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addProperties.py
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addProperties.py
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"""
Function: addMolweight
adds the column Molweight to paralogFull.tab and writes out to
paralogMolweight.tab
--------------------
Felix Kruger
momo.sander@googlemail.com
"""
def addMolweight(key, path, params):
import queryDevice
import os
infile = open(path, 'r')
lines = infile.readlines()
infile.close()
out = open('_'.join([path,"sed"]) ,'w')
out.write('%s\tmolweight\n'%lines[0].rstrip('\n') )
header = lines[0].split('\t')
molregnos = {}
for i, col in enumerate(header):
if col == key:
idx = i
break
for line in lines[1:]:
elements = line.split('\t')
molregno = int(elements[idx])
molregnos[molregno] = 0
molstr = "','".join(map(str, molregnos.keys()))
print "Looking up mw_freebase for ", len(molregnos.keys()), "cmpds."
data = queryDevice.queryDevice("SELECT distinct molregno, mw_freebase FROM compound_properties WHERE molregno IN('%s')"% molstr, params)
for tup in data:
molregno = int(tup[0])
molweight = tup[1]
molregnos[molregno] = molweight
for line in lines[1:]:
elements = line.split('\t')
molregno = int(elements[idx])
molweight = molregnos[molregno]
out.write("%s\t%s\n"%(line.rstrip('\n'), molweight ))
out.close()
os.system('mv %s %s'% ('_'.join([path,"sed"]), path))
def addChembl_id(key, path, params):
import queryDevice
import os
infile = open(path, 'r')
lines = infile.readlines()
infile.close()
out = open('_'.join([path,"sed"]) ,'w')
out.write('%s\tchembl_id\n'%lines[0].rstrip('\n') )
header = lines[0].split('\t')
molregnos = {}
for i, col in enumerate(header):
if col == key:
idx = i
break
for line in lines[1:]:
elements = line.split('\t')
molregno = int(elements[idx])
molregnos[molregno] = 0
molstr = "','".join(map(str, molregnos.keys()))
print "Looking up chembl_id for ", len(molregnos.keys()), "cmpds."
data = queryDevice.queryDevice("SELECT distinct molregno, chembl_id FROM molecule_dictionary WHERE molregno IN('%s')"% molstr, params)
for tup in data:
molregno = int(tup[0])
chembl_id = tup[1]
molregnos[molregno] = chembl_id
for line in lines[1:]:
elements = line.split('\t')
molregno = int(elements[idx])
chembl_id = molregnos[molregno]
out.write("%s\t%s\n"%(line.rstrip('\n'), chembl_id ))
out.close()
os.system('mv %s %s'% ('_'.join([path,"sed"]), path))
def addTargetClass(level, key, path, params):
import queryDevice
import os
infile = open(path, 'r')
lines = infile.readlines()
infile.close()
out = open('_'.join([path,"sed"]) ,'w')
out.write('%s\ttarget_class_%s\n'%(lines[0].rstrip('\n'), level))
header = lines[0].split('\t')
accessions = {}
for i, col in enumerate(header):
if col == key:
idx = i
break
for line in lines[1:]:
elements = line.split('\t')
acc = elements[idx]
accessions[acc] = 0
accStr = "','".join(map(str, accessions.keys()))
data = queryDevice.queryDevice("SELECT protein_accession, %s FROM target_class tc JOIN target_dictionary td ON td.tid = tc.tid WHERE protein_accession IN('%s') "%(level, accStr), params)
for tup in data:
acc = tup[0]
targetClass = tup[1]
accessions[acc] = targetClass
for line in lines[1:]:
elements = line.split('\t')
acc = elements[idx]
targetClass = accessions[acc]
out.write("%s\t%s\n"%(line.rstrip('\n'), targetClass ))
out.close()
os.system('mv %s %s'% ('_'.join([path,"sed"]), path))
def addSeq100(path):
import os
infile = open(path, 'r')
lines = infile.readlines()
infile.close()
out = open('_'.join([path,"sed"]) ,'w')
out.write('%s\tseqId\n'%lines[0].rstrip('\n'))
for line in lines[1:]:
out.write("%s\t%s\n"%(line.rstrip('\n'), 100 ))
out.close()
os.system('mv %s %s'% ('_'.join([path,"sed"]), path))
def addPrefName(key, path, params):
import queryDevice
import os
infile = open(path, 'r')
lines = infile.readlines()
infile.close()
out = open('_'.join([path,"sed"]) ,'w')
out.write('%s\tprefName_%s\n'%(lines[0].rstrip('\n'), key))
header = lines[0].split('\t')
accessions = {}
for i, col in enumerate(header):
if col == key:
idx = i
break
for line in lines[1:]:
elements = line.split('\t')
acc = elements[idx]
accessions[acc] = 0
accStr = "','".join(map(str, accessions.keys()))
data = queryDevice.queryDevice("SELECT protein_accession, pref_name FROM target_dictionary WHERE protein_accession IN('%s') "% accStr, params)
for tup in data:
acc = tup[0]
prefName = tup[1]
accessions[acc] = prefName
for line in lines[1:]:
elements = line.split('\t')
acc = elements[idx]
prefName = accessions[acc]
out.write("%s\t\"%s\"\n"%(line.rstrip('\n'), prefName))
out.close()
os.system('mv %s %s'% ('_'.join([path,"sed"]), path))