def main():
# Get the protein codes (these can also be stored in a file and retrieved)
keyCodes = hlp.getProtienCodes('E.Coli.txt')
for keyCode in keyCodes:
pdbSearchCode = keyCode[1:5]
pdbPath = 'protiens/' + pdbSearchCode + '/' + pdbSearchCode + '.pdb'
dsspPath = 'protiens/' + pdbSearchCode + '/' + pdbSearchCode + '.dssp'
if not os.path.exists(dsspPath):
print dsspPath + " doesn't exists \n"
pass
else :
csvPath = 'protiens/' + pdbSearchCode + '/' + pdbSearchCode
purgePath = 'protiens/' + pdbSearchCode + '/'
hlp.purgeFiles(purgePath, ".csv")
infile = open(dsspPath, "r")
for line in infile:
if(re.match(".*#.*",line)):
#line = infile.next()
# c = csv.writer(open(csvPath,"wb+"))
# c.writerow(["Residue No.","Amino Acid","Structure"])
for line in infile:
suffix = re.split("\W+", line)[3] + '.csv'
# print csvPath
if not os.path.exists(csvPath + '_' + suffix):
c = csv.writer(open(csvPath + '_' + suffix,"wb+"))
c.writerow(["Residue No.", "Residue Class", "Amino Acid", "Structure"])
splitLine = re.split("\W+",line)
if( not (splitLine[3].isdigit() or splitLine[4].isdigit())):
# print splitLine[2]+" "+splitLine[4]+" "+splitLine[5]
c.writerow([splitLine[2], splitLine[3], splitLine[4], splitLine[5]])
infile.close()
sys.exit(0)
def main():
residueClass = raw_input("Please enter the Residue class: (Eg. A,B,C.....) ")
residueClass = residueClass.upper()
groupCount = int(raw_input("Please enter the grouping constant: "))
# print residueClass
# print groupCount
keyCodes = hlp.getProtienCodes("E.Coli.txt")
keyCodes = hlp.cleanProtienCodes(keyCodes)
keyCodes = list(set(keyCodes))
for keyCode in keyCodes:
targetFile = 'protiens/' + keyCode + '/' + keyCode + '_' + residueClass + '.csv'
if os.path.exists(targetFile):
infile = open(targetFile, 'r')
infile.next()
residueNum = []
aminoAcid = []
structure = []
codons = []
for line in infile:
# print line
residueNum.append(getResidueNum(line))
aminoAcid.append(getAminoAcids(line))
structure.append(getStructures(line))
codons.append(getCodons(line))
print keyCode, len(residueNum)
getGroupedCSV(residueNum, aminoAcid, structure, codons, groupCount, keyCode)
def main():
keyCodes = hlp.getProtienCodes('E.Coli.txt')
hlp.makeDirStructure(keyCodes)
for keyCode in keyCodes:
pdbSearchCode = keyCode[1:5]
print pdbSearchCode
url = 'http://www.rcsb.org/pdb/files/' + pdbSearchCode + '.pdb' # REST API for fetching pdb files
pdbPath = 'protiens/' + pdbSearchCode + '/' + pdbSearchCode + '.pdb'
# pdb file for respective protein is fetched only if it doean't exist
if not os.path.exists(pdbPath):
response = urllib2.urlopen(url)
pdbData = response.read()
pdbFile = open(pdbPath, 'w')
pdbFile.write(pdbData)
pdbFile.close()
dsspPath = 'protiens/' + pdbSearchCode + '/' + pdbSearchCode + '.dssp'
if os.path.exists(pdbPath) and not os.path.exists(dsspPath):
pdbToDSSP(pdbPath, pdbSearchCode) # Converting the pdb file to dssp
