User:ShawnDouglas/scripts

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

DNA sequence manipulation

• reverse complement & remove whitespace

<syntaxhighlight lang="python"> complement = string.maketrans('ACGTacgt','TGCAtgca') def comp(s):

 return s.translate(complement)[::-1]

def nowhite(s):

 return .join([c for c in s if c in string.letters])

</syntaxhighlight>

• replace mac return character ('\r') with unix return ('\n')

cat foo | tr '\r' '\n' > bar
mv bar foo