def main(args):
count = 0
with open(args.wordlist) as f:
for _ in f:
count += 1
i = 0
bar = progress.ProgressMeter(count)
with open(args.wordlist) as f:
for pwd in f:
pwd = pwd.strip()
if try_password(args.keychain, pwd):
print '\n\nfound password: %s' % pwd
break
bar.nextItem()
i += 1
if i >= 16:
i = 0
sys.stdout.write('\r%s %s ' % (bar, pwd))
sys.stdout.flush()
parbg.transition_table = 'hroest.srmTransitions_' + background
parbg.peptide_table = 'hroest.srmPeptides_' + background
background = True
cmadd = parbg.peptide_table.split('.')[1]
bgpar = parbg
else: bgpar = par
self = mycollider
self.pepids = self._get_unique_pepids_toptransitions(par, cursor)
MAX_UIS = par.max_uis
common_filename = par.get_common_filename()
self.min_transitions = []
start = time.time()
progressm = progress.ProgressMeter(total=len(self.pepids), unit='peptides')
for i, pep in enumerate(self.pepids):
p_id = pep['parent_id']
q1 = pep['q1']
if not use_randomized_transitions and not use_above_precursor:
transitions = self._get_all_transitions_toptransitions(par, pep, cursor)
elif use_above_precursor:
import c_getnonuis
transitions = c_getnonuis.calculate_transitions_ch(
((pep['q1'], pep['mod_sequence'], p_id),), [1], 0, 20000)
#get all singly charged y ions above the precursor
y_series = [(t[0], 0) for t in transitions[:len(transitions)/2] if t[0] > q1]
y_series.reverse()
y_series = y_series[:5]
transitions = y_series
elif use_randomized_transitions:
q = """
select modified_sequence, peptide_key, parent_id, q1_charge, q1, ssrcalc, isotope_nr
from %(peptide_table)s where q1 between %(lowq1)s and %(highq1)s
%(qadd)s
""" % {'peptide_table' : peptide_table,
'lowq1' : min_q1 ,
'highq1' : max_q1,
'qadd' : qadd
}
print q
cursor.execute(q)
print "Obtained all peptides"
alltuples = list(cursor.fetchall() )
progressm = progress.ProgressMeter(total=len(alltuples), unit='peptides')
prepare = []
total_transitions = 0
total_assays = 0
for kk, pep in enumerate(alltuples):
q3_low, q3_high = [400, 1200]
q3_low, q3_high = [400, 1400]
q3charges = [1,2]
q3charges = [1]
#q3_low, q3_high = [0, 12000]
#
#new way to calculate the precursors
transitions = c_getnonuis.calculate_transitions_ch(
((-2, pep[0], -1),), q3charges, q3_low, q3_high)
#print pep, len(pep[0]), len(transitions)
total_transitions += len(transitions)
def refresh(self, **kw):
# Clear line
sys.stdout.write(self.ESC + '[2K')
self.reset_cursor()
sys.stdout.write(self.get_meter(**kw))
# Are we finished?
if self.count >= self.total:
sys.stdout.write('\n')
sys.stdout.flush()
# Timestamp
self.last_refresh = time.time()
if __name__ == '__main__':
import progress
import time
import random
total = 100
p = progress.ProgressMeter(total=total)
## for i in range(total):
## p.update(1)
## time.sleep(.1)
while total > 0:
cnt = random.randint(1,10)
p.update(cnt)
total -= cnt
time.sleep(random.random()*1.)