User:ShawnDouglas/scripts
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PCR
- /make-pcr-oligos.py - given target sequence, generate oligos that can be used for PCR assembly of that sequence
- /random-sequence.py - generate random DNA sequence of specified length
- /primer.py - given upstream and downstream sense sequence of region to amplify, print out correct primers
Nanostructures
- /toehold.py - given input sequence generate N-mers orthogonal (to seq and its complement) to be used as toeholds
- /hexgui.py - Tk GUI for honeycomb lattice program
Misc
- reverse complement
complement = string.maketrans('ACGTacgt','TGCAtgca') def comp(s): return s.translate(complement)[::-1]
- replace mac return character ('\r') with unix return ('\n')
cat foo | tr '\r' '\n' > bar mv bar foo
- print first n chars of STDIN
<syntax type="python">
- !/usr/bin/python
import string import sys import fileinput
def nowhite(s):
return .join([c for c in s if c in string.letters])
seq =
if len(sys.argv) > 1:
n = int(sys.argv[1])
else:
sys.exit("usage: " + sys.argv[0] + " [length]")
- read in sequence
for line in fileinput.input("-"):
seq = seq + nowhite(line)
- seq = seq[offset:] + seq[:offset] # wrap around first offset bases
- print last n chars
- print seq[-n:]
- print first n chars
print seq[:n] </syntax>
- Check for restriction site
<syntax type="python">
- return True if s DOES contain any restriction sites
- return False if s DOES NOT contain any restriction sites
def hasresite(s):
BamHI = 'ggatcc' EcoRI = 'gaattc' FokI = 'ggatg' HindIII = 'aagctt' BglII = 'agatct' XbaI = 'tctaga' XhoI = 'ctcgag' BbvCIA = 'cctcagc' BbvCIB = comp(BbvCIA)
result = False
if s.count(BamHI) > 0: #print 'BamHI found' result = True elif s.count(EcoRI) > 0: #print 'EcoRI found' result = True elif s.count(FokI) > 0: #print 'FokI found' result = True elif s.count(HindIII) > 0: #print 'HindIII found' result = True elif s.count(BglII) > 0: #print 'BglII found' result = True elif s.count(XbaI) > 0: #print 'XbaI found' result = True elif s.count(XhoI) > 0: #print 'XhoI found' result = True elif s.count(BbvCIA) > 0: #print 'BbvCI.IA found' result = True elif s.count(BbvCIB) > 0: #print 'BbvCI.IB found' result = True
return result
</syntax>