class TestMultiProcessingLog(unittest.TestCase):
def setUp(self):
self.dirname = os.path.dirname(os.path.abspath(__file__))
self.fastafile = os.path.join(self.dirname, "..", "data", 'smallDB.fasta')
self.db = ProteinDB()
self.db.readFasta(self.fastafile)
self.P31946 = self.db.proteinDictionary['P31946']
def test_readFasta(self):
self.code1 = self.P31946.code1
self.code2 = self.P31946.code2
self.modres = self.P31946.modres
self.ncbi_tax_id = self.P31946.ncbi_tax_id
self.description = self.P31946.description
self.sequence = self.P31946.sequence
print self.code1
print self.code2
print self.modres
print self.ncbi_tax_id
print self.description
print self.sequence
def test_get_proteins_containing_peptide(
self): #To-Do : test with some peptides present and not present. Also shared peptides.
pass
def test_pseudoreverseDB(
self): #To-Do : Pseudo-reverse and check a couple of reversed proteins. Pseudo-reverse the DB twice, and check the DB is equal.
pass
def writeDigestFile(fastafile, enzyme, minPepLength=5, missedCleavages=0):
base = os.path.splitext(fastafile)[0]
digest = base + '_digest.tsv'
dynfile = base + '_simulation.tsv'
headers = ['protein_code', 'sequence']
peptidelib = {}
db = ProteinDB()
db.readFasta(fastafile)
try:
writer = csv.writer(open(digest, 'w'), dialect='excel-tab')
except:
print("something went wrong while trying to write the file :",
massfile)
sys.exit(1)
writer.writerow(headers)
protein_cnt = 0
for code, protein in db.proteinDictionary.items():
protein_cnt += 1
if protein_cnt % 5000 == 0: print("%s proteins stored" % protein_cnt)
peptides = protein.digest(enzyme,
minLength=minPepLength,
missedCleavages=missedCleavages)
for peptide in peptides:
wr_row = [protein.code2, peptide]
writer.writerow(wr_row)
def main(argv):
fasta = argv[0]
fasta_new = fasta + ".new"
#Read fasta file
protDB = ProteinDB()
protDB.readFasta(fasta)
for protein in protDB.proteinDictionary.values() :
code1 = protein.code1
code2 = protein.code2
if len(code1) == 0 : code1 = code2
if len(code2) == 0 : code2 = code1
protein.code1 = code2
protein.code2 = code1
protDB.writeFastaFile(fasta_new, chunksize = -1, format="sp")
def main(argv):
fasta = argv[0]
fasta_new = fasta + ".new"
#Read fasta file
protDB = ProteinDB()
protDB.readFasta(fasta)
for protein in protDB.proteinDictionary.values():
code1 = protein.code1
code2 = protein.code2
if len(code1) == 0: code1 = code2
if len(code2) == 0: code2 = code1
protein.code1 = code2
protein.code2 = code1
protDB.writeFastaFile(fasta_new, chunksize=-1, format="sp")
class TestUnitProtein(unittest.TestCase):
def setUp(self):
#>sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=H**o sapiens GN=YWHAB PE=1 SV=3
#MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS
#WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFY
#LKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFY
#YEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGD
#AGEGEN
self.dirname = os.path.dirname(os.path.abspath(__file__))
self.fastafile = os.path.join(self.dirname, "..", "data", 'smallDB.fasta')
self.db = ProteinDB()
self.db.readFasta(self.fastafile)
self.P31946 = self.db.proteinDictionary['P31946']
self.trypsin = {'terminus': 'C', 'cleave': ['K', 'R'], 'exceptions': ['KP', 'RP']}
self.Lys_N = {'terminus': 'N', 'cleave': ['K'], 'exceptions': []}
self.pep_tryp1 = 'TAFDEAIAELDTLNEESYK'
self.pep_Lys_N = 'KGDYFRYLSEVASGDN'
def test_proteinWeight(self):
pass
def test_digest(self):
self.P31946_peptides_trypsin = self.P31946.digest(self.trypsin)
self.assertIn(self.pep_tryp1, self.P31946_peptides_trypsin,
"A tryptic peptide has not been found after tryptic digestion of a protein!")
self.assertNotIn(self.pep_Lys_N, self.P31946_peptides_trypsin,
"A non tryptic peptide has been found after tryptic digestion of a protein!")
self.P31946_peptides_Lys_N = self.P31946.digest(self.Lys_N)
self.assertNotIn(self.pep_tryp1, self.P31946_peptides_Lys_N,
"A tryptic peptide has been found after tryptic digestion of a protein!")
self.assertIn(self.pep_Lys_N, self.P31946_peptides_Lys_N,
"A Lys-N peptide has not been found after tryptic digestion of a protein!")
def writeDigestFile(fastafile,enzyme, minPepLength = 5, missedCleavages = 0) :
base = os.path.splitext(fastafile)[0]
digest = base + '_digest.tsv'
dynfile = base + '_simulation.tsv'
headers = ['protein_code','sequence']
peptidelib = {}
db = ProteinDB()
db.readFasta(fastafile)
try :
writer = csv.writer(open(digest,'w'), dialect='excel-tab')
except :
print "something went wrong while trying to write the file :" , massfile
sys.exit(1)
writer.writerow(headers)
protein_cnt = 0
for code, protein in db.proteinDictionary.iteritems() :
protein_cnt += 1
if protein_cnt % 5000 == 0 : print "%s proteins stored" % protein_cnt
peptides = protein.digest(enzyme, minLength = minPepLength, missedCleavages = missedCleavages)
for peptide in peptides :
wr_row = [protein.code2, peptide]
writer.writerow(wr_row)
def writeMassFile(fastafile,enzyme, abundances, dynrange, minPepLength = 5, peptidesID = 0, minPepProteinID = 1) :
base = os.path.splitext(fastafile)[0]
massfile = base + '_mass.tsv'
dynfile = base + '_simulation.tsv'
headers = ['protein_code','weight','num_of_peptides']
headers_dyn = ['protein_code','num_of_peptides','peptide','dyn_range','protein_abundance','pep_estimated_intensity','peptide_shared_with_detected_proteins']
peptidelib = {} # dictionary containing the simulated detectability and the protein abundances : peptides = [ detectability , { "SEQUENCE1" : { code1 : Abundance1, ...}, ... }]
db = ProteinDB()
db.readFasta(fastafile)
try :
writer = csv.writer(open(massfile,'w'), dialect='excel-tab')
except :
print("something went wrong while trying to write the file :" , massfile)
sys.exit(1)
if dynrange :
try :
writer_dyn = csv.writer(open(dynfile,'w'), dialect='excel-tab')
except :
print("something went wrong while trying to write the file :" , dynfile)
sys.exit(1)
if len(abundances) > 0 : headers.extend(['protein_abundance'])
writer.writerow(headers)
if dynrange : writer_dyn.writerow(headers_dyn)
protein_cnt = 0
for code, protein in db.proteinDictionary.items() :
protein_cnt += 1
if protein_cnt % 5000 == 0 : print("%s proteins stored" % protein_cnt)
peptides = protein.digest(enzyme, minLength = minPepLength)
wr_row = [protein.code2, protein.proteinWeight(), len(peptides)]
this_abundance = -1
if protein.code2 in abundances :
this_abundance = abundances[protein.code2]
wr_row.extend([this_abundance])
writer.writerow(wr_row)
if dynrange and this_abundance > 0 :
for pep in peptides :
if pep not in peptidelib : peptidelib[pep] = [ randomPepdist() , {protein : float(this_abundance) }]
else : peptidelib[pep][1][protein] = float(this_abundance)
protein_cnt = 0
all_peptides = []
for code, protein in db.proteinDictionary.items() :
protein_cnt += 1
if protein_cnt % 5000 == 0 : print("%s proteins simulated" % protein_cnt)
if protein.code2 not in abundances : continue
this_abundance = -1
this_abundance = abundances[protein.code2]
if this_abundance < 0 : continue
peptides = protein.digest(enzyme, minLength = minPepLength)
for pep in peptides :
if pep not in peptidelib : continue
#print peptidelib[pep][0] , list(peptidelib[pep][1].itervalues())
intensity = peptidelib[pep][0] * sum( list(peptidelib[pep][1].values()) )
proteins_txt = ""
if len(peptidelib[pep][1]) > 1 :
proteins_txt = ",".join( [ str(i.code2) for i in peptidelib[pep][1].keys()] )
wr_row = [protein.code2, len(peptides), pep, peptidelib[pep][0], this_abundance ,intensity,proteins_txt]
all_peptides.append(wr_row)
writer_dyn.writerow(wr_row)
#Sort the peptides by estimated intensity
all_peptides = sorted(all_peptides, key= lambda x: (-x[5]))
protein_peptides = {}
pep2_cnt = 0 # Count peptides that are in proteins with at least another peptide already identified. IF it is the second peptide of the protein identified, count it twice so that we count the first one
pep_idx = 0
while pep2_cnt < peptidesID and pep_idx < len(all_peptides) :
this_peptide = all_peptides[pep_idx]
this_sequence = this_peptide[2]
this_protcode = this_peptide[0]
this_intensity = this_peptide[5]
if this_peptide[0] not in protein_peptides : protein_peptides[this_protcode] = { this_sequence : this_intensity }
else :
protein_peptides[this_protcode][this_sequence] = this_intensity
if len(protein_peptides[this_protcode]) == minPepProteinID : pep2_cnt += minPepProteinID
elif len(protein_peptides[this_protcode]) > minPepProteinID: pep2_cnt += 1
pep_idx += 1
#Count the number of proteins with 2 or more peptides, and proteins with only 1 peptide
protein_2peps = 0
protein_1pep = 0
for protein in protein_peptides.values() :
#print len(protein), protein
if len(protein) >= minPepProteinID : protein_2peps += 1
else : protein_1pep += 1
print("Number of proteins identified with at least %s peptides (given %s identified peptides) : %s" % (minPepProteinID,peptidesID,protein_2peps))
print("Number of proteins identified with less than %s peptides (given %s identified peptides) : %s" % (minPepProteinID,peptidesID,protein_1pep))
def writeMassFile(fastafile,
enzyme,
abundances,
dynrange,
minPepLength=5,
peptidesID=0,
minPepProteinID=1):
base = os.path.splitext(fastafile)[0]
massfile = base + '_mass.tsv'
dynfile = base + '_simulation.tsv'
headers = ['protein_code', 'weight', 'num_of_peptides']
headers_dyn = [
'protein_code', 'num_of_peptides', 'peptide', 'dyn_range',
'protein_abundance', 'pep_estimated_intensity',
'peptide_shared_with_detected_proteins'
]
peptidelib = {
} # dictionary containing the simulated detectability and the protein abundances : peptides = [ detectability , { "SEQUENCE1" : { code1 : Abundance1, ...}, ... }]
db = ProteinDB()
db.readFasta(fastafile)
try:
writer = csv.writer(open(massfile, 'w'), dialect='excel-tab')
except:
print "something went wrong while trying to write the file :", massfile
sys.exit(1)
if dynrange:
try:
writer_dyn = csv.writer(open(dynfile, 'w'), dialect='excel-tab')
except:
print "something went wrong while trying to write the file :", dynfile
sys.exit(1)
if len(abundances) > 0: headers.extend(['protein_abundance'])
writer.writerow(headers)
if dynrange: writer_dyn.writerow(headers_dyn)
protein_cnt = 0
for code, protein in db.proteinDictionary.iteritems():
protein_cnt += 1
if protein_cnt % 5000 == 0: print "%s proteins stored" % protein_cnt
peptides = protein.digest(enzyme, minLength=minPepLength)
wr_row = [protein.code2, protein.proteinWeight(), len(peptides)]
this_abundance = -1
if protein.code2 in abundances:
this_abundance = abundances[protein.code2]
wr_row.extend([this_abundance])
writer.writerow(wr_row)
if dynrange and this_abundance > 0:
for pep in peptides:
if pep not in peptidelib:
peptidelib[pep] = [
randomPepdist(), {
protein: float(this_abundance)
}
]
else:
peptidelib[pep][1][protein] = float(this_abundance)
protein_cnt = 0
all_peptides = []
for code, protein in db.proteinDictionary.iteritems():
protein_cnt += 1
if protein_cnt % 5000 == 0: print "%s proteins simulated" % protein_cnt
if protein.code2 not in abundances: continue
this_abundance = -1
this_abundance = abundances[protein.code2]
if this_abundance < 0: continue
peptides = protein.digest(enzyme, minLength=minPepLength)
for pep in peptides:
if pep not in peptidelib: continue
#print peptidelib[pep][0] , list(peptidelib[pep][1].itervalues())
intensity = peptidelib[pep][0] * sum(
list(peptidelib[pep][1].itervalues()))
proteins_txt = ""
if len(peptidelib[pep][1]) > 1:
proteins_txt = ",".join(
[str(i.code2) for i in peptidelib[pep][1].iterkeys()])
wr_row = [
protein.code2,
len(peptides), pep, peptidelib[pep][0], this_abundance,
intensity, proteins_txt
]
all_peptides.append(wr_row)
writer_dyn.writerow(wr_row)
#Sort the peptides by estimated intensity
all_peptides = sorted(all_peptides, key=lambda x: (-x[5]))
protein_peptides = {}
pep2_cnt = 0 # Count peptides that are in proteins with at least another peptide already identified. IF it is the second peptide of the protein identified, count it twice so that we count the first one
pep_idx = 0
while pep2_cnt < peptidesID and pep_idx < len(all_peptides):
this_peptide = all_peptides[pep_idx]
this_sequence = this_peptide[2]
this_protcode = this_peptide[0]
this_intensity = this_peptide[5]
if this_peptide[0] not in protein_peptides:
protein_peptides[this_protcode] = {this_sequence: this_intensity}
else:
protein_peptides[this_protcode][this_sequence] = this_intensity
if len(protein_peptides[this_protcode]) == minPepProteinID:
pep2_cnt += minPepProteinID
elif len(protein_peptides[this_protcode]) > minPepProteinID:
pep2_cnt += 1
pep_idx += 1
#Count the number of proteins with 2 or more peptides, and proteins with only 1 peptide
protein_2peps = 0
protein_1pep = 0
for protein in protein_peptides.itervalues():
#print len(protein), protein
if len(protein) >= minPepProteinID: protein_2peps += 1
else: protein_1pep += 1
print "Number of proteins identified with at least %s peptides (given %s identified peptides) : %s" % (
minPepProteinID, peptidesID, protein_2peps)
print "Number of proteins identified with less than %s peptides (given %s identified peptides) : %s" % (
minPepProteinID, peptidesID, protein_1pep)