/
analyse_seqs.py
executable file
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/
analyse_seqs.py
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'''
Python script to analyse DNA single-stranded tile sequences. Run with --help for options. Python2 and python3 compatible.
Shipped with DNA single-stranded tile (SST) sequence designer used in the following publication.
"Diverse and robust molecular algorithms using reprogrammable DNA self-assembly"
Woods*, Doty*, Myhrvold, Hui, Zhou, Yin, Winfree. (*Joint first co-authors)
Nature, 2019
'''
import math,sys,os,time,itertools,pickle
import argparse as argparse
from sst_dsd import pfunc, binding, mfe_binding, RNAduplex_multiple
from atam2ssts import eval_colocated_end_pair
import re
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
from multiprocessing.pool import ThreadPool
# from lru_cache import lru_cache # this was used when we had a hand-rolled lru_cache, but it's now in Python 3
try:
from functools import lru_cache
except ImportError:
# in case this is python2
from lru_cache import lru_cache
from datetime import datetime
global_thread_pool = ThreadPool()
MORE_NEGAIVE_ENERGY_IS_MORE_FAVOURABLE = True
NEGATE = not MORE_NEGAIVE_ENERGY_IS_MORE_FAVOURABLE
#############################################################################
# Define constants and inputs
#############################################################################
_default_temp_in_C = 53.0 # if the user does not specify a temperature, we use this value
_threaded = True
_bad_first_algo_conflict_threshold = -8.0
_lower_thres_correct_binding = -10.8
_check_double_mismatches = False # Setting to False speeds up lattice binding analysis
_num_helices=16
_bad_lattice_binding_to_arbitrary_lattice_threshold = -10.0
# Some output filenames
filelist = ['nupack domain pair binding V RNAduplex domain pair (1999) - non-wc.pdf',
'nupack domain pair binding V RNAduplex domain pair (1999) - wc.pdf',
'dG of lattice+tile-lattice-tile V binding(tile,lattice).pdf',
'nupack pair binding V RNAduplex pair (1999).pdf',
'nupack pair binding V RNAduplex pair (2004).pdf',
'RNAduplex pair (1999) V RNAduplex pair (2004).pdf',
'nupack pair mfe V RNAduplex pair.pdf',
'nupack pair binding V nupack pair mfe.pdf']
#############################################################################
# args e.g. --help
#############################################################################
def parse_args():
parser = argparse.ArgumentParser(description=
'''Python3 script that runs a barrage of energetics tests on DNA-tile sequences.
If you are running a non-algorithmic tile set please use option -nl (to turn off
some tests and prevent errors). Input is given as a text file in IDT format, for example:
# Example 1
# Algorithmic SST example. Note that sequences may contain T bases with an ("internal") biotin modification, denoted "/iBiodT/".
# Strand domains (that encode aTAM tile-glues) are separated by a single space. Comments are ignored by the analysis code.
#
U3;10->10;sw,AGTGTGTTTTT AGTTCGATGT AGAGGCTTTT ATCAGAGGGAA,25nm,STD
U3;10->10;se,ACTCGTTCTT TTCCC/iBiodT/CTGAT TCCTCCAATTA AAAAACGCAA,25nm,STD
U3;10->11;nw,AAGAACCACT TTCGTCAAATT ATACATCACCT AACCCACCAA,25nm,STD
# Example 2
# Non-algorithmic example, tile names do not have any ";" symbols.
# This example shows that tiles need not have four domains/glues.
#
tile_name1,AATCCTAGAA ATTGTTATTTC ATGTATACAAA GATAGATCAG,25nm,STD
tile_name2,AACTAGAAAC CTTAGGAATT,25nm,STD
tile_name3,TAATACTTTCA TTTATCATCG CTACATTCTT ATTTGTTTATC,25nm,STD
The script makes use of pfunc and mfe from NUPACK, and RNAduplex from ViennaRNA, and assumes these
three executables are available.
''',
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog= '''Example usage:
python analyse_seqs.py input_file.idt
''')
#parser.add_argument('-s', '--seqs', required=True, # action="store_true",
# help="Specify a batch file that contains one or more image filenames to process.", default="")
# parser.add_argument('-o', '--check', required=False, action="store_true", # action="store", dest="query",
# help="Use with --batch. Check orientation of ribbons. Produces ribbon image files, some of which may be incorrectly orientated.", default="")
parser.add_argument('files', nargs='*') # default=os.getcwd()
#_StoreAction(option_strings=[], dest='files', nargs='*', const=None, default='', type=None, choices=None, help=None, metavar=None)
#parser.add_argument('-s', '--strands', required=False, action="store_true", # action="store", dest="query",
# help="Analyse secondary structure energy of individual strands.", default="")
parser.add_argument('-T', '--temperature', required=False, type=float, # action="store", dest="query",
help="Temperature in C to analyse sequences. Default temperature is 53.0 C")
parser.add_argument('-nl', '--no-lattice-binding', required=False, action="store_true", # action="store", dest="query",
help="Do not run analysis of lattice-binding properties (includes analysis of algorithmic errors which is probably only relevant for algorithmic tile sets).", default="")
parser.add_argument('-nd', '--no-domains', required=False, action="store_true", # action="store", dest="query",
help="Do not run domain-level secondary structure analysis.", default="")
parser.add_argument('-ns', '--no-strand-analysis', required=False, action="store_true", # action="store", dest="query",
help="Do not run strand-level/tile-level secondary structure analysis.", default="")
parser.add_argument('-np', '--no-tile-pairs', required=False, action="store_true", # action="store", dest="query",
help="Do not run the (expensive) tile pair test, nor the domain pair test.", default="")
parser.add_argument('-nm', '--no-mfe-analysis', required=False, action="store_true", # action="store", dest="query",
help="Do not run (expensive) mfe analysis.", default="")
parser.add_argument('-p', '--pickle', required=False, action="store_true", # action="store", dest="query",
help="Use python pickle lbrary to save processed data. Useful when doing time-consuming calculations and want the data for further processing.", default="")
parser.add_argument('-b', '--bins', required=False, type=int, # action="store", dest="query",
help="Number of bins in histogram plots.")
parser.add_argument('-nst', '--non-standard-tiles', required=False, action="store_true", # action="store", dest="query",
help="Tiles that do not have exactly 4 domains.", default="")
args = parser.parse_args()
if not (args.files):
parser.error('Error: no input filename specified. Please specify a .idt file with DNA sequences for processing.')
return args
#############################################################################
# Run analysis
#############################################################################
import string
# maketrans is in string if python2 but in str if python3
try:
_wctable = str.maketrans('ACGTacgt_-','TGCAtgca_-')
except AttributeError:
_wctable = string.maketrans('ACGTacgt_-','TGCAtgca_-')
def wc(seq):
'''Return reverse Watson-Crick complement of seq'''
return seq.translate(_wctable)[::-1]
def run_analysis(f,directory,temp_in_C,domain_analysis=1,strand_analysis=1,tile_pair_check=1,
lattice_binding_analysis=1,run_mfe=1,non_standard_tiles=0,pickle_data=0,num_bins=-1):
domains, domains_with_biotin = read_domains_from_idt_order(f,non_standard_tiles)
names, seqs, seqs_bt, seq_ws, seq_ws_bt = read_strand_data_from_idt_order(f)
if not tile_pair_check: num_tile_and_domain_pairs = -1 # -1 means do not do the tile pair, nor domain pair, check
else: num_tile_and_domain_pairs = 0 # 0 means do the tile pair, and domain pair, check (for fast debugging/testing: num_tile_and_domain_pairs>1 means only check the first num_tile_and_domain_pairs pairs)
# strand level analysis
if strand_analysis:
run_strand_analysis(seqs,seqs_bt,domains,domains_with_biotin,temp_in_C,
num_tile_pairs=num_tile_and_domain_pairs, run_mfe=mfe_analysis,
directory=directory,pickle_data=pickle_data,num_bins=num_bins)
if domain_analysis:
# domain level analysis
analyse_domains(names,seqs,seqs_bt,domains,domains_with_biotin,
seq_ws,seq_ws_bt,temp_in_C,num_domain_pairs=num_tile_and_domain_pairs,
directory=directory,non_standard_tiles=non_standard_tiles,pickle_data=pickle_data,num_bins=num_bins) # num_tile_pairs ,num_domain_pairs=num_tile_pairs
if lattice_binding_analysis and not non_standard_tiles:
print('\nStarting lattice binding analysis')
list_of_pairs_of_lists,descriptors = run_lattice_binding_analysis(f,directory,temp_in_C,num_bins=num_bins)
plot_energies2(list_of_pairs_of_lists, labels=descriptors,
xaxis='dG of lattice+tile-lattice-tile',yaxis='binding(tile,lattice)',
title_info='',plot_dir=directory)
#convert_scatter_plots_to_jpg(f, directory)
#print('Done with: run_analysis()')
# analyze sequences at the 'strand' level of abstraction
def run_strand_analysis(seqs,seqs_bt,domains,domains_with_biotin,temp_in_C,
num_tile_pairs=False,run_mfe=False,directory='plots/',pickle_data=0,num_bins=-1):
'''Analyse `strand' energetics: secondary structure, and strand pair interactions'''
print('running analysis on strands')
description = '' # f[1]
if not os.path.exists(directory):
print(directory)
os.makedirs(directory)
pickle_directory = directory+'pickle/'
if pickle_data:
if not os.path.exists(pickle_directory):
os.makedirs(pickle_directory)
print(' run_strand_analysis(): plots will be placed in: '+directory+ pickle_data*(', pickled datastructures will be placed in: ' + pickle_directory))
print(str(len(seqs_bt))+' sequences (where we leave in biotin markers), ' + str(len(seqs))+' sequences (where we do not leave in biotin markers)')
print(str(len([s for s in seqs_bt if '/iBiodT/' in s])) +' sequences with biotin markers')
if all([len(s)==42 for s in seqs] ): print('All strands are of length 42 bases')
else: 'Some strands are not of length 42 bases'
print(str(len(domains))+' unique domains (glue sequences), ' +str(len([d for d in domains if len(d)==10])) + ' of length 10, '+str(len([d for d in domains if len(d)==11])) + ' of length 11')
sys.stdout.flush()
# domain secondary structure
#print 'analysing domain secondary structure';sys.stdout.flush()
#print temp_in_C
#domain_energies = [pfunc(d, temp_in_C, NEGATE) for d in domains]
#histogram([domain_energies],labels=[description],xaxis='energy (kcal/mol)',yaxis='',title='domain secondary structure',plot_dir=directory)
#pickle.dump(domain_energies, open( pickle_directory+"domain_secondary_structure.p", "wb" ) )
# strand secondary structure
sys.stdout.write('analysing tile (strand) secondary structure: '); sys.stdout.flush()
sec_struct_energies = [pfunc(s, temp_in_C, NEGATE) for s in seqs]
sys.stdout.write(str(len(sec_struct_energies))+' tiles\n'); sys.stdout.flush()
histogram([sec_struct_energies],labels=[description],xaxis='energy (kcal/mol)',yaxis='',title='internal tile secondary structure (via Nupack pfunc)',plot_dir=directory,num_bins=num_bins)
if pickle_data:
pickle.dump(sec_struct_energies, open(pickle_directory+"sec_struct_energies.p", "wb" ) )
# tile pair analysis
if num_tile_pairs != -1:
sys.stdout.write('analysing tile pairs: ');sys.stdout.flush()
seq_pairs = get_seq_pairs(seqs)
if num_tile_pairs>0 : seq_pairs = seq_pairs[:num_tile_pairs]
print(str(len(seq_pairs)) + ' tile pairs to process');sys.stdout.flush()
RNAduplex_pair_energies = tile_pair_RNAduplex_energies(seq_pairs,temp_in_C)
RNAduplex_pair_energies_2004 = tile_pair_RNAduplex_energies(seq_pairs,temp_in_C,NA_parameter_set='dna_mathews2004.par')
histogram([RNAduplex_pair_energies],labels=[description],xaxis='energy (kcal/mol)',yaxis='',title='tile pairs - RNAduplex (1999)',plot_dir=directory,num_bins=num_bins)
histogram([RNAduplex_pair_energies_2004],labels=[description],xaxis='energy (kcal/mol)',yaxis='',title='tile pairs - RNAduplex (2004)',plot_dir=directory,num_bins=num_bins)
binding_pair_energies = tile_pair_NUPACK_binding_energies(seq_pairs,temp_in_C)
histogram([binding_pair_energies],labels=[description],xaxis='energy (kcal/mol)',yaxis='',title='tile pairs - nupack binding',plot_dir=directory,num_bins=num_bins)
scatter_plot_energies(binding_pair_energies, RNAduplex_pair_energies, xaxis='nupack pair binding', yaxis='RNAduplex pair (1999)', title_info='',plot_dir=directory) #,xthreshold=9.3,ythreshold=9.3
scatter_plot_energies(binding_pair_energies, RNAduplex_pair_energies_2004, xaxis='nupack pair binding', yaxis='RNAduplex pair (2004)', title_info='',plot_dir=directory) #,xthreshold=9.3,ythreshold=9.3
scatter_plot_energies(RNAduplex_pair_energies, RNAduplex_pair_energies_2004, xaxis='RNAduplex pair (1999)', yaxis='RNAduplex pair (2004)', title_info='',plot_dir=directory)
if run_mfe and num_tile_pairs != -1:
mfe_pair_energies = tile_pair_NUPACK_mfe_energies(seq_pairs,temp_in_C)
histogram([mfe_pair_energies],labels=[description],xaxis='energy (kcal/mol)',yaxis='',title='tile pairs - nupack mfe',plot_dir=directory,num_bins=num_bins)
scatter_plot_energies(mfe_pair_energies, RNAduplex_pair_energies, xaxis='nupack pair mfe', yaxis='RNAduplex pair', title_info='',plot_dir=directory)
scatter_plot_energies(binding_pair_energies, mfe_pair_energies, xaxis='nupack pair binding', yaxis='nupack pair mfe', title_info='',plot_dir=directory)
descriptors = ['RNAduplex (1999)','RNAduplex (2004)','NUPACK binding','NUPACK mfe']
histogram([RNAduplex_pair_energies,RNAduplex_pair_energies_2004,binding_pair_energies,mfe_pair_energies],labels=descriptors,xaxis='energy (kcal/mol)',yaxis='',title='tile pair energies',plot_dir=directory,num_bins=num_bins)
if pickle_data:
pickle.dump(mfe_pair_energies, open( pickle_directory+"mfe_pair_energies.p", "wb" ) )
elif not run_mfe and num_tile_pairs != -1:
descriptors = ['RNAduplex (1999)','RNAduplex (2004)','NUPACK binding']
histogram([RNAduplex_pair_energies,RNAduplex_pair_energies_2004,binding_pair_energies],labels=descriptors,xaxis='energy (kcal/mol)',yaxis='',title='tile pair energies',plot_dir=directory,num_bins=num_bins)
#descriptors = ['binding v RNAduplex (1999)','binding v RNAduplex (2004)','mfe v RNAduplex (1999)','mfe v RNAduplex (2004)']
#pickle.dump(RNAduplex_pair_energies, open( pickle_directory+"RNAduplex_pair_energies.p", "wb" ) )
#pickle.dump(binding_pair_energies, open( pickle_directory+"binding_pair_energies.p", "wb" ) )
#pickle.dump(seqs, open( pickle_directory+"seqs.p", "wb" ) )
#pickle.dump(seq_pairs, open( pickle_directory+"seq_pairs.p", "wb" ) )
#if run_mfe: return seqs, seq_pairs, sec_struct_energies, binding_pair_energies, RNAduplex_pair_energies, binding_pair_energies, mfe_pair_energies
#else: return seqs, seq_pairs, sec_struct_energies, binding_pair_energies, RNAduplex_pair_energies, binding_pair_energies
def lattice_binding_spacer(strand,lattice_end_top,lattice_spacer,lattice_end_bottom,temp_in_C):
'''Strand is string with 4 single-whitespace delimited domains. lattice is of the form domain+lattice_spacer+domain,
where lattice_spacer is typically 'TTTTT'.'''
tile1_domains = strand.split(' ')
dG_sticky_ends_bound = max(binding(tile1_domains[1]+tile1_domains[2],lattice_end_top+ lattice_spacer +lattice_end_bottom,temp_in_C),
binding(tile1_domains[1]+tile1_domains[2],lattice_end_top+wc(lattice_spacer)+lattice_end_bottom,temp_in_C))
dG_tube_ends_after = max(pfunc(tile1_domains[0]+ lattice_spacer +tile1_domains[3],temp_in_C, NEGATE),
pfunc(tile1_domains[0]+wc(lattice_spacer)+tile1_domains[3],temp_in_C, NEGATE))
dG_strand_before = pfunc(''.join(tile1_domains),temp_in_C, NEGATE)
dG_tube_ends_before = max(pfunc(lattice_end_top+ lattice_spacer +lattice_end_bottom,temp_in_C, NEGATE),
pfunc(lattice_end_top+wc(lattice_spacer)+lattice_end_bottom,temp_in_C, NEGATE))
dG = dG_sticky_ends_bound + dG_tube_ends_after - dG_strand_before - dG_tube_ends_before # + dG_adjustment
return dG
_bad_single_mismatch_threshold = 10.0
def run_lattice_binding_analysis(f,directory,temp_in_C,lattice_spacer='TTTTT',num_bins=-1):
# check for "first" algo conflicts (single mismatches that are the first error in a proofreading block)
# first with empty lattice_spacer
_,_,_ = analyse_algo_conflicts(f,directory,temp_in_C=temp_in_C,lattice_spacer='',threaded=True,num_bins=num_bins)
# then with lattice_spacer='TTTTT'
_,_,_ = analyse_algo_conflicts(f,directory,temp_in_C=temp_in_C,lattice_spacer=lattice_spacer,threaded=True,num_bins=num_bins)
_,_,_ = analyse_algo_conflicts(f,directory,temp_in_C=temp_in_C,lattice_spacer=lattice_spacer,threaded=False,num_bins=num_bins)
correct_dG_algo,mismatch_below_algo,mismatch_above_algo = analyse_algo_conflicts(f,directory,temp_in_C=temp_in_C,lattice_spacer=lattice_spacer,threaded=True)
# check for generalised algo conflicts (single mismatches)
analyse_row_conflicts(f,directory, temp_in_C=temp_in_C,lattice_spacer=lattice_spacer,normed=True,check_double_mismatches=_check_double_mismatches,num_bins=num_bins)
analyse_row_conflicts(f,directory,temp_in_C=temp_in_C,lattice_spacer=lattice_spacer,normed=False,check_double_mismatches=_check_double_mismatches,num_bins=num_bins)
_,_,_ = lattice_binding_energies_detailed(f,directory,temp_in_C=temp_in_C,lattice_spacer=lattice_spacer,threaded=True,num_bins=num_bins)
_,_,_ = lattice_binding_energies_detailed(f,directory,temp_in_C=temp_in_C,lattice_spacer=lattice_spacer,threaded=False,num_bins=num_bins)
correct_dG,mismatch_below_dG,mismatch_above_dG = lattice_binding_energies_detailed(f,directory,temp_in_C=temp_in_C,lattice_spacer=lattice_spacer,threaded=True,num_bins=num_bins)
correct_binding,mismatch_below_binding,mismatch_above_binding = lattice_binding_energies_simplified(f,directory,temp_in_C=temp_in_C,lattice_spacer=lattice_spacer,num_bins=num_bins)
list_of_pairs_of_lists = [[correct_dG,correct_binding],
[mismatch_below_dG,mismatch_below_binding],
[mismatch_above_dG,mismatch_above_binding]]
descriptors = ['correct binding',
'1 mismatch (below)',
'1 mismatch (above)']
return list_of_pairs_of_lists,descriptors
def algo_format_tile_name(n):
return len(n.split(";"))==3 and n.split(";")[2] in ['ne','nw','se','sw']
def analyse_row_conflicts(f,directory,temp_in_C,lattice_spacer='TTTTT',check_double_mismatches=False,normed=True,threaded=True,num_bins=-1):
'''Nupack binding() energy of row-conflicting tile (single-mismatch that can arise
during correct and incorrect growth) ... TODO: explain row-conflict'''
names, _, _, seqs, seqs_bt = read_strand_data_from_idt_order(f)
domains, domains_incl_biotin_labels = read_domains_from_idt_order(f)
is_algo_tile_set = True
for n in names:
if not algo_format_tile_name(n):
is_algo_tile_set = False
if not is_algo_tile_set:
print("The input tile set seems to not be an algorithmic tile set (based on it's tile names), hence I'm skipping execution of analyse_row_conflicts().")
return 0
if not os.path.exists(directory): os.makedirs(directory)
print(' analyse_row_conflicts(), lattice binding analysis from file: '+f+'\n plots will be placed in: ' + directory)
names_seqs = list(zip(names,seqs))
#threaded = False # _threaded # threaded code is not yet implemented
num_tiles_processed = 0
correct_growth_energies = []
single_mismatch_below_energies = []
single_mismatch_above_energies = []
double_mismatch_energies = []
double_mismatch_crazy_energies = []
thres = _bad_single_mismatch_threshold
helix_tiles = [[] for i in range(_num_helices+1)]
for helix in range(_num_helices):
for tile_name, tile_seq in names_seqs:
if tile_helix(tile_name) == helix:
helix_tiles[helix].append( (tile_name, tile_seq) )
for tile1_name, tile1_seq in names_seqs:
if num_tiles_processed%10==0 and num_tiles_processed>0: sys.stdout.write(str(num_tiles_processed))
num_tiles_processed += 1
sys.stdout.write('.'); sys.stdout.flush()
correct_growth_energies.append(lattice_binding_spacer(tile1_seq,
wc(tile1_seq.split(' ')[2]),
lattice_spacer,
wc(tile1_seq.split(' ')[1]),
temp_in_C))
# mismatch above:
for tile2_name,tile2_seq in helix_tiles[ (tile_helix(tile1_name)+1) % _num_helices ]:
# i.e. both tile1 and tile2 are "e"ast or both are "w"est within their pf blocks
if tile_dir(tile1_name)[1] == tile_dir(tile2_name)[1] and tile1_seq.split(' ')[2] != wc(tile2_seq.split(' ')[0]): # really I should check tile names intead of seqs here
e = lattice_binding_spacer(tile1_seq,
tile2_seq.split(' ')[0],
lattice_spacer,
wc(tile1_seq.split(' ')[1]),
temp_in_C)
single_mismatch_above_energies.append(e)
if e > thres:
print_lattice_mismatch_above(e, tile2_seq.split(' ')[0], tile2_name, tile1_seq, tile1_name, wc(tile1_seq.split(' ')[1]) )
# mismatch below:
h = (tile_helix(tile1_name)-1) % _num_helices
if h == 0: h = 16
for tile2_name,tile2_seq in helix_tiles[ h ]:
# i.e. one of tile1, tile2 is "e"ast and the other is "w"est within their pf blocks
if tile_dir(tile1_name)[1] != tile_dir(tile2_name)[1] and tile1_seq.split(' ')[1] != wc(tile2_seq.split(' ')[3]): # really I should check tile names intead of seqs here
e = lattice_binding_spacer(tile1_seq,
wc(tile1_seq.split(' ')[2]),
lattice_spacer,
tile2_seq.split(' ')[3],
temp_in_C)
single_mismatch_below_energies.append(e)
if e > thres:
print_lattice_mismatch_below(e, tile1_seq.split(' ')[2], tile1_seq, tile1_name, wc(tile2_seq.split(' ')[3]), tile2_name)
list_of_lists_of_energies= [correct_growth_energies,single_mismatch_below_energies,single_mismatch_above_energies]
labels=['correct growth ({} energies)'.format(len(correct_growth_energies)),
'one mismatch below ({} energies)'.format(len(single_mismatch_below_energies)),
'one mismatch above ({} energies)'.format(len(single_mismatch_above_energies))]
# Mismatch below and above (double mismatch)
if check_double_mismatches:
# double mismatches that do preserve row/direction
for tile_below_name,tile_below_seq in helix_tiles[ h ]: # h was defined above
double_mismatch_res = [global_thread_pool.apply_async(lattice_binding_spacer, args=(tile1_seq,
tile_above_seq.split(' ')[0],
lattice_spacer,
tile_below_seq.split(' ')[3],
temp_in_C)) for tile_above_name,tile_above_seq in helix_tiles[ (tile_helix(tile1_name)+1) % _num_helices ] \
if tile1_seq.split(' ')[1] != wc(tile_below_seq.split(' ')[3]) and \
tile1_seq.split(' ')[2] != wc(tile_above_seq.split(' ')[0]) and \
tile_dir(tile1_name)[1] != tile_dir(tile_below_name)[1] and \
tile_dir(tile1_name)[1] == tile_dir(tile_above_name)[1]]
double_mismatch_energies.extend([result.get() for result in double_mismatch_res])
# double mismatches that do not preserve row/direction
for tile_below_name,tile_below_seq in helix_tiles[ h ]: # h was defined above
double_mismatch_crazy_res = [global_thread_pool.apply_async(lattice_binding_spacer, args=(tile1_seq,
tile_above_seq.split(' ')[0],
lattice_spacer,
tile_below_seq.split(' ')[3],
temp_in_C)) for tile_above_name,tile_above_seq in helix_tiles[ (tile_helix(tile1_name)+1) % _num_helices ] \
if tile1_seq.split(' ')[1] != wc(tile_below_seq.split(' ')[3]) and \
tile1_seq.split(' ')[2] != wc(tile_above_seq.split(' ')[0])]
double_mismatch_crazy_energies.extend([result.get() for result in double_mismatch_crazy_res])
if check_double_mismatches:
list_of_lists_of_energies.extend( [double_mismatch_crazy_energies, double_mismatch_energies] )
labels.extend(['double mismatch, arbitrary ({} energies)'.format(len(double_mismatch_crazy_energies)),
'double mismatch, row/dir preserving ({} energies)'.format(len(double_mismatch_energies))])
histogram(list_of_lists_of_energies,labels=labels,
xaxis='energy (kcal/mol)',yaxis='',
title='growth on right (dG before-after binding, 1'+ ' and 2'*check_double_mismatches +' mismatch'+'es'*check_double_mismatches+', lattice spacer is '+lattice_spacer*(bool(lattice_spacer))+'empty string'*(not(bool(lattice_spacer)))+', not normalised'*(not normed)+')', #; for {} tiles)'.format(len(names_seqs)),
label_size=12,legend_font_size=9,
plot_dir=directory,normed=normed,xmin=-18,num_bins=num_bins) # ,xmin=4,xmax=18
return correct_growth_energies,single_mismatch_below_energies,single_mismatch_above_energies,double_mismatch_energies
def lattice_binding_energies_detailed(f,directory,temp_in_C=53,lattice_spacer='TTTTT',threaded=True,num_bins=-1):
'''Nupack binding() energy of tile binding of right (non-seeded end) of
nanotube with zero or one mistmatches'''
names, _, _, seqs, seqs_bt = read_strand_data_from_idt_order(f)
domains, domains_incl_biotin_labels = read_domains_from_idt_order(f)
if not os.path.exists(directory): os.makedirs(directory)
print('lattice_binding_energies_detailed(), lattice binding analysis from file:\n'+f+' plots will be placed in: ' + directory)
names_seqs = list(zip(names,seqs))
num_tiles_processed = 0
correct_growth_energies = []
single_mismatch_below_energies = []
single_mismatch_above_energies = []
bad_conflicts = ''
for tile1_name, tile1_seq in names_seqs:
tile1_domains = tile1_seq.split(' ')
if threaded:
if num_tiles_processed%10==0 and num_tiles_processed>0: sys.stdout.write(str(num_tiles_processed))
sys.stdout.write('.'); sys.stdout.flush()
num_tiles_processed += 1
correct_growth_energies.append(lattice_binding_spacer(tile1_seq,
wc(tile1_domains[2]),
lattice_spacer,
wc(tile1_domains[1]),
temp_in_C))
mismatch_below_res = [global_thread_pool.apply_async(lattice_binding_spacer, args=(tile1_seq,
#wc(tile1_domains[2])+'TTTTT'+tile2_seq.split(' ')[3],
wc(tile1_domains[2]),
lattice_spacer,
tile2_seq.split(' ')[3],
temp_in_C)) for _,tile2_seq in names_seqs if wc(tile1_seq.split(' ')[1])!=tile2_seq.split(' ')[3]]
single_mismatch_below_energies = single_mismatch_below_energies + [result.get() for result in mismatch_below_res]
mismatch_above_res = [global_thread_pool.apply_async(lattice_binding_spacer, args=(tile1_seq,
#tile2_seq.split(' ')[0]+'TTTTT'+wc(tile1_domains[1]),
tile2_seq.split(' ')[0],
lattice_spacer,
wc(tile1_domains[1]),
temp_in_C)) for _,tile2_seq in names_seqs if wc(tile1_seq.split(' ')[2])!=tile2_seq.split(' ')[0] ]
single_mismatch_above_energies = single_mismatch_above_energies + [result.get() for result in mismatch_above_res]
else: # not threaded
thres = _bad_lattice_binding_to_arbitrary_lattice_threshold
correct_growth_energies.append(lattice_binding_spacer(tile1_seq,
wc(tile1_domains[2]),
lattice_spacer,
wc(tile1_domains[1]),
temp_in_C))
for tile2_name,tile2_seq in names_seqs:
# mismatch below
if wc(tile1_domains[1])!=tile2_seq.split(' ')[3]:
e = lattice_binding_spacer(tile1_seq,
wc(tile1_domains[2]),
lattice_spacer,
tile2_seq.split(' ')[3],
temp_in_C)
single_mismatch_below_energies.append(e)
if e < thres:
bad_conflicts += print_lattice_mismatch_below(e, wc(tile1_seq.split(' ')[2]),
tile1_seq, tile1_name,
tile2_seq.split(' ')[3],
'mismatch: dom 3 of '+tile2_name)
bad_conflicts += str('{0:.2f}'.format(eval_colocated_end_pair(tile1_seq.split(' ')[1],tile2_seq.split(' ')[3],temp_in_C))) +' = eval_colocated_end_pair('+str( tile1_seq.split(' ')[1])+','+str(tile2_seq.split(' ')[3])+','+str(temp_in_C)+')\n'
# mismatch above
if wc(tile1_domains[2])!=tile2_seq.split(' ')[0]:
e = lattice_binding_spacer(tile1_seq,
tile2_seq.split(' ')[0],
lattice_spacer,
wc(tile1_domains[1]),
temp_in_C)
single_mismatch_above_energies.append(e)
if e < thres:
bad_conflicts += print_lattice_mismatch_above(e, tile2_seq.split(' ')[0],
'mismatch: dom 0 of tile '+tile2_name,
tile1_seq, tile1_name,
wc(tile1_seq.split(' ')[1]))
bad_conflicts += str('{0:.2f}'.format(eval_colocated_end_pair(tile2_seq.split(' ')[0], tile1_seq.split(' ')[2], temp_in_C)))+' = eval_colocated_end_pair('+str(tile2_seq.split(' ')[0])+','+str(tile1_seq.split(' ')[2])+','+str(temp_in_C)+')\n'
if not threaded:
with open(directory+'bad_arbitrary_lattice_conflicts - '+lattice_spacer+'.txt', 'w') as f:
f.write('Showing erroneous attachments with energy $\leq ' +str(thres) +'$ kcal/mol for single-match and single-mismatch binding events ' +'to arbitrary (correct or incorrect) lattices. These errors ' +'may or may not respect proofreading block tile-position.')
f.write('\\begin{footnotesize}\\begin{verbatim}\n')
f.write(bad_conflicts)
f.write('\\end{verbatim}\\end{footnotesize}\n')
histogram([correct_growth_energies,single_mismatch_below_energies,single_mismatch_above_energies],
labels=['correct growth ({} energies)'.format(len(correct_growth_energies)),
'one mismatch below ({} energies)'.format(len(single_mismatch_below_energies)),
'one mismatch above ({} energies)'.format(len(single_mismatch_above_energies))
],
xaxis='energy (-kcal/mol)',yaxis='',
label_size=12,legend_font_size=9,
title='growth on right (detailed binding, incorrect and correct lattices, lattice spacer '+lattice_spacer*(bool(lattice_spacer))+'is empty string'*(not(bool(lattice_spacer)))+')', #; for {} tiles)'.format(len(names_seqs)),
plot_dir=directory,xmin=-18,
num_bins=num_bins) # xmin=4,xmax=18
sys.stdout.write('\n')
return correct_growth_energies,single_mismatch_below_energies,single_mismatch_above_energies
def lattice_binding_energies_simplified(f,directory, temp_in_C=53, lattice_spacer='TTTTT',num_bins=-1):
'''Nupack binding() energy of tile binding of right of nanotube with no mistmatches
or one mismatch'''
names, _, _, seqs, seqs_bt = read_strand_data_from_idt_order(f)
domains, domains_incl_biotin_labels = read_domains_from_idt_order(f)
if not os.path.exists(directory): os.makedirs(directory)
print('lattice_binding_energies_simplified(), lattice binding analysis from file:\n'+f+' plots will be placed in: ' + directory)
names_seqs = list(zip(names,seqs))
threaded = _threaded
num_tiles_processed = 0
correct_growth_energies = []
single_mismatch_below_energies = []
single_mismatch_above_energies = []
for tile1_name, tile1_seq in names_seqs:
tile1_domains = tile1_seq.split(' ')
sys.stdout.write('.')
if num_tiles_processed%10==0 and num_tiles_processed>0: sys.stdout.write(str(num_tiles_processed))
#if num_tiles_processed%10==0: sys.stdout.write('.')
sys.stdout.flush()
num_tiles_processed += 1
#correct_growth_energies.append(binding(tile1_domains[1],wc(tile1_domains[1]),temp_in_C)+binding(tile1_domains[2],wc(tile1_domains[2]),temp_in_C))
correct_growth_energies.append(binding(tile1_domains[1]+tile1_domains[2],
wc(tile1_domains[2])+lattice_spacer+wc(tile1_domains[1]),
temp_in_C))
# mismatch below
results1 = [global_thread_pool.apply_async(binding, args=(tile1_domains[1]+tile1_domains[2],
wc(tile1_domains[2])+lattice_spacer+tile2_seq.split(' ')[3],
temp_in_C)) for _,tile2_seq in names_seqs if wc(tile1_seq.split(' ')[1])!=tile2_seq.split(' ')[3]]
single_mismatch_below_energies = single_mismatch_below_energies + [result.get() for result in results1]
# mismatch above
results2 = [global_thread_pool.apply_async(binding, args=(tile1_domains[1]+tile1_domains[2],
tile2_seq.split(' ')[0]+lattice_spacer+wc(tile1_domains[1]),
temp_in_C)) for _,tile2_seq in names_seqs if wc(tile1_seq.split(' ')[2])!=tile2_seq.split(' ')[0] ]
single_mismatch_above_energies = single_mismatch_above_energies + [result.get() for result in results2]
histogram([correct_growth_energies,single_mismatch_below_energies,single_mismatch_above_energies],
labels=['correct growth ({} energies)'.format(len(correct_growth_energies)),
'one mismatch below ({} energies)'.format(len(single_mismatch_below_energies)),
'one mismatch above ({} energies)'.format(len(single_mismatch_above_energies))
],
xaxis='energy (-kcal/mol)',yaxis='',
title='growth on right (simplified binding(), lattice spacer is '+lattice_spacer*(bool(lattice_spacer))+'empty string'*(not(bool(lattice_spacer)))+')',
label_size=12,legend_font_size=9,
plot_dir=directory,xmin=-18,
num_bins=num_bins) # ,xmin=4,xmax=18
return correct_growth_energies,single_mismatch_below_energies,single_mismatch_above_energies
def tile_helix(tile_name):
'''return helix number for tile with name tile_name'''
n = tile_num(tile_name)
d = tile_dir(tile_name)
#if n%2==0:
if d == 'nw' or d == 'se' : return 2*n
elif d == 'sw': return 2*n-1
elif d == 'ne': return (2*n+1) % _num_helices
else: sys.exit('Exiting program: Error in tile name. Was expecting a tile name with two semi-colons followed by one of nw,ne,se,sw. E.g. U6;00->00;ne.')
def tile_dir(name):
return name[10:12]
def tile_num(name):
return int(name[1:2])
def analyse_algo_conflicts(f,directory,temp_in_C=53,lattice_spacer='TTTTT',threaded=True,num_bins=-1):
'''binding() energy of algorithmic conflicting tile (single-mismatches that can arise
as the first error from a locally-correct lattice)'''
names, _, _, seqs, seqs_bt = read_strand_data_from_idt_order(f)
domains, domains_incl_biotin_labels = read_domains_from_idt_order(f)
if not os.path.exists(directory): os.makedirs(directory)
print(' the next few plots will be placed in: ' + directory)
names_seqs = list(zip(names,seqs))
print(' analysing single mismatches that are the first error in a \
locally correct lattice (aka first algorithmic conflicts) using \
the function analyse_algo_conflicts(), from file: ' + f +\
' (iterating through '+str(len(names_seqs))+' strands):')
num_tiles_processed = 0
correct_growth_energies = []
single_mismatch_below_energies = []
single_mismatch_above_energies = []
thres = _bad_first_algo_conflict_threshold
lower_thres_correct_binding = _lower_thres_correct_binding
bad_conflicts = ''
weak_correct_bindings = ''
for tile1_name, tile1_seq in names_seqs:
tile1_domains = tile1_seq.split(' ')
if threaded:
if num_tiles_processed%10==0 and num_tiles_processed>0: sys.stdout.write(str(num_tiles_processed))
sys.stdout.write('.')
sys.stdout.flush()
num_tiles_processed += 1
correct_growth_energies.append(lattice_binding_spacer(tile1_seq,
wc(tile1_seq.split(' ')[2]),
lattice_spacer,
wc(tile1_seq.split(' ')[1]),
temp_in_C))
mismatch_below_res = [global_thread_pool.apply_async(lattice_binding_spacer, args=(tile1_seq,
wc(tile1_seq.split(' ')[2]),
lattice_spacer,
wc(tile2_seq.split(' ')[1]),
temp_in_C)) \
for _,tile2_seq in names_seqs \
if tile1_seq.split(' ')[2]==tile2_seq.split(' ')[2] and \
tile1_seq.split(' ')[1]!=tile2_seq.split(' ')[1]]
single_mismatch_below_energies = single_mismatch_below_energies + [result.get() for result in mismatch_below_res]
mismatch_above_res = [global_thread_pool.apply_async(lattice_binding_spacer, args=(tile1_seq,
wc(tile2_seq.split(' ')[2]),
lattice_spacer,
wc(tile1_seq.split(' ')[1]),
temp_in_C)) \
for _,tile2_seq in names_seqs \
if tile1_seq.split(' ')[1]==tile2_seq.split(' ')[1] and \
tile1_seq.split(' ')[2]!=tile2_seq.split(' ')[2]]
single_mismatch_above_energies = single_mismatch_above_energies + [result.get() for result in mismatch_above_res]
else: # not threaded
e = lattice_binding_spacer(tile1_seq,
wc(tile1_seq.split(' ')[2]),
lattice_spacer,
wc(tile1_seq.split(' ')[1]),
temp_in_C)
correct_growth_energies.append(e)
if e > lower_thres_correct_binding:
weak_correct_bindings += print_lattice_binding(e, tile1_seq, tile1_name)
for tile2_name,tile2_seq in names_seqs:
# mismatch below
if tile1_seq.split(' ')[2]==tile2_seq.split(' ')[2] and tile1_seq.split(' ')[1]!=tile2_seq.split(' ')[1]:
e = lattice_binding_spacer(tile1_seq,
wc(tile1_seq.split(' ')[2]),
lattice_spacer,
wc(tile2_seq.split(' ')[1]), # there was previously an eror here
temp_in_C)
single_mismatch_below_energies.append(e)
if e < thres:
#print_lattice_mismatch_below(energy, top_output, tile_seq, tile_name, bottom_output, bottom_name):
bad_conflicts += print_lattice_mismatch_below(e, wc(tile1_seq.split(' ')[2]), tile1_seq, tile1_name, wc(tile2_seq.split(' ')[1]), 'mismatch: dom 3 of tile WC to dom 1 of '+tile2_name)
bad_conflicts += str('{0:.2f}'.format(eval_colocated_end_pair(tile1_seq.split(' ')[1],wc(tile2_seq.split(' ')[1]),temp_in_C))) +' = eval_colocated_end_pair('+str( tile1_seq.split(' ')[1])+','+str(wc(tile2_seq.split(' ')[1]))+','+str(temp_in_C)+')\n'
# mismatch above
if tile1_seq.split(' ')[1]==tile2_seq.split(' ')[1] and tile1_seq.split(' ')[2]!=tile2_seq.split(' ')[2]:
e = lattice_binding_spacer(tile1_seq,
wc(tile2_seq.split(' ')[2]),
lattice_spacer,
wc(tile1_seq.split(' ')[1]),
temp_in_C)
single_mismatch_above_energies.append(e)
if e < thres:
bad_conflicts += print_lattice_mismatch_above(e, wc(tile2_seq.split(' ')[2]), 'mismatch: dom 0 of tile WC to dom 2 of '+tile2_name, tile1_seq, tile1_name, wc(tile1_seq.split(' ')[1]))
bad_conflicts += str('{0:.2f}'.format(eval_colocated_end_pair(wc(tile2_seq.split(' ')[2]), tile1_seq.split(' ')[2], temp_in_C)))+' = eval_colocated_end_pair('+str(wc(tile2_seq.split(' ')[2]))+','+str(tile1_seq.split(' ')[2])+','+str(temp_in_C)+')\n'
if not threaded:
with open(directory+'bad_first_algo_conflicts - '+lattice_spacer+'.txt', 'w') as f:
f.write('Showing erroneous attachments with energy $\leq ' +str(thres) +'$ kcal/mol for single mismatches (algorithmic conflicts) that occur as ' +'the first error in a proofreading block.')
f.write('\\begin{footnotesize}\\begin{verbatim}\n')
f.write(bad_conflicts)
f.write('\\end{verbatim}\\end{footnotesize}\n')
#f.write('Done writing ' +str(len(bad_conflicts))+ ' characters')
#f.close()
with open(directory+'weak_correct_bindings - '+lattice_spacer+'.txt', 'w') as f:
f.write('Showing correct lattice attachments with energy $\geq '+str(lower_thres_correct_binding)+'$ kcal/mol.')
f.write('\\begin{footnotesize}\\begin{verbatim}\n')
f.write(weak_correct_bindings)
f.write('\\end{verbatim}\\end{footnotesize}\n')
histogram([correct_growth_energies,single_mismatch_below_energies,single_mismatch_above_energies],
labels=['correct growth ({} energies)'.format(len(correct_growth_energies)),
'one mismatch below ({} energies)'.format(len(single_mismatch_below_energies)),
'one mismatch above ({} energies)'.format(len(single_mismatch_above_energies))
],
xaxis='energy (kcal/mol)',yaxis='count',
title='correct and algorithmic error attachments to a valid lattice'+' (lattice spacer is empty)'*(not(bool(lattice_spacer))), #; for {} tiles)'.format(len(names_seqs)),
filename='algorithmic error (first), dG before and after, mismatches above and below, lattice spacer is '+lattice_spacer*(bool(lattice_spacer))+'empty string'*(not(bool(lattice_spacer))), #; for {} tiles)'.format(len(names_seqs)),
normed=0,label_size=12,legend_font_size=9,plot_dir=directory,
xmin=min(-17.1,min(correct_growth_energies+single_mismatch_below_energies+single_mismatch_above_energies)),
xmax=0,
num_bins=num_bins) # was ymax=282
histogram([correct_growth_energies,single_mismatch_below_energies+single_mismatch_above_energies],
labels=['{} correct attachments'.format(len(correct_growth_energies)),
'{} algorithmic errors'.format(len(single_mismatch_below_energies+single_mismatch_above_energies))
],
xaxis='energy (kcal/mol)',yaxis='count',
title= 'correct and algorithmic error attachments to a valid lattice'+' (lattice spacer is empty)'*(not(bool(lattice_spacer))), #; for {} tiles)'.format(len(names_seqs)),
filename='algorithmic error (first), dG before and after, lattice spacer is '+lattice_spacer*(bool(lattice_spacer))+'empty string'*(not(bool(lattice_spacer)))+')', #; for {} tiles)'.format(len(names_seqs)),
normed=0,label_size=12,legend_font_size=9,plot_dir=directory,
xmin=min(-17.1,min(correct_growth_energies+single_mismatch_below_energies+single_mismatch_above_energies)),
xmax=0,
num_bins=num_bins) # was ymax=282
sys.stdout.write('\n')
return correct_growth_energies,single_mismatch_below_energies,single_mismatch_above_energies
def print_lattice_binding(energy, tile_seq, tile_name):
s = '\n'
s += str('{0:.2f}'.format(energy)) + ' binding strength\n'
s += '<-' + wc(tile_seq.split(' ')[2])[::-1]+'\n'
s += ' /' +tile_seq.split(' ')[2]+'-'+tile_seq.split(' ')[3]+'-> '+tile_name+'\n'
s += ' \\' +tile_seq.split(' ')[1][::-1]+'-'+tile_seq.split(' ')[0][::-1]+'\n'
s += ' -' + wc(tile_seq.split(' ')[1]) +'->\n'
return s
def print_lattice_mismatch_below(energy, top_output, tile_seq, tile_name, bottom_output, bottom_name):
s = '\n'
s += str('{0:.2f}'.format(energy)) + ' strength mismatch\n'
s += '<-' + top_output[::-1]+'\n'
s += ' /' +tile_seq.split(' ')[2]+'-'+tile_seq.split(' ')[3]+'-> '+tile_name+'\n'
s += ' \\' +tile_seq.split(' ')[1][::-1]+'-'+tile_seq.split(' ')[0][::-1]+'\n'
s += ' -' + bottom_output +'-> '+bottom_name +'\n'
#print s ; sys.stdout.flush()
return s
def print_lattice_mismatch_above(energy, top_output, top_name, tile_seq, tile_name, bottom_output):
s = '\n'
s += str('{0:.2f}'.format(energy)) + ' strength mismatch\n'
s += '<-' + top_output[::-1]+' '+top_name + '\n'
s += ' /' +tile_seq.split(' ')[2]+'-'+tile_seq.split(' ')[3]+'-> '+tile_name+'\n'
s += ' \\' +tile_seq.split(' ')[1][::-1]+'-'+tile_seq.split(' ')[0][::-1]+'\n'
s += ' -' + bottom_output +'->\n'
#print s; sys.stdout.flush()
return s
def analyse_domains(names,seqs,seqs_bt,domains,domains_incl_biotin_labels,
seq_ws,seq_ws_bt,temp_in_C=53.0,num_domain_pairs=False,
directory='plots_tmp/',non_standard_tiles=0,pickle_data=0,num_bins=-1):
'''Analyse domain sequences'''
print('\ndomain analysis: plots will be placed in: ' + directory)
#print 'Analysing sequences from file:\n' + filename + '\n' +str(len(domains))+' unique domains, ' +str(len(domains_incl_biotin_labels))+' domains (leaving in biotin labels), ' + str(len([d for d in domains if len(d)==10])) + ' of length 10, '+str(len([d for d in domains if len(d)==11])) + ' of length 11' ; sys.stdout.flush()
print(' analysing tile input and output sec structure'); sys.stdout.flush()
if non_standard_tiles:
print(seq_ws)
seq_ws = [s.split()[0]+' '+s.split()[2]+' '+s.split()[3]+' '+s.split()[5] for s in seq_ws if len(s.split())==6]
print(seq_ws)
input_energies = analyse_input_pairs(seq_ws, temp_in_C)
output_energies = analyse_output_pairs(seq_ws, temp_in_C)
lattice_input_energies_correct_binding = analyse_lattice_input_energies_correct_binding(seq_ws, temp_in_C)
histogram([input_energies,lattice_input_energies_correct_binding,output_energies],
labels=['input','lattice (correct)','output'],xaxis='energy (kcal/mol)',yaxis='',
title='tile input, lattice and output secondrary structure (ss)',plot_dir=directory,
num_bins=num_bins)
scatter_plot_energies(input_energies, lattice_input_energies_correct_binding, xaxis='input sec struct', yaxis='lattice sec struct (correct binding)', title_info='',plot_dir=directory) #,xthreshold=9.3,ythreshold=9.3
# domain secondary structure
sys.stdout.write(' analysing domain secondary structure: '); sys.stdout.flush()
domain_energies = [pfunc(d, temp_in_C, NEGATE) for d in domains]
sys.stdout.write(str(len(domain_energies))+ ' domains\n')
strong_doms = [d.replace('/iBiodT/','T') for d in domains_incl_biotin_labels if '/iBiodT/' in d]
# in the following line I should replace d.replace('/iBiodT/','T') with d:
weak_doms = [d for d in domains_incl_biotin_labels if '/iBiodT/' not in d]
strong_doms_energies = [pfunc(d, temp_in_C, NEGATE) for d in strong_doms]
weak_doms_energies = [pfunc(d, temp_in_C, NEGATE) for d in weak_doms]
if len(strong_doms_energies)>0 and len(weak_doms_energies):
histogram([weak_doms_energies,strong_doms_energies],labels=['domains','domains with biotin'],
xaxis='energy (kcal/mol)',yaxis='',title='domain secondary structure energy histogram (via NUPACK pfunc)',
plot_dir=directory,
num_bins=num_bins)
else:
#weak_doms_energies.extend(strong_doms_energies)
histogram([domain_energies],labels=['domains'],xaxis='energy (kcal/mol)',yaxis='',
title='domain secondary structure (pfunc)',plot_dir=directory,
num_bins=num_bins)
if num_domain_pairs != -1:
sys.stdout.write(' analysing domain pairs: ');sys.stdout.flush()
domains_pairs = get_seq_pairs(domains)
print(str(len(domains_pairs)) + ' domain pairs to process'); sys.stdout.flush()
if num_domain_pairs>0:
domains_pairs = domains_pairs[:num_domain_pairs]
print('Warning: I am merely going to analyse a strict subset ('+str(len(domains_pairs))+') of all domain pairs')
#if num_domain_pairs: domains_pairs = domains_pairs[:num_domain_pairs]
#sys.stdout.write(' analysing domain pair secondary structure: '); sys.stdout.flush()
#print(str(len(domains_pairs)) + ' strand pairs to process');sys.stdout.flush()
non_wc_domains_pairs = [p for p in domains_pairs if p[0]!=wc(p[1])]
wc_domains_pairs = [p for p in domains_pairs if p[0]==wc(p[1])]
RNAduplex_non_wc_domains_pairs_energies = tile_pair_RNAduplex_energies(non_wc_domains_pairs,temp_in_C)
# unpaired strands get RNAduplex energy of ~ -100, so set those to -5:
if MORE_NEGAIVE_ENERGY_IS_MORE_FAVOURABLE:
RNAduplex_non_wc_domains_pairs_energies = [e if e > -100 else -5 for e in RNAduplex_non_wc_domains_pairs_energies ]
else:
RNAduplex_non_wc_domains_pairs_energies = [e if e < 100 else 5 for e in RNAduplex_non_wc_domains_pairs_energies ]
threshold = 3.0
print(str(len( [e for e in RNAduplex_non_wc_domains_pairs_energies if e > threshold ]))+' non-wc domain pairs with energy > '+str(threshold))
RNAduplex_wc_domains_pairs_energies = tile_pair_RNAduplex_energies(wc_domains_pairs,temp_in_C)
histogram([RNAduplex_wc_domains_pairs_energies,RNAduplex_non_wc_domains_pairs_energies],
labels=['wc domains','non-wc domains'],xaxis='energy (kcal/mol)',yaxis='',
title='domain pair (RNAduplex)',plot_dir=directory,
num_bins=num_bins)
non_wc_binding_pair_energies = tile_pair_NUPACK_binding_energies(non_wc_domains_pairs,temp_in_C)
scatter_plot_energies(non_wc_binding_pair_energies, RNAduplex_non_wc_domains_pairs_energies, xaxis='nupack domain pair binding', yaxis='RNAduplex domain pair (1999)', title_info='non-wc',plot_dir=directory) #,xthreshold=9.3,ythreshold=9.3
wc_binding_pair_energies = tile_pair_NUPACK_binding_energies(wc_domains_pairs,temp_in_C)
scatter_plot_energies(wc_binding_pair_energies, RNAduplex_wc_domains_pairs_energies, xaxis='nupack domain pair binding', yaxis='RNAduplex domain pair (1999)', title_info='wc',plot_dir=directory) #,xthreshold=9.3,ythreshold=9.3
histogram([wc_binding_pair_energies,non_wc_binding_pair_energies],
labels=[str(len(wc_binding_pair_energies))+ ' WC domain pairs',str(len(non_wc_binding_pair_energies))+' non-WC domain pairs'],
xaxis='energy (kcal/mol)',yaxis='',
normed=1,label_size=12,legend_font_size=9,
title='domain pair (nupack binding())',plot_dir=directory,
num_bins=num_bins)
#############################################################################
# Reading from idt-formatted files (with extension .idt)
#############################################################################
def get_lines_from_file(filename):
'''Returns uncommented and non-empty lines from a text file'''
with open(filename, 'r') as f:
lines = f.readlines()
lines = [line[:line.find('#')].strip() for line in lines]
lines = [line for line in lines if len(line) > 0]
return lines
def is_DNA_sequence(s):
return set(s.replace('/iBiodT/','').replace(' ','')).issubset('ACTG')
def get_DNA_sequences_from_idt_file(f):
return get_testtube_DNA_sequences_from_idt_file(f) + get_plate_DNA_sequences_from_idt_file(f)
def get_testtube_lines_from_idt_file(f):
lines = get_lines_from_file(f)
return [l for l in lines if len(l.split(','))==4 and is_DNA_sequence(l.split(',')[1]) and 'guard' not in l]
def get_plate_lines_from_idt_file(f):
'''Ignores any line containing the word guard'''
lines = get_lines_from_file(f)
return [l for l in lines if len(l.split(','))==4 and is_DNA_sequence(l.split(',')[2]) and 'guard' not in l]
def read_strand_data_from_idt_order(f):
tiles = get_testtube_lines_from_idt_file(f)
tile_names = [l.split(',')[0].replace(' ','').replace('\n','').replace('\r','').lstrip().strip() for l in tiles]
tile_seqs_without_biotin_labels = [tile.split(',')[1].replace('/iBiodT/','T').replace(' ','').replace('\n','').replace('\r','').lstrip().strip() for tile in tiles]
tile_seqs_with_biotin_labels = [tile.split(',')[1].replace(' ','').replace('\n','').replace('\r','').lstrip().strip() for tile in tiles]
tile_seqs_with_whitespace_between_doms = [tile.split(',')[1].replace('/iBiodT/','T').replace('\n','').replace('\r','').lstrip().strip() for tile in tiles]
tile_seqs_biotins_whitespace_between_doms = [tile.split(',')[1].replace('\n','').replace('\r','').lstrip().strip() for tile in tiles]
tiles = get_plate_lines_from_idt_file(f)
tile_names += [l.split(',')[1].replace(' ','').replace('\n','').replace('\r','').lstrip().strip() for l in tiles]
tile_seqs_without_biotin_labels += [tile.split(',')[2].replace('/iBiodT/','T').replace(' ','').replace('\n','').replace('\r','').lstrip().strip() for tile in tiles]
tile_seqs_with_biotin_labels += [tile.split(',')[2].replace(' ','').replace('\n','').replace('\r','').lstrip().strip() for tile in tiles]
tile_seqs_with_whitespace_between_doms += [tile.split(',')[2].replace('/iBiodT/','T').replace('\n','').replace('\r','').lstrip().strip() for tile in tiles]
tile_seqs_biotins_whitespace_between_doms += [tile.split(',')[2].replace('\n','').replace('\r','').lstrip().strip() for tile in tiles]
if len(tile_seqs_without_biotin_labels) == 0:
exit('There are 0 DNA strands. Did you give the correct input? Strands should be specified in idt file format. Run with --help to get an example.')
if len(tile_names) != len(tile_seqs_without_biotin_labels):
exit('Error: there are '+str(len(tile_names))+ ' strand names and '+str(len(tile_seqs_without_biotin_labels))+'strands!')
return tile_names, tile_seqs_without_biotin_labels, tile_seqs_with_biotin_labels, tile_seqs_with_whitespace_between_doms, tile_seqs_biotins_whitespace_between_doms
def read_domains_from_idt_order(filename, non_standard_tiles=0):
_, _, _, tile_seqs_with_whitespace_between_doms, tile_seqs_biotins_whitespace_between_doms = read_strand_data_from_idt_order(filename)
doms = []
doms_with_biotin = []
for l in tile_seqs_with_whitespace_between_doms:
doms.extend(l.replace('\n','').replace('\r','').split(' ') )
for l in tile_seqs_biotins_whitespace_between_doms:
doms_with_biotin.extend(l.replace('\n','').replace('\r','').split(' ') )
return list(set(doms)), list(set(doms_with_biotin))
def flatten(l):
return [item for sublist in l for item in sublist]
#############################################################################
# Plots
#############################################################################
def histogram(data, labels='', xaxis='', yaxis='', title='', filename='', plot_dir='', log_scale=False,
normed=1, xmin=0, xmax=0, ymin=0, ymax=0, label_size=12, legend_font_size=12, show_mean_min_max=1,
legend_location='upper left',num_bins=-1):
'''Plot a histogram. By default data is normalized (area under curve sums to 1 for each dataset (curve colour))'''
min_data = 10000; max_data = -10000
# Fix up function param types/formatting
if filename=='': filename=title
if type(data)!=list: data = [data]
if labels=='':labels=['' for _ in data]
if title!='': filename = title
else: filename = '_'.join(l for l in labels)
pp = PdfPages(plot_dir + filename + '.pdf')
colours = itertools.cycle(['r','b','g','y'])
for i,d in enumerate(data):
if d!= []: #assert len(d)!=0
min_data = min(min_data,min(d))
max_data = max(max_data,max(d))
if num_bins==-1: num_bins = int(min(50, math.ceil(math.sqrt(len(flatten(data))) +1) ))
step_size = (max_data-min_data)/num_bins
bins = [min_data+(i*step_size) for i in range(num_bins)]
for i,d in enumerate(data):
if d != []:
ax = plt.hist(d, bins,
density=normed, #normed=normed, # normed is depreciated, so using density instead
range=[2.0,18.0],
histtype='stepfilled',
facecolor=next(colours), alpha=0.5, edgecolor='black',
label=labels[i] + show_mean_min_max*((labels[i]!='')*', '+'mean='+str('{0:.2f}'.format(sum(d)/float(len(d))))+', min='+str('{0:.2f}'.format(min(d)))+', max='+str('{0:.2f}'.format(max(d)))))
if xmin!=0 or xmax!=0:
plt.xlim(xmin, xmax)
if ymin!=0 or ymax!=0:
plt.ylim(ymin, ymax)
else:
from numpy import isnan
if all(isnan(v) for v in ax[0]):
pp.savefig(); plt.clf(); pp.close()
print("Warning: unable to make plot with the following data\n"+str(data)+