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pdbDisulfide_interXray_gz.py
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pdbDisulfide_interXray_gz.py
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"""Echo command line arguments
"""
__author__ = "Jason Wong"
__version__ = "$Revision: 1.0 $"
__date__ = "$Date: 2017/04/27 10:06:20 $"
__copyright__ = "Copyright (c) 2017 Jason WH Wong"
__license__ = "UNSW Faculty of Medicine"
import sys
import os
import getopt
import tokenize
import StringIO
import gzip
import copy
class pdb:
prot = ""
pos = {}
revpos = {}
start = 0
end = 0
chain = ""
AA = {}
class uniprot:
ID = ""
SSBond = []
pdbs = []
class exBedGraph:
def __init__(self):
self.outFile = None
self.pdbDir = None
self.mapFile = None
self.Prots = {}
self.pdbMap = {}
# Reads the residue level map file from PDBSWS, such that for every PDB chain the corresponding Uniprot
# start, end, and positions of cysteine residues are recorded.
def readInputMap(self):
print "Processing BigMap file..."+os.path.basename(self.bigmapFile)
f = open(self.bigmapFile,'r')
c = 0
for line in f:
if len(line) > 5:
if c%421977 == 0:
print "."
line = ' '.join(line.split())
tmp = line.split(" ")
tmpID = tmp[0].swapcase()+tmp[1]
if len(tmp) > 7:
try:
tmpPDB = self.pdbMap[tmpID]
#if tmp[3] == 'CYS':
if tmp[6] == 'C': # only store cysteine positions to save memory
try:
tmpPDB.pos[int(tmp[4])]=int(tmp[7])
except ValueError:
tmpPDB.pos[int(tmp[4][:-1])]=int(tmp[7])
try:
tmpPDB.revpos[int(tmp[7])]=int(tmp[4])
except ValueError:
tmpPDB.revpos[int(tmp[7])]=int(tmp[4][:-1])
try:
tmpPDB.AA[int(tmp[4])]=tmp[3]
except ValueError:
tmpPDB.AA[int(tmp[4][:-1])]=tmp[3]
if tmpPDB.end < int(tmp[7]):
tmpPDB.end = int(tmp[7])
self.pdbMap[tmpID] = tmpPDB
except KeyError:
try:
tmpPDB = pdb()
tmpPDB.prot = tmp[5]
#if tmp[3] == 'CYS':
if tmp[6] == 'C':
try:
tmpPDB.pos[int(tmp[4])]=int(tmp[7])
except ValueError:
tmpPDB.pos[int(tmp[4][:-1])]=int(tmp[7])
try:
tmpPDB.revpos[int(tmp[7])]=int(tmp[4])
except ValueError:
tmpPDB.revpos[int(tmp[7])]=int(tmp[4][:-1])
tmpPDB.start = int(tmp[7])
tmpPDB.end = 0
try:
tmpPDB.AA[int(tmp[4])]=tmp[3]
except ValueError:
tmpPDB.AA[int(tmp[4][:-1])]=tmp[3]
tmpPDB2 = pdb()
tmpPDB2.prot = tmpPDB.prot
tmpPDB2.pos = copy.deepcopy(tmpPDB.pos)
tmpPDB2.revpos = copy.deepcopy(tmpPDB.revpos)
tmpPDB2.start = tmpPDB.start
tmpPDB2.end = tmpPDB.end
tmpPDB2.AA = copy.deepcopy(tmpPDB.AA)
tmpPDB.pos.clear()
tmpPDB.revpos.clear()
self.pdbMap[tmpID] = tmpPDB2
except:
a = None
except IndexError:
a = None
c+=1
print "PDBs: "+str(len(self.pdbMap))
# Builds a list of all UniProt IDs in the database and for each of these store all disulfide bonds present and all PDB chains
# associated with that Uniprot ID
def processPDB(self):
# Creates an object holder for each UniProt protein with a list of disulfide bonds and PDB chains
print "Processing Input file..."+os.path.basename(self.mapFile)
f = open(self.mapFile,'r')
for line in f:
line = line[:-1]
tmp = line.split(" ")
tmpProt = uniprot()
tmpProt.ID = tmp[2]
tmpProt2 = uniprot()
tmpProt2.ID = tmpProt.ID
tmpProt2.SSBond = tmpProt.SSBond[:]
tmpProt2.pdbs = tmpProt.pdbs[:]
self.Prots[tmpProt2.ID] = tmpProt2
f.close()
print "Uniprots: "+str(len(self.Prots))
# Start populating the disulfide bond and PDB chains list for each Uniprot protein entry.
print "Reading PDB..."+os.path.basename(self.pdbDir)
dirList = os.listdir(self.pdbDir)
for fname in dirList:
if fname.find(".ent") != -1:
print self.pdbDir+"//"+fname
f = gzip.open(self.pdbDir+"//"+fname,'r')
header = ""
expt = ""
starts = {}
ends = {}
hasSS = 0
chains = []
for line in f:
if line[0:6] == "HEADER":
line = line[:-1].strip()
header = line[-4:]
print "HEAD: "+header
elif line[0:6] =="EXPDTA":
line = ' '.join(line[:-1].split())
expt = line.split(" ")[1]
expt = expt.split(",")[0]
#print "EXPT: "+expt
if expt <> "X-RAY":
print "NOT XRAY!!!"
break
elif line[0:6] =="SSBOND":
hasSS = 1
line = ' '.join(line.split())
bond = line.split(" ")
pos1 = bond[4]
pos2 = bond[7]
#print line
try:
tmpID1 = header+bond[3]
tmpID2 = header+bond[6]
except:
#print "invalid SSBOND line"
continue
tmpPDB1 = None
tmpPDB2 = None
try:
tmpPDB1 = self.pdbMap[tmpID1]
except:
#print "Uniprot C1 not found"
continue
try:
tmpPDB2 = self.pdbMap[tmpID2]
except KeyError, k:
#print "Uniprot C2 not found: "+str(k)
continue
SS = tmpPDB1.start
SE = tmpPDB1.end
try:
AAC1 = tmpPDB1.pos[int(bond[4])]
except KeyError:
#print "no C1"
continue
except ValueError:
try:
AAC1 = tmpPDB1.pos[int(bond[4][:-1])]
except KeyError:
#print "no C1"
continue
try:
AAC2 = tmpPDB2.pos[int(bond[7])]
except KeyError:
#print "no C2"
continue
except ValueError:
try:
AAC2 = tmpPDB2.pos[int(bond[7][:-1])]
except KeyError:
#print "no C2"
continue
if AAC2 < AAC1:
tmp = AAC1
AAC1 = AAC2
AAC2 = tmp
if tmpPDB1.prot == tmpPDB2.prot and bond[3] == bond[6]: #Uniprot and Chains are the same
try:
curProt = self.Prots[tmpPDB1.prot]
if expt.find("X-RAY") != -1:
found = 0
for i in curProt.pdbs:
if i == tmpID1:
found = 1
if found == 0:
curProt.pdbs.append(tmpID1)
found = 0
pos = 0
for i in curProt.SSBond:
if i[0] == int(AAC1) and i[1] == int(AAC2):
tmplist = i[2][:]
tmplist.append(tmpID1)
tmpposlist = i[3][:]
tmpposlist.append(str(self.pdbMap[tmpID1].revpos[AAC1])+"-"+str(self.pdbMap[tmpID1].revpos[AAC2]))
curProt.SSBond[pos] = ((i[0],i[1],tmplist[:],tmpposlist[:]))
found = 1
pos+=1
if found == 0:
IDlist = []
poslist = []
IDlist.append(tmpID1)
poslist.append(str(self.pdbMap[tmpID1].revpos[AAC1])+"-"+str(self.pdbMap[tmpID1].revpos[AAC2]))
curProt.SSBond.append((int(AAC1),int(AAC2),IDlist[:],poslist[:]))
self.Prots[tmpPDB1.prot] = curProt
except KeyError:
print "Not found: "+tmpPDB1.prot
elif line[0:5] == "DBREF" and line.find("UNP") <> -1:
tmpc = line.split(" ")
#print line
chains.append(tmpc[3])
elif line[0:4] =="ATOM":
if hasSS == 0:
for k in chains:
try:
curProt = self.Prots[self.pdbMap[header+k].prot]
curProt.pdbs.append(header+k)
except KeyError:
print header+k
break
f.close()
# Outputs results and also work out whether each disulfide bond listed is missing in any other PDB chain and for what reason
def outputRes(self):
print "Output results file..."+os.path.basename(self.outFile)
out = open(self.outFile,'w')
for key in self.Prots.keys():
curProt = self.Prots[key]
uniqXray = [] # Bonds that are only in one structure because not covered by any other
commonXray = [] # Bonds that appear more than once
missXray = [] # Bonds that is in one structure but not another yet is covered
for i in curProt.SSBond:
for k in curProt.pdbs:
found = 0
for j in i[2]:
if k == j:
found =1
if found == 0:
curPDB = self.pdbMap[k]
if curPDB.start <= i[0] and curPDB.end >= i[1]: # if PDB covers bond
found1 = 0
found2 = 0
for key,val in curPDB.pos.items():
if i[0] == val:
found1 = 1
if i[1] == val:
found2 = 1
out.write(curProt.ID+"\t"+str(i[0])+"\t"+str(i[1])+"\t"+str(i[2])+"\t"+str(i[3])+"\t")
try:
out.write(str(curPDB.revpos[i[0]])+"\t")
except KeyError:
out.write("X\t")
try:
out.write(str(curPDB.revpos[i[1]]))
except KeyError:
out.write("X")
if found1 ==1 and found2 ==1 and curPDB.AA[curPDB.revpos[i[0]]] == "CYS" and curPDB.AA[curPDB.revpos[i[1]]] == "CYS":
out.write("\tSSMissing"+"\t"+k)
found3 = 0
for x in i[2]:
if x.find(k[:-1]) <> -1:
found3 = 1
if found3 == 1:
out.write("\t1\n")
else:
out.write("\t0\n")
else:
out.write("\tSSMutant"+"\t"+k+"\t-\n")
else:
out.write(curProt.ID+"\t"+str(i[0])+"\t"+str(i[1])+"\t"+str(i[2])+"\t"+str(i[3])+"\t")
try:
out.write(str(curPDB.revpos[i[0]])+"\t")
except KeyError:
out.write("X\t")
try:
out.write(str(curPDB.revpos[i[1]]))
except KeyError:
out.write("X")
out.write("\tNonOverlap"+"\t"+k+"\t"+str(curPDB.start)+"-"+str(curPDB.end)+"\n")
out.close()
def ParseCommandLine(self, Arguments):
try:
(Options, Args) = getopt.getopt(Arguments, "hi:m:o:b:")
except:
print "Unknown option entered"
print UsageInfo
sys.exit(1)
OptionsSeen = {}
for (Option, Value) in Options:
OptionsSeen[Option] = 1
if Option == "-i":
self.pdbDir = Value
elif Option == "-m":
self.mapFile = Value
elif Option == "-b":
self.bigmapFile = Value
elif Option == "-o":
self.outFile = Value
else:
print "** Unknown option:", Option, Value
if not self.pdbDir:
print "\n* Error: -i missing"
print UsageInfo
sys.exit(1)
UsageInfo = """
pdbDisulfide_interXray_gz.py - Checks for disulfide bonds that are in the PDB chain of a XRay structure but not in others.
Parameters:
-i [FILENAME] input PDB directory (contains .ent.gz files directly from PDB)
-m [FILENAME] Chain level map file from PDBSWS (http://www.bioinf.org.uk/pdbsws/pdbsws_chain.txt.gz)
-b [FILENAME] Residue level map file from PDBSWS (http://www.bioinf.org.uk/pdbsws/pdbsws_res.txt.gz)
-o [Output] Output file
Example:
pdbDisulfide_interXray_gz -i ~/Z/DB/pdb/ -m ~/Z/DB/pdb/pdb_uniprot_chain_map.lst.2 -b ~/Z/DB/pdb_uniprot_map.lst.2 -o ~/Z/Data/disulfide/interXRay_all_out.txt
"""
def Main(exBed= None):
global MAX_RESULTS_FILES_TO_PARSE
if not exBed:
exBed = exBedGraph()
exBed.ParseCommandLine(sys.argv[1:])
exBed.readInputMap()
exBed.processPDB()
exBed.outputRes()
if __name__ == "__main__":
try:
import psyco
psyco.full()
except:
print ""
#TestMain()
Main()