def setUp(self):
try:
import c_getnonuis
self.transitions = test_shared.transitions_def1
self.collisions = test_shared.collisions_def1
self.pep1 = test_shared.peptide1
self.pep2 = test_shared.peptide2
self.transitions_12_between300_1500 = test_shared.transitions_12_between300_1500
self.pep1_yseries = test_shared.pep1_yseries
self.pep1_bseries = test_shared.pep1_bseries
tuples = []
tuples.append(self.pep1)
tuples.append(self.pep2)
self.tuples = tuple(tuples)
self.R = Residues('mono')
class Minimal:
pass
self.par = Minimal()
self.par.q3_window = 4.0
self.par.ppm = False
self.q3_high = 1500
self.q3_low = 300
self.MAX_UIS = 5
self.par.bions = True
self.par.yions = True
self.par.aions = False
self.par.aMinusNH3 = False
self.par.bMinusH2O = False
self.par.bMinusNH3 = False
self.par.bPlusH2O = False
self.par.yMinusH2O = False
self.par.yMinusNH3 = False
self.par.cions = False
self.par.xions = False
self.par.zions = False
self.par.MMinusH2O = False
self.par.MMinusNH3 = False
except ImportError:
pass
def _process(self, line):
"""Parses DOM records.
Records consist of 4 tab deliminated fields;
sid, pdbid, residues, hierarchy
"""
#For example ::
#
#d1sctg_ 1sct g: 1.001.001.001.001.001
#d1scth_ 1sct h: 1.001.001.001.001.001
#d1flp__ 1flp - 1.001.001.001.001.002
#d1moh__ 1moh - 1.001.001.001.001.002
line = line.rstrip() # no trailing whitespace
columns = line.split("\t") # separate the tab-delineated cols
if len(columns) != 4:
raise ValueError("I don't understand the format of %s" % line)
self.sid, pdbid, res, self.hierarchy = columns
self.residues = Residues(res)
self.residues.pdbid = pdbid
def getSeqMap(self, residues):
"""Get the sequence map for a collection of residues.
residues -- A Residues instance, or a string that can be converted into
a Residues instance.
"""
if type(residues) == StringType:
residues = Residues(residues)
pdbid = residues.pdbid
frags = residues.fragments
if not frags:
frags = (('_', '', ''), ) # All residues of unnamed chain
seqMap = None
for frag in frags:
chainid = frag[0]
if chainid == '' or chainid == '-' or chainid == ' ' or chainid == '_':
chainid = '_'
id = pdbid + chainid
sm = self[id]
#Cut out fragment of interest
start = 0
end = len(sm.res)
if frag[1]: start = int(sm.index(frag[1], chainid))
if frag[2]: end = int(sm.index(frag[2], chainid) + 1)
sm = sm[start:end]
if seqMap == None:
seqMap = sm
else:
seqMap += sm
return seqMap
def __init__(self):
self.peptides = []
self.R = Residues('mono')
class SRMColliderController():
def __init__(self):
self.peptides = []
self.R = Residues('mono')
def initialize(self, db_used, default_org_prefix, db_tables_map):
self.db_used = db_used
self.default_org_prefix = default_org_prefix
self.db_tables_map = db_tables_map
def get_sample_peptides_html(self):
sample_peptides = """
AFGIPVNTFSSEVVTLWYR
AIPAPHEILTSNVVTR
VTDISTGIYK
GYSENPVENSQFLTEYVATR
ETLVGFMTEYVATR
IQDPQMTGYVSTR
ATMVGTPYWMAPEIVNQK
TNSFVGTEEYLAPEVIR
TNSFVGTEEYIAPEVIR
LINSIADTFVGTSTYMSPER
"""
sample_peptides_html = ''
for s in sample_peptides.split():
sample_peptides_html += s + '<br/>'
return sample_peptides_html
def parse_srmcollider_form(self, form, genomes_that_require_N15_data):
peptides_raw = form.getvalue('peptides')
q1_w = float(form.getvalue('q1_window') )
q3_w = float(form.getvalue('q3_window') )
ssr_w = float(form.getvalue('ssr_window') )
high = float(form.getvalue('high_mass') )
low = float(form.getvalue('low_mass') )
genome = form.getvalue('genome')
isotope = int(form.getvalue('isotope') )
uis = int(form.getvalue('uis') )
ions = {'aions' : bool(form.getvalue('aions' )),
'aMinusNH3': bool(form.getvalue('aMinusNH3' )),
'bions' : bool(form.getvalue('bions' )),
'bMinusH2O': bool(form.getvalue('bMinusH2O' )),
'bMinusNH3': bool(form.getvalue('bMinusNH3' )),
'bPlusH2O' : bool(form.getvalue('bPlusH2O' )),
'cions' : bool(form.getvalue('cions' )),
'xions' : bool(form.getvalue('xions' )),
'yions' : bool(form.getvalue('yions' )),
'yMinusH2O': bool(form.getvalue('yMinusH2O' )),
'yMinusNH3': bool(form.getvalue('yMinusNH3' )),
'zions' : bool(form.getvalue('zions' )),
'MMinusH2O': bool(form.getvalue('MMinusH2O' )),
'MMinusNH3': bool(form.getvalue('MMinusNH3' )),
}
missed = int(form.getvalue('missed') )
oxMet = bool(form.getvalue('oxMet') )
Deamid = bool(form.getvalue('Deamid') )
chargeCheck = bool(form.getvalue('chargeCheck') )
try:
table_used = self.db_tables_map[ genome ]
except KeyError:
print "Genome not recognized";
exit()
#create the parameter object
par = collider.SRM_parameters()
par.dontdo2p2f = False #do not look at 2+ parent / 2+ fragment ions
par.q1_window = q1_w / 2.0
par.q3_window = q3_w / 2.0
par.ssrcalc_window = ssr_w / 2.0
par.ppm = False
par.considerIsotopes = True
par.isotopes_up_to = isotope
par.q3_range = [low, high]
par.peptide_tables = [self.db_used + self.default_org_prefix + table_used]
par.transition_table = self.db_used + '.srmTransitions_' + table_used
par.__dict__.update( ions )
par.max_mods = -1
par.max_MC = -1
par.add_sql_select = ""
par.select_by = "modified_sequence"
par.eval()
par.query2_add = ''
if not oxMet and not Deamid:
par.query2_add = ' and modifications = 0 '
elif oxMet and not Deamid:
par.query2_add = " and modified_sequence not like '%N[115]%' "
elif not oxMet and Deamid:
par.query2_add = " and modified_sequence not like '%M[147]%' "
if missed == 0:
par.query2_add += ' and missed_cleavages = 0 '
if missed == 1:
par.query2_add += ' and missed_cleavages <= 1 '
par.chargeCheck = chargeCheck
par.genome = genome
par.uis = uis
# check whether we need to recalculate the residues for N15
if genome in genomes_that_require_N15_data:
self.R.recalculate_monisotopic_data_for_N15()
parser = PeptideParser(self.R)
# try to parse transition list. If it doesnt work, try to parse the
# input as single peptide sequences.
try:
self.peptides = parser.parse_transition_list(peptides_raw)
seqs, input_sequences = parser.get_seqs(self.peptides)
except AssertionError:
self.peptides = []
if len(self.peptides) == 0:
try:
self.peptides = parser.parse_transition_csv(peptides_raw)
seqs, input_sequences = parser.get_seqs(self.peptides)
except AssertionError:
self.peptides = []
if len(self.peptides) == 0:
# sanitize input: all input is already sanitized except myinput and genome
seqs, input_sequences = parser.sanitize_peptide_input(peptides_raw)
for s in input_sequences:
peptide = DDB.Peptide();
peptide.set_sequence(s)
peptide.charge = 2
self.peptides.append(peptide)
parser.calculate_default_fragmenation(self.peptides, par)
par.seqs = seqs
par.input_sequences = input_sequences
return par
def getNonuniqueObjects(self, nonunique):
# Syntax
## tmplist.append( python::make_tuple(series[k],
## q1_used, 0, peptide_key, curr_ion, snumber, precursor.attr("modified_sequence"), ssrcalc, isotope_nr, ch));
res = {}
for key in nonunique:
nonunique_obj = []
for n in nonunique[key]:
o = NonUnique()
o.q3 = n[0]
o.q1 = n[1]
o.dummy = n[2]
o.peptide_key = n[3]
o.ion_type = n[4]
o.ion_number = n[5]
o.sequence = n[6]
o.ssrcalc = n[7]
o.isotope_nr = n[8]
o.charge = n[9]
nonunique_obj.append(o)
res[key] = nonunique_obj
return res
def parse_skyline(self, data):
# Parse Skyline reports:
# 1. Fix unique peptide identifier from skyline (use modified sequence + charge)
# 2. replace modifications AA[+n] with AA[mass] for parsing
import csv
result = ""
header = True
mod_mapping = self.R.mod_mapping
for line in csv.reader( data.split("\n")):
if len(line) < 8: continue
if header: header = False; continue
line[0] = line[1] + "/" + line[2]
nextline = ",".join(line) + "\n"
for mmap in mod_mapping:
nextline = nextline.replace(mmap, mod_mapping[mmap])
result += nextline
return result
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
*
* Program : SRMCollider
* Author : Hannes Roest <*****@*****.**>
* Date : 13.11.2012
"""
import srmcollider_website_helper
import DDB, collider, sys
from Residues import Residues
R = Residues('mono')
peptideparser = srmcollider_website_helper.PeptideParser(R)
###########################################################################
# Parse options
from optparse import OptionParser, OptionGroup
usage = "usage: %prog [options]"
parser = OptionParser(usage=usage)
group = OptionGroup(parser, "Run options")
group.add_option("--in",
dest="inputfile",
type="str",
help="Input file with one peptide sequence per line")
group.add_option("--out",
dest="outputfile",
type="str",
help="Output file in mProphet format")
parser.add_option_group(group)
def __init__(self):
self.peptides = []
self.R = Residues('mono')
class SRMColliderController():
"""
Main controller for the website
Parses the main form using parse_srmcollider_form or Skyline input using parse_skyline.
"""
def __init__(self):
self.peptides = []
self.R = Residues('mono')
def initialize(self, db_used, default_org_prefix, db_tables_map):
self.db_used = db_used
self.default_org_prefix = default_org_prefix
self.db_tables_map = db_tables_map
def get_sample_peptides_html(self):
sample_peptides = """
AFGIPVNTFSSEVVTLWYR
AIPAPHEILTSNVVTR
VTDISTGIYK
GYSENPVENSQFLTEYVATR
ETLVGFMTEYVATR
IQDPQMTGYVSTR
ATMVGTPYWMAPEIVNQK
TNSFVGTEEYLAPEVIR
TNSFVGTEEYIAPEVIR
LINSIADTFVGTSTYMSPER
"""
sample_peptides_html = ''
for s in sample_peptides.split():
sample_peptides_html += s + '<br/>'
return sample_peptides_html
def parse_srmcollider_form(self, form, genomes_that_require_N15_data):
peptides_raw = form.getvalue('peptides')
q1_w = float(form.getvalue('q1_window') )
q3_w = float(form.getvalue('q3_window') )
ssr_w = float(form.getvalue('ssr_window') )
high = float(form.getvalue('high_mass') )
low = float(form.getvalue('low_mass') )
genome = form.getvalue('genome')
isotope = int(form.getvalue('isotope') )
uis = int(form.getvalue('uis') )
ions = {'aions' : bool(form.getvalue('aions' )),
'aMinusNH3': bool(form.getvalue('aMinusNH3' )),
'bions' : bool(form.getvalue('bions' )),
'bMinusH2O': bool(form.getvalue('bMinusH2O' )),
'bMinusNH3': bool(form.getvalue('bMinusNH3' )),
'bPlusH2O' : bool(form.getvalue('bPlusH2O' )),
'cions' : bool(form.getvalue('cions' )),
'xions' : bool(form.getvalue('xions' )),
'yions' : bool(form.getvalue('yions' )),
'yMinusH2O': bool(form.getvalue('yMinusH2O' )),
'yMinusNH3': bool(form.getvalue('yMinusNH3' )),
'zions' : bool(form.getvalue('zions' )),
'MMinusH2O': bool(form.getvalue('MMinusH2O' )),
'MMinusNH3': bool(form.getvalue('MMinusNH3' )),
}
missed = int(form.getvalue('missed') )
oxMet = bool(form.getvalue('oxMet') )
Deamid = bool(form.getvalue('Deamid') )
chargeCheck = bool(form.getvalue('chargeCheck') )
try:
table_used = self.db_tables_map[ genome ]
except KeyError:
print "Genome not recognized";
exit()
#create the parameter object
par = collider.SRM_parameters()
par.dontdo2p2f = False #do not look at 2+ parent / 2+ fragment ions
par.q1_window = q1_w / 2.0
par.q3_window = q3_w / 2.0
par.ssrcalc_window = ssr_w / 2.0
par.ppm = False
par.considerIsotopes = True
par.isotopes_up_to = isotope
par.q3_range = [low, high]
par.peptide_tables = [self.db_used + self.default_org_prefix + table_used]
par.transition_table = self.db_used + '.srmTransitions_' + table_used
par.__dict__.update( ions )
par.max_mods = -1
par.max_MC = -1
par.add_sql_select = ""
par.select_by = "modified_sequence"
par.eval()
par.query2_add = ''
if not oxMet and not Deamid:
par.query2_add = ' and modifications = 0 '
elif oxMet and not Deamid:
par.query2_add = " and modified_sequence not like '%N[115]%' "
elif not oxMet and Deamid:
par.query2_add = " and modified_sequence not like '%M[147]%' "
if missed == 0:
par.query2_add += ' and missed_cleavages = 0 '
if missed == 1:
par.query2_add += ' and missed_cleavages <= 1 '
par.chargeCheck = chargeCheck
par.genome = genome
par.uis = uis
# check whether we need to recalculate the residues for N15
if genome in genomes_that_require_N15_data:
self.R.recalculate_monisotopic_data_for_N15()
parser = PeptideParser(self.R)
# try to parse transition list. If it doesnt work, try to parse the
# input as single peptide sequences.
try:
self.peptides = parser.parse_transition_list(peptides_raw)
seqs, input_sequences = parser.get_seqs(self.peptides)
except AssertionError:
self.peptides = []
if len(self.peptides) == 0:
try:
self.peptides = parser.parse_transition_csv(peptides_raw)
seqs, input_sequences = parser.get_seqs(self.peptides)
except AssertionError:
self.peptides = []
if len(self.peptides) == 0:
# sanitize input: all input is already sanitized except myinput and genome
seqs, input_sequences = parser.sanitize_peptide_input(peptides_raw)
for s in input_sequences:
peptide = DDB.Peptide();
peptide.set_sequence(s)
peptide.charge = 2
self.peptides.append(peptide)
parser.calculate_default_fragmenation(self.peptides, par)
par.seqs = seqs
par.input_sequences = input_sequences
return par
def getNonuniqueObjects(self, nonunique):
# Syntax
## tmplist.append( python::make_tuple(series[k],
## q1_used, 0, peptide_key, curr_ion, snumber, precursor.attr("modified_sequence"), ssrcalc, isotope_nr, ch));
res = {}
for key in nonunique:
nonunique_obj = []
for n in nonunique[key]:
o = NonUnique()
o.q3 = n[0]
o.q1 = n[1]
o.dummy = n[2]
o.peptide_key = n[3]
o.ion_type = n[4]
o.ion_number = n[5]
o.sequence = n[6]
o.ssrcalc = n[7]
o.isotope_nr = n[8]
o.charge = n[9]
nonunique_obj.append(o)
res[key] = nonunique_obj
return res
def parse_skyline(self, data):
# Parse Skyline reports:
# 1. Fix unique peptide identifier from skyline (use modified sequence + charge)
# 2. replace modifications AA[+n] with AA[mass] for parsing
import csv
result = ""
header = True
mod_mapping = self.R.mod_mapping
for line in csv.reader( data.split("\n")):
if len(line) < 8: continue
if header: header = False; continue
line[0] = line[1] + "/" + line[2]
nextline = ",".join(line) + "\n"
for mmap in mod_mapping:
nextline = nextline.replace(mmap, mod_mapping[mmap])
result += nextline
return result
def setUp(self):
self.limit = 100
self.limit_large = 100
self.limit = 300
self.limit_large = 600
try:
import MySQLdb
#db_l = MySQLdb.connect(read_default_file="~/.my.cnf.local")
db = MySQLdb.connect(read_default_file="~/.srm.cnf")
cursor = db.cursor()
self.cursor = cursor
par = test_shared.get_default_setup_parameters()
par.use_sqlite = True
par.q1_window = 1.2 / 2.0
par.q3_window = 2.0 / 2.0
par.ssrcalc_window = 4 / 2.0
par.ssrcalc_window = 9999 / 2.0
par.peptide_tables = ['hroest.srmPeptides_yeast']
par.transition_table = 'hroest.srmTransitions_yeast'
par.isotopes_up_to = 3
self.mycollider = collider.SRMcollider()
par.select_by = "id"
self.par = par
self.min_q1 = 440
self.max_q1 = 450
## For debugging
##self.max_q1 = 440.18
##par.q1_window = 0.009 / 2.0
##par.q3_window = 2.0 / 2.0
##par.isotopes_up_to = 1
import Residues
R = Residues.Residues('mono')
isotope_correction = par.isotopes_up_to * R.mass_diffC13 / min(
par.parent_charges)
start = time.time()
query = """
select modified_sequence, transition_group, parent_id, q1_charge, q1, ssrcalc, isotope_nr, 0, 0
from %s where q1 between %s and %s
#and isotope_nr = 0
""" % (par.peptide_tables[0], self.min_q1 -
par.q1_window, self.max_q1 + par.q1_window)
cursor.execute(query)
self.alltuples = list(cursor.fetchall())
#print "len alltuples", len(self.alltuples)
query = """
select modified_sequence, transition_group, parent_id, q1_charge, q1, ssrcalc, isotope_nr, 0, 0
from %s where q1 between %s - %s and %s
and isotope_nr = 0
""" % (par.peptide_tables[0], self.min_q1 -
par.q1_window, isotope_correction,
self.max_q1 + par.q1_window)
cursor.execute(query)
self.alltuples_isotope_correction = list(cursor.fetchall())
#print "len alltuples zero", len(self.alltuples_isotope_correction)
self.myprecursors = Precursors()
# myprecursors.getFromDB(par, db.cursor(), self.min_q1 - par.q1_window, self.max_q1 + par.q1_window)
##### LEGACY getFromDB -- have isotope_nr = 0 in there!
# Get all precursors from the DB within a window of Q1
lower_q1 = self.min_q1 - par.q1_window
upper_q1 = self.max_q1 + par.q1_window
self.myprecursors.precursors = []
isotope_correction = par.isotopes_up_to * R.mass_diffC13 / min(
par.parent_charges)
q = """
select modified_sequence, transition_group, parent_id, q1_charge, q1, ssrcalc, modifications, missed_cleavages, isotopically_modified
from %(peptide_table)s where q1 between %(lowq1)s - %(isotope_correction)s and %(highq1)s
and isotope_nr = 0
""" % {
'peptide_table': par.peptide_tables[0],
'lowq1': lower_q1, # min_q1 - par.q1_window
'highq1': upper_q1, # max_q1 + par.q1_window,
'isotope_correction': isotope_correction
}
cursor.execute(q)
for res in cursor.fetchall():
p = Precursor()
p.initialize(*res)
# Only include those precursors that are actually have isotopes in the specified range
if (p.included_in_isotopic_range(lower_q1, upper_q1, par)):
self.myprecursors.precursors.append(p)
##### END LEGACY getFromDB
self.precursors_to_evaluate = self.myprecursors.getPrecursorsToEvaluate(
self.min_q1, self.max_q1)
except Exception as inst:
print "something went wrong"
print inst
def setUp(self):
try:
import MySQLdb
self.database_available = True
except ImportError:
print """Module MySQLdb not available.
Please install it if you want to use it.
Use the following command (on Ubuntu systems):
sudo apt-get install python-mysqldb
"""
self.database_available = False
try:
self.db = MySQLdb.connect(read_default_file=mysql_conf_file)
self.database_available = True
except MySQLdb.OperationalError as e:
print "Could not connect to database: Please check the configuration in test/test_db.py!\n", e
self.database_available = False
class Minimal:
def get_q3_window_transitions(self, q3):
if self.ppm:
return [
q3 - self.q3_window * 10**(-6) * q3,
q3 + self.q3_window * 10**(-6) * q3
]
else:
return [q3 - self.q3_window, q3 + self.q3_window]
self.par = Minimal()
self.par.q3_window = 4.0
self.par.ppm = False
self.MAX_UIS = 5
self.q3_high = 1500
self.q3_low = 300
self.par.q1_window = 1.2 / 2.0
self.par.ssrcalc_window = 9999
self.par.query2_add = ' and isotope_nr = 0 '
self.par.peptide_tables = [test_database + '.srmPeptides_human']
self.par.transition_table = test_database + '.srmTransitions_human'
self.par.print_query = False
self.par.select_floor = False
self.par.isotopes_up_to = 3
self.par.select_by = "id"
self.par.parent_charges = [2, 3]
self.par.bions = True
self.par.yions = True
self.par.aions = False
self.par.aMinusNH3 = False
self.par.bMinusH2O = False
self.par.bMinusNH3 = False
self.par.bPlusH2O = False
self.par.yMinusH2O = False
self.par.yMinusNH3 = False
self.par.cions = False
self.par.xions = False
self.par.zions = False
self.par.MMinusH2O = False
self.par.MMinusNH3 = False
def returntrue():
return True
self.par.do_b_y_only = returntrue
def returnrange():
return self.q3_low, self.q3_high
self.par.get_q3range_collisions = returnrange
#self.par.get_q3_window_transitions = get_q3_window_transitions
#self.par.get_q3_window_transitions = collider.SRM_parameters.get_q3_window_transitions
import sys
self.R = Residues('mono')
self.acollider = collider.SRMcollider()
self.aparamset = collider.testcase(testdatabase=test_database)
