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[[IGEM:Harvard/2006/Container_Design_4/Python_Code/Full_Code_Final|Full Code - Finalized 7/11]]
<div class="tabs-blue">
= Modified Versions of William's Code - Finalized 7/11/06 =
<ul>
<pre>
<li>[[IGEM:Harvard/2006/DNA nanostructures|Project Overview]]</li>
#!/usr/bin/python
<li id = "current">[[IGEM:Harvard/2006/DNA_nanostructures/Designs|Designs]]</li>
<li>[[IGEM:Harvard/2006/DNA_nanostructures/Notebook|Notebook]]</li>
<li>[[IGEM:Harvard/2006/DNA_nanostructures/Protocols|Protocols]]</li>
<li>[[IGEM:Harvard/2006/DNA_nanostructures/Presentations|Presentations]]</li>
<li>[[IGEM:Harvard/2006/DNA_nanostructures/Literature|Literature]]</li>
</ul>
</div>
<br style="clear:both">


import sys
<div class = "tabs-blue">
# for regular expression matching
<ul>
import re
<li>[[IGEM:Harvard/2006/Container Design 1|Design 1]]</li>
# for reading structures in from files
<li>[[IGEM:Harvard/2006/Container Design 2|Design 2]]</li>
import pickle
<li>[[IGEM:Harvard/2006/Container Design 3|Design 3]]</li>
from honeycomb_pointers_v1 import *
<li id = "current">[[IGEM:Harvard/2006/Container Design 4|Design 4]]</li>
from pointers_to_sequences_v1 import *
<li>[[IGEM:Harvard/2006/Container Design 5|Design 5]]</li>
<li>[[IGEM:Harvard/2006/Container Design 6|Design 6]]</li>
</ul>
</div>
<br style = "clear:both">


filename = raw_input('Enter the filename for the text-based node lattice array: ')
<div class="tabs-blue">
num_zones = int(raw_input('Enter the number of 42bp zones per double helix: '))
<ul>
#filename = 'lid_1_ascii.txt'
<li>[[IGEM:Harvard/2006/Container_Design_4|Design 4 Overview]]</li>
#num_zones = 3
<li>[[IGEM:Harvard/2006/Container_Design_4/Schematics|Schematics]]</li>
periodic_structure_flag = False
<li>[[IGEM:Harvard/2006/Container_Design_4/Scaffold Sequences|Scaffold]]</li>
<li id = "current">[[IGEM:Harvard/2006/Container_Design_4/Python Code|Code]]</li>
<li>[[IGEM:Harvard/2006/Container_Design_4/Latch Sequences|Latches]]</li>
<li>[[IGEM:Harvard/2006/Container_Design_4/Oligos|Final Oligo List]]</li>
</ul>
</div>
<br style="clear:both">


node_ra = read_text_format_node_array(filename)
print_node_lattice_array(node_ra)
TPP_ra = token_pointer_pair_array(node_ra, num_zones, periodic_structure_flag)
path_ra = token_pointer_path_array(TPP_ra)
OTP_ra = oligo_token_pointer_array(path_ra)
check_token_representation(OTP_ra, TPP_ra)


 
==Modifications and Additions to Dr. Shih's Code==
# Print out the longest path, just for fun
The code is fairly general with the exception of the Pickle Scripts which generate lists specific to Design 4 and some hardcoded lists under Oligo Sorting
longest_path = []
*[[IGEM:Harvard/2006/Container_Design_4/Python_Code/Full_Code_Final|Full Code - Finalized 7/11]]<br>
for path in path_ra:
*[[IGEM:Harvard/2006/Container_Design_4/Python_Code/Split_Oligos|Oligo Splitting]]<br>
if len(path) > len(longest_path):
*[[IGEM:Harvard/2006/Container_Design_4/Python_Code/Add_Aptamers|Adding Aptamers]]<br>
longest_path = path
*[[IGEM:Harvard/2006/Container_Design_4/Python_Code/Add_Latches|Adding Latches]]<br>
print_path(longest_path, TPP_ra)
*[[IGEM:Harvard/2006/Container_Design_4/Python_Code/Oligo_Sorting|Oligo Sorting]]<br>
 
*[[IGEM:Harvard/2006/Container_Design_4/Python_Code/Pickle_Scripts|Pickle Scripts]]<br>
#####
*[[IGEM:Harvard/2006/Container_Design_4/Python_Code/Print_Oligo_Grid|Print Oligo Grid]]<br>
# Oligo splitting - this time reading from a file and not asking for user
== Other Useful Scripts==
# input
*[[IGEM:Harvard/2006/Container_Design_4/Python_Code/Split_Scaffold|Split Scaffold]]<br>
#####
fin_barrel = None
fin_lid = None
 
try:
fin_barrel = open("barrel_oligos_to_split.txt", "r")
fin_lid = open("lid_oligos_to_split.txt", "r")
except IOError, e:
print "Error in file IO: ", e
 
# Ask the user if they are running a lid or a barrel
 
shape = int(raw_input("Enter 1 if you are running a barrel, 2 if lid: "))
if (shape == 1):
oligos_to_split = pickle.load(fin_barrel)
elif (shape == 2):
oligos_to_split = pickle.load(fin_lid)
else:
print 'Please modify code or run with lid or 30hb barrel'
 
new_OTP_ra = OTP_ra[:]
for pair in oligos_to_split:
oligo_num = pair[0]
print oligo_num
num_toks = pair[1]
print num_toks
      new_OTP_ra = split_oligo(new_OTP_ra, oligo_num, num_toks)
 
      print new_OTP_ra
    print len(OTP_ra)
      print len(new_OTP_ra)
 
# if it's the barrel design and so that all the numbers aren't messed
# up, the 7bp token on the start of strand 10 needs to be removed
# because it's going to be left unpaired
 
if (shape == 1):
new_OTP_ra = new_OTP_ra[:61] + new_OTP_ra[62:]
 
if fin_barrel: fin_barrel.close()
if fin_lid: fin_lid.close()
 
 
 
 
####
# generate and print the oligo token grid
####
 
# Initialize the grid with all periods
num_strands = len(TPP_ra)
num_subzones = len(TPP_ra[0])
 
sub_token_visit_ra = ['.' for subzone_num in range(num_subzones)]
grid_ra = [sub_token_visit_ra[:] for strand_num in range(num_strands)]
 
oligo_num = 0
for oligo in new_OTP_ra:
grid_ra = generate_oligo_path(oligo, oligo_num, grid_ra)
oligo_num = oligo_num + 1
print grid_ra
 
print_all_oligos(grid_ra, num_strands, num_subzones)
 
####
# Generate oligo sequences
####
strand_ra = strand_array('lid_1_scaffold.txt', TPP_ra)
token_ra = token_array(strand_ra)
oligo_ra = oligo_array(new_OTP_ra, token_ra)
 
# The array of oligos that does have the oligos split but does not have the
# aptamers or latches added.
original_oligo_ra = oligo_ra[:]
latch_2_oligo_ra = oligo_ra[:]
 
#####
# Add apts this time using file input instead of user input
#####
 
# Constants
apt_seq = 'GGTTGGTGTGGTTGG'
T_linker = 'TTT'
 
fin_barrel = None
       
try:
        fin_barrel = open("barrel_apts_to_add.txt", "r")
except IOError, e:
        print "Error in file IO: ", e
       
if (shape == 1):
    apts_to_add = pickle.load(fin_barrel)
 
for apt_specs in apts_to_add:
oligo_num = apt_specs[0]
type = apt_specs[1]
if (type == 1):
# apt is pointing in so add 'I' as a flag at the end
oligo_ra[oligo_num] = oligo_ra[oligo_num] + T_linker + apt_seq + 'I'
elif (type == 2):
# apt is pointing out so add 'O' as a flag
oligo_ra[oligo_num] = oligo_ra[oligo_num] + T_linker + apt_seq + 'O'
else:
# incorrect type
print 'Bad input - aptamer needs to be pointing in or out'
 
#####
# Add latches
#####
 
fin_barrel = None
fin_lid1 = None
fin_lid2 = None
fin_barrel_design2 = None
fin_lid1_design2 = None
fin_lid2_design2 = None
               
try:
        fin_barrel = open("barrel_latches_to_add.txt", "r")
fin_lid1 = open("lid1_latches_to_add.txt", "r")
fin_lid2 = open("lid2_latches_to_add.txt", "r")
fin_barrel_design2 = open("barrel_latches_to_add_design2.txt", "r")
fin_lid1_design2 = open("lid1_latches_to_add_design2.txt", "r")
fin_lid2_design2 = open("lid2_latches_to_add_design2.txt", "r")
except IOError, e:
        print "Error in file IO: ", e
 
 
if (shape == 1):
        latches_to_add = pickle.load(fin_barrel)
latches_to_add_d2 = pickle.load(fin_barrel_design2)
elif (shape == 2):
# Ask which lid is being run
print 'What lid are you running?'
type = int(raw_input('Enter 1 if lid1, 2 if lid2: '))
if (type == 1):
latches_to_add = pickle.load(fin_lid1)
latches_to_add_d2 = pickle.load(fin_lid1_design2)
elif (type == 2):
latches_to_add = pickle.load(fin_lid2)
latches_to_add_d2 = pickle.load(fin_lid2_design2)
 
       
# note: latch sequence includes any linker Ts already
for latch_specs in latches_to_add:
oligo_num = latch_specs[0]
        latch = latch_specs[1]
oligo_ra[oligo_num] = oligo_ra[oligo_num] + latch
 
for latch_specs in latches_to_add_d2:
oligo_num = latch_specs[0]
latch = latch_specs[1]
latch_2_oligo_ra[oligo_num] = latch_2_oligo_ra[oligo_num] + latch
 
 
#####
# oligo sorting
#####
#
barrel_core = [0, 3, 4, 5, 6, 8, 9, 10, 12, 13, 14, 15, 16, 18, 19, 20, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77]
barrel_latch = [21, 27, 43, 60]
barrel_aptamer_out = [2, 7, 17, 23]
barrel_aptamer_in = [1, 11, 36, 47]
lid_core = [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]
lid_latch = [2, 29]
 
# output all oligos
output_file = file('lid_1_all_oligos.txt', 'w')
for oligo in oligo_ra:
output_file.write(oligo + '\n')
output_file.close()
 
if (shape == 1):
# barrel output
barrel_oligos_file = file('barrel_oligos_sorted.txt', 'w')
# output barrel core oligos
barrel_oligos_file.write('Core Oligos' + '\n')
barrel_oligos_file.close()
# to append the file needs to be reopened in append mode.
barrel_oligos_file = file('barrel_oligos_sorted.txt', 'a')
 
for oligo_num in barrel_core:
barrel_oligos_file.write(str(oligo_num) + ' : ' + oligo_ra[oligo_num] + '\n')
 
# out + apts
barrel_oligos_file.write('\n' + 'Out + Apts' + '\n')
for oligo_num in barrel_aptamer_out:
barrel_oligos_file.write(str(oligo_num) + ' : ' + oligo_ra[oligo_num] + '\n')
# out - apts
barrel_oligos_file.write('\n' + 'Out - Apts' + '\n')
for oligo_num in barrel_aptamer_out:
barrel_oligos_file.write(str(oligo_num) + ' : ' + original_oligo_ra[oligo_num] + '\n')
# in - apts
barrel_oligos_file.write('\n' + 'In - Apts' + '\n')
for oligo_num in barrel_aptamer_in:
barrel_oligos_file.write(str(oligo_num) + ' : ' + original_oligo_ra[oligo_num] + '\n')
 
# in + apts
barrel_oligos_file.write('\n' + 'In + Apts' +'\n')
for oligo_num in barrel_aptamer_in:
barrel_oligos_file.write(str(oligo_num) + ' : ' + oligo_ra[oligo_num] + '\n')
# barrel oligos with latches - two oligo design
barrel_oligos_file.write('\n' + 'Oligos with Latches - Design 1' + '\n')
for oligo_num in barrel_latch:
barrel_oligos_file.write(str(oligo_num) + ' : ' + oligo_ra[oligo_num] + '\n')
# barrel oligos with latches - four oligo design
barrel_oligos_file.write('\n' + 'Oligos with Latches - Design 2\n')
for oligo_num in barrel_latch:
barrel_oligos_file.write(str(oligo_num) + ' Design 2: ' + latch_2_oligo_ra[oligo_num] + '\n')
 
# barrel oligos replacing all latches
barrel_oligos_file.write('\n' + 'Oligos replacing all latches\n')
for oligo_num in barrel_latch:
barrel_oligos_file.write(str(oligo_num) + ' : ' + original_oligo_ra[oligo_num] + '\n')
 
barrel_oligos_file.close()
 
 
if (shape == 2):
# lid output
 
# output lid core oligos
# we first open the file for writing because we want to clear
# anything that was there before. Then we close it and reopen it
# in append mode.
lid_oligos_file = file('lid1_oligos_sorted.txt', 'w')
lid_oligos_file.write('Lid Core' + '\n')
lid_oligos_file.close()
lid_oligos_file = file('lid1_oligos_sorted.txt', 'a')
for oligo_num in lid_core:
lid_oligos_file.write(str(oligo_num) + ' : ' + oligo_ra[oligo_num] + '\n')
 
# output lid oligos with latches -- 2 oligo design
lid_oligos_file.write('\nLid Latch Oligos - 2 Oligo Design\n')
for oligo_num in lid_latch:
lid_oligos_file.write(str(oligo_num) + ' : ' + oligo_ra[oligo_num] + '\n')
 
# output lid oligos with latches -- 4 oligo design
lid_oligos_file.write('\nLid Latch Oligos - 4 Oligo Design\n')
for oligo_num in lid_latch:
lid_oligos_file.write(str(oligo_num) + ' Design 2 : ' + latch_2_oligo_ra[oligo_num] + '\n')
 
# output lid oligos that replace those with latches
lid_oligos_file.write('\nLid Replacement Oligos - No Latches\n')
for oligo_num in lid_latch:
lid_oligos_file.write(str(oligo_num) + ' : ' + original_oligo_ra[oligo_num] + '\n')
lid_oligos_file.close()
 
sys.stdout.write('\n\n\n\n\n\n')
 
 
</pre>
 
[[IGEM:Harvard/2006/Container_Design_4/Python_Code/Split_Scaffold|Split Scaffold]]
 
==Split Oligos From User Input==
Script for splitting up as many oligos as you want (USING USER INPUT). The first part goes in main. The second part goes in honeycomb_pointers_v1.py
<pre>
 
#####
# Oligo splitting:
# get new list of oligos given user input specifying which oligo to cut
#####
 
num_to_split = int(raw_input('How many oligos do you want to split?'))
i = 0
new_OTP_ra = OTP_ra[:]
while i < num_to_split: 
 
        oligo_num = int(raw_input('Enter the number oligo you wish to split:'))
        print '\n'
        print 'How many tokens should the first new oligo be?'
        num_toks = int(raw_input('Number of toks starting from 5 prime: '))
 
        new_OTP_ra = split_oligo(new_OTP_ra, oligo_num, num_toks)
       
        print new_OTP_ra
        print len(OTP_ra)
        print len(new_OTP_ra)
        i = i + 1
 
####
# given an oligo to split, split it and return the new list of oligos
####   
def split_oligo(new_OTP_ra, oligo_num, num_toks):
       
        print new_OTP_ra[oligo_num]
 
        original_oligo = new_OTP_ra[oligo_num]
       
        oligo_1 = original_oligo[:num_toks] 
        oligo_2 = original_oligo[num_toks:]
        print oligo_1
        print'\n'
        print oligo_2
               
        new_OTP_ra[oligo_num] = oligo_1
        new_OTP_ra.insert(oligo_num + 1, oligo_2)
        return new_OTP_ra   
 
 
</pre>
 
 
==Split Oligos From File Input==
Script for splitting up oligos automatically (FILE INPUT). (make sure to import pickle at the top). This part goes in main. Further down is the file
to read from essentially (uses pickle)
 
<pre>
#####
# Oligo splitting - this time reading from a file and not asking for user
# input
#####
fin_barrel = None
fin_lid = None
       
try:
        fin_barrel = open("barrel_oligos_to_split.txt", "r")
        fin_lid = open("lid_oligos_to_split.txt", "r")
except IOError, e:
        print "Error in file IO: ", e
       
# Ask the user if they are running a lid or a barrel
shape = int(raw_input("Enter 1 if you are running a barrel, 2 if lid: "))
if (shape == 1):
        oligos_to_split = pickle.load(fin_barrel)
elif (shape == 2):
        oligos_to_split = pickle.load(fin_lid)
else:
        print 'Please modify code or run with lid or 30hb barrel'
 
 
new_OTP_ra = OTP_ra[:]
for pair in oligos_to_split:
        oligo_num = pair[0]
        print oligo_num
        num_toks = pair[1]
        print num_toks
 
        new_OTP_ra = split_oligo(new_OTP_ra, oligo_num, num_toks)
       
        print new_OTP_ra
        print len(OTP_ra)
        print len(new_OTP_ra)
 
# if it's the barrel design and so that all the numbers aren't messed
# up, the 7bp token on the start of strand 10 needs to be removed
# because it's going to be left unpaired
if (shape == 1):
        new_OTP_ra = new_OTP_ra[:61] + new_OTP_ra[62:]
 
if fin_barrel: fin_barrel.close()
if fin_lid: fin_lid.close()
       
</pre>
 
==Pickle Split Parameters==
<pre>
### split = [[oligo_num, num_tokens for oligo_1 - from 5prime], ... ]
 
import pickle
 
fout_barrel = None
fout_lid = None
 
try:
        fout_barrel = open("barrel_oligos_to_split.txt", "w")
        fout_lid = open("lid_oligos_to_split.txt", "w")
except IOError, e:
        print "Error in file IO: ", e
 
barrel_split = [[56, 2], [57, 3], [41, 3], [26, 3], [21, 4]]
lid_split = [[27, 4], [2, 4]]
 
pickle.dump(barrel_split, fout_barrel)
pickle.dump(lid_split, fout_lid)
 
# clean up if they're open
if fout_barrel:
        fout_barrel.close()
if fout_lid:
        fout_lid.close()
</pre>
 
 
==Add aptamers==
<pre>
#######
# Add aptamers to the ends of the appropriate oligos.
#######
 
# Constants
apt_seq = 'GGTTGGTGTGGTTGG'
T_linker = 'TTT'
       
print oligo_ra
num_aptamers = int(raw_input('How many aptamers do you want to add? '))
i = 0 
while i < num_aptamers:
        oligo_num = int(raw_input('Which oligo needs an aptamer? '))
        if oligo_num < len(oligo_ra):
                # Add the aptamer to that oligo
                oligo_ra[oligo_num] = oligo_ra[oligo_num] + T_linker + apt_seq
                i = i + 1
        else:
                print 'oligo ' + str(oligo_num) + ' out of range.'
 
print oligo_ra
</pre>
 
==Add aptamers using File Input rather than User Input==
<pre>
#####
# Add apts this time using file input instead of user input
#####
                       
# Constants
apt_seq = 'GGTTGGTGTGGTTGG'
T_linker = 'TTT'
                       
fin_barrel = None
                       
try:
        fin_barrel = open("barrel_apts_to_add.txt", "r")
except IOError, e:
        print "Error in file IO: ", e
 
# Ask the user if they are running a lid or a barrel
shape = int(raw_input("Enter 1 if you are running a barrel, 2 if lid: "))
if (shape == 1): 
        apts_to_add = pickle.load(fin_barrel)
        for apt_specs in apts_to_add:
                oligo_num = apt_specs[0]
                type = apt_specs[1]
                if (type == 1):
                        # apt is pointing in so add 'I' as a flag at the end
                        oligo_ra[oligo_num] = oligo_ra[oligo_num] + T_linker + apt_seq + 'I'
                elif(type == 2):
                        # apt is pointing out so add 'O' as a flag
                        oligo_ra[oligo_num] = oligo_ra[oligo_num] + T_linker + apt_seq + 'O'
                else:
                        # incorrect type
                        print 'Bad input - aptamer needs to be pointing in or out'
 
</pre>
 
 
 
==Print Aptamer Oligos==
Oligo sorting - find an print out those with aptamers
 
<pre>
 
##### 
# oligo sorting
#####
 
# sort based on whether or not there's an aptamer attached to the end of
# an oligo
       
apt = re.compile('TTTGGTTGGTGTGGTTGG')
oligo_num = 0
for oligo in oligo_ra: 
        m = apt.search(oligo)
        if m:
                print 'Match found: ', oligo + ' : ' + str(oligo_num)
        else:
                print 'No match' + str(oligo_num)
        oligo_num = oligo_num + 1
 
 
</pre>
 
==Modifications to honeycomb_v1 scripts==
*Modifications to William's program to print each oligo number next to what tokens it represents
<pre>
oligo_num = 0
for oligo in OTP_ra:
        for token in oligo:
                print str(oligo_num) + ": ", token
        oligo_num = oligo_num + 1
</pre>
 
*Modifications to William's program to print a grid of oligo numbers completely filled in
* add this part to main (AAA or BBB)
<pre>
####
# generate and print the oligo grid
####
 
# Initialize the grid with all periods
num_strands = len(TPP_ra)
num_subzones = len(TPP_ra[0])
 
sub_token_visit_ra = ['.' for subzone_num in range(num_subzones)]
grid_ra = [sub_token_visit_ra[:] for strand_num in range(num_strands)]
       
oligo_num = 0
for oligo in OTP_ra:
        grid_ra = generate_oligo_path(oligo, oligo_num, grid_ra)
        oligo_num = oligo_num + 1
print grid_ra
       
print_all_oligos(grid_ra, num_strands, num_subzones)
 
</pre>
 
* add this part to honeycomb_pointers_v1.py
<pre>
# The idea here is to have a function that adds the numbers of one oligo path
# to the appropriate places in the big grid array. Eventually this will be printed
# in main. Also it needs to be initialized in main. Oligo_path is the path of
# one oligo, while grid_ra is the grid that is constantly being updated until
# it is printed in main. oligo_num is number that will be inputed to the grid_ra.
                       
def generate_oligo_path(oligo_path, oligo_num, grid_ra):
        num_path_tokens = len(oligo_path)
               
# Assign visits
        for path_token_num in range(num_path_tokens):
                token = oligo_path[path_token_num]
                strand = token[0]
                subzone = token[1]
                grid_ra[strand][subzone] = oligo_num
       
       
        return grid_ra
 
def print_all_oligos(grid_ra, num_strands, num_subzones):
        spacer = '  '
        for strand_num in range(num_strands):
                for subzone_num in range(num_subzones):
                        visitor_string = str(grid_ra[strand_num][subzone_num]) 
                        sys.stdout.write(visitor_string)
                        sys.stdout.write(spacer[:4 - len(visitor_string)])
                sys.stdout.write('\n') 
</pre>
 
== honeycomb_pointers_v1.py ==
 
<pre>
#!/usr/bin/python
 
import sys
 
######
# This function reads in the node array from a text file
# It adds a border of nodes automatically
######
def read_text_format_node_array(filename):
# Read in file
input_file = file(filename, 'r')
lines = input_file.readlines()
input_file.close()
row_string_ra = [line[:-1] for line in lines]
 
# Check to make sure each line is the same length
no_length_violation = True
length = len(row_string_ra[0])
for row_string in row_string_ra:
if len(row_string) != length and len(row_string) != 0:
sys.stdout.write('ERROR: Not all lines of inputted node lattice array are the same length.\n')
sys.stdout.write('Length is ' + str(len(row_string)) + '\n')
no_length_violation = False
 
# Parse into pre node array
pre_node_ra = []
for row_string in row_string_ra:
num_row_nodes = len(row_string)/3
sub_pre_node_ra = []
for row_node_num in range(num_row_nodes):
sub_pre_node_ra.append(row_string[row_node_num*3:row_node_num*3 + 3])
if sub_pre_node_ra != []:
pre_node_ra.append(sub_pre_node_ra)
 
# Parse pre node array into node array
num_rows = len(pre_node_ra)/2
num_row_nodes = len(pre_node_ra[0])
node_ra = [['.' for row_node_num in range(num_row_nodes + num_row_nodes%2 + 2)]]
for row_num in range(num_rows):
sub_node_ra = ['.']
for row_node_num in range(num_row_nodes):
pre_node_string = pre_node_ra[row_num*2 + (row_node_num + row_num)%2][row_node_num]
if pre_node_string == '...':
node = '.'
else:
node = int(pre_node_string)
sub_node_ra.append(node)
sub_node_ra.append('.')
if num_row_nodes%2 == 1:
sub_node_ra.append('.')
node_ra.append(sub_node_ra)
node_ra.append(['.' for row_node_num in range(num_row_nodes + num_row_nodes%2 + 2)])
 
# Check for parity violations
num_parity_violations = 0
for row_num in range(num_rows):
for row_node_num in range(num_row_nodes):
node = node_ra[row_num][row_node_num]
if node != '.':
if (node + row_num + row_node_num)%2 == 1:
sys.stdout.write('ERROR: Parity violation for strand ' + str(node) + '.\n')
sys.stdout.write('Parity is the row number plus the row-node number.\n')
sys.stdout.write('Make sure even-numbered strands are on even-parity nodes.\n')
sys.stdout.write('Make sure odd-numbered strands are on odd-parity nodes.\n')
num_parity_violations += 1
 
if num_parity_violations > 0 and no_length_violations == True:
return
else:
return node_ra
 
 
 
 
 
 
######
# This function prints the node lattice array in a honeycomb format
######
def print_node_lattice_array(node_ra):
sys.stdout.write('\nNODE LATTICE ARRAY\n')
zeroes = '000'
for y in range(len(node_ra)):
even_row_string = ''
odd_row_string = '  '
for x in range(len(node_ra[0])):
string_element = str(node_ra[y][x])
if string_element == '.':
string_element += '..'
else:
string_element = zeroes[:3 - len(string_element)] + string_element
if x%2 == 0:
even_row_string += string_element + '  '
else:
odd_row_string += string_element + '  '
if y%2 == 0:
sys.stdout.write(even_row_string + '\n')
sys.stdout.write(odd_row_string + '\n')
else:
sys.stdout.write(odd_row_string + '\n')
sys.stdout.write(even_row_string + '\n')
sys.stdout.write('\n')
sys.stdout.write('\n\n')
 
return
 
 
 
 
 
 
######
# This function inputs the node array and the number of 42bp zones
# and returns a token pointer pair array
######
def token_pointer_pair_array(node_ra, num_zones, periodic_structure_flag):
# Initialize the offset array
even_offset_ra = [[ 0,  1], [ 0, -1], [-1, 0]]
odd_offset_ra  = [[ 0, -1], [ 0,  1], [ 1, 0]]
offset_ra = [even_offset_ra, odd_offset_ra]
 
#Initialize the token pointer pair array
strand_list_ra = []
for sub_node_ra in node_ra:
for node in sub_node_ra:
if node != '.' and strand_list_ra.count(node) == 0:
strand_list_ra.append(node)
num_strands = len(strand_list_ra)
 
TPP_ra = []
num_subzones = num_zones*6
for strand_num in range(num_strands):
sub_TPP_ra = []
for token_num in range(num_subzones):
if strand_num%2 == 0:
previous_TP = [strand_num, (token_num + 1)%num_subzones]
if previous_TP[1] == 0 and periodic_structure_flag == False:
previous_TP[1] = -1
next_TP = [strand_num, (token_num - 1)%num_subzones]
if next_TP[1] == (num_subzones - 1) and periodic_structure_flag == False:
next_TP[1] = -1
sub_TPP_ra.append([previous_TP, next_TP])
else:
previous_TP = [strand_num, (token_num - 1)%num_subzones]
if previous_TP[1] == (num_subzones - 1) and periodic_structure_flag == False:
previous_TP[1] = -1
next_TP = [strand_num, (token_num + 1)%num_subzones]
if next_TP[1] == 0 and periodic_structure_flag == False:
next_TP[1] = -1
sub_TPP_ra.append([previous_TP, next_TP])
TPP_ra.append(sub_TPP_ra)
 
 
# Introduce crossovers based on the node array
for donor_y in range(len(node_ra)):
for donor_x in range(len(node_ra[0])):
donor_strand_num = node_ra[donor_y][donor_x]
if donor_strand_num != '.':
for position in range(3):
parity = (donor_y + donor_x)%2
acceptor_y = donor_y + offset_ra[parity][position][0]
acceptor_x = donor_x + offset_ra[parity][position][1]
acceptor_strand_num = node_ra[acceptor_y][acceptor_x]
if acceptor_strand_num != '.':
for zone_num in range(num_zones):
subzone_num = zone_num*6 + position*2 + 1 - parity
TPP_ra[donor_strand_num][subzone_num][1] = [acceptor_strand_num, subzone_num]
TPP_ra[acceptor_strand_num][subzone_num][0] = [donor_strand_num, subzone_num]
return TPP_ra
 
 
 
 
 
 
######
# This function inputs the token pointer pair array
# and returns an array of token_pointer_paths
######
def token_pointer_path_array(TPP_ra):
sub_visits_ra = [0 for i in range(len(TPP_ra[0]))]
visits_ra = [sub_visits_ra[:] for i in range(len(TPP_ra))]
path_ra = []
 
 
for strand_num in range(len(TPP_ra)):
for subzone_num in range(len(TPP_ra[0])):
if visits_ra[strand_num][subzone_num] == 0:
previous_TP = TPP_ra[strand_num][subzone_num][0]
next_TP = TPP_ra[strand_num][subzone_num][1]
num_visits = 100 * len(path_ra) + 1
visits_ra[strand_num][subzone_num] = num_visits
sub_path_ra = [[strand_num, subzone_num]]
upstream_done = False
while not upstream_done:
if previous_TP[1] == -1:
upstream_done = True
elif visits_ra[previous_TP[0]][previous_TP[1]] > 0:
upstream_done = True
else:
sub_path_ra.insert(0, previous_TP)
num_visits += 1
visits_ra[previous_TP[0]][previous_TP[1]] = num_visits
previous_TP = TPP_ra[previous_TP[0]][previous_TP[1]][0]
downstream_done = False
while not downstream_done:
if next_TP[1] == -1:
downstream_done = True
elif visits_ra[next_TP[0]][next_TP[1]] > 0:
downstream_done = True
else:
sub_path_ra.append(next_TP)
num_visits += 1
visits_ra[next_TP[0]][next_TP[1]] = num_visits
next_TP = TPP_ra[next_TP[0]][next_TP[1]][1]
# Make sure that the path begins between subzones, not in the middle of a subzone
if (sub_path_ra[0][0] + sub_path_ra[0][1])%2 == 0:
sub_path_ra = sub_path_ra[1:] + sub_path_ra[:1]
path_ra.append(sub_path_ra)
 
 
 
num_tokens_visited = 0
for sub_path_ra in path_ra:
num_tokens_visited += len(sub_path_ra)
 
sys.stdout.write('The number of tokens visited is ' + str(num_tokens_visited) + '.\n')
 
path_length_ra = [0 for i in range(1100)]
for sub_path_ra in path_ra:
path_length_ra[len(sub_path_ra)] += 1
 
for length in range(1100):
if path_length_ra[length] != 0:
sys.stdout.write('The number of paths with length ' + str(length) + ' is ' + str(path_length_ra[length]) + '.\n')
return path_ra
 
 
 
 
 
 
######
# This function inputs the token pointer path array
# and returns a list of oligos as lists of six token pointers
######
def oligo_token_pointer_array(path_ra):
OTP_ra = []
for sub_path_ra in path_ra:
for oligo_num in range(len(sub_path_ra)/6):
OTP_ra.append(sub_path_ra[oligo_num*6:oligo_num*6 + 6])
# Take care of the remainders
if len(sub_path_ra)%6 != 0:
OTP_ra.append(sub_path_ra[-(len(sub_path_ra)%6):])
return OTP_ra
 
 
 
 
 
 
######
# This function checks to make sure each token is represented once and only once
# in the oligo token pointer lists
######
def check_token_representation(OTP_ra, TPP_ra):
CTP_ra = []
for sub_OTP_ra in OTP_ra:
for TP in sub_OTP_ra:
CTP_ra.append(TP)
 
num_strands = len(TPP_ra)
num_subzones = len(TPP_ra[0])
problems = False
 
# Check each token for single presence
for strand_num in range(num_strands):
for token_num in range(num_subzones):
if CTP_ra.count([strand_num, token_num]) == 0:
sys.stdout.write(str([strand_num, token_num]) + ' not present.\n')
problems = True
elif CTP_ra.count([strand_num, token_num]) > 1:
sys.stdout.write(str([strand_num, token_num]) + ' present more than once.\n')
problems = True
if problems == False:
sys.stdout.write('Each token is represented once and only once in the oligo token pointer lists.\n')
 
return
 
 
 
 
 
######
# This function prints the oligo path on the strand token lattice
# It is fun to see how the paths twist around the lattice
# You can use this function to help debug your program
######
def print_path(sub_path_ra, TPP_ra):
sys.stdout.write('\nONE PATH ARRAY\n')
 
num_strands = len(TPP_ra)
num_subzones = len(TPP_ra[0])
num_path_tokens = len(sub_path_ra)
# Initialize strand token lattice
sub_token_visit_ra = ['.' for subzone_num in range(num_subzones)]
token_visit_ra = [sub_token_visit_ra[:] for strand_num in range(num_strands)]
 
 
# Assign visits
for path_token_num in range(num_path_tokens):
token = sub_path_ra[path_token_num]
strand = token[0]
subzone = token[1]
token_visit_ra[strand][subzone] = path_token_num
 
# Print out strand token lattice
spacer = '  '
for strand_num in range(num_strands):
for subzone_num in range(num_subzones):
visitor_string = str(token_visit_ra[strand_num][subzone_num])
sys.stdout.write(visitor_string)
sys.stdout.write(spacer[:4 - len(visitor_string)])
sys.stdout.write('\n')
sys.stdout.write('\n')
return
# The idea here is to have a function that adds the numbers of one oligo path
# to the appropriate places in the big grid array. Eventually this will be printed
# in main. Also it needs to be initialized in main. Oligo_path is the path of
# one oligo, while grid_ra is the grid that is constantly being updated until
# it is printed in main. oligo_num is number that will be inputed to the grid_ra.
 
def generate_oligo_path(oligo_path, oligo_num, grid_ra):
num_path_tokens = len(oligo_path)
       
# Assign visits
        for path_token_num in range(num_path_tokens):
                token = oligo_path[path_token_num]
                strand = token[0]
                subzone = token[1]
                grid_ra[strand][subzone] = oligo_num
               
       
return grid_ra
 
 
def print_all_oligos(grid_ra, num_strands, num_subzones):
        spacer = '  '
        for strand_num in range(num_strands):
                for subzone_num in range(num_subzones):
                        visitor_string = str(grid_ra[strand_num][subzone_num])
                        sys.stdout.write(visitor_string)
                        sys.stdout.write(spacer[:4 - len(visitor_string)])
                sys.stdout.write('\n')
       
 
 
####
# given an oligo to split, split it and return the new list of oligos
####
def split_oligo(new_OTP_ra, oligo_num, num_toks):
 
print new_OTP_ra[oligo_num]
 
original_oligo = new_OTP_ra[oligo_num]
 
oligo_1 = original_oligo[:num_toks]
oligo_2 = original_oligo[num_toks:]
print oligo_1
print'\n'
print oligo_2
new_OTP_ra[oligo_num] = oligo_1
new_OTP_ra.insert(oligo_num + 1, oligo_2)
return new_OTP_ra
 
 
sys.stdout.write('Honeycomb pointers module installed.\n')
 
<\pre>

Latest revision as of 07:38, 27 July 2006





Modifications and Additions to Dr. Shih's Code

The code is fairly general with the exception of the Pickle Scripts which generate lists specific to Design 4 and some hardcoded lists under Oligo Sorting

Other Useful Scripts

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