'
#+++++++++++ File Parseing Etc +++++++++++
usage = """python %prog scopeOut.xml [scopeOut.xml ...]"""
parser = optparse.OptionParser(usage)
(opts, args) = parser.parse_args()
if len(sys.argv) == 1:
parser.print_help()
exit(0)
for xml in args:
out = xml.replace('.xml','.xms')
motifs = parseScopeXML(xml)
toXMSfile(motifs,out)
