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
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