User:ShawnDouglas/scripts: Difference between revisions
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ShawnDouglas (talk | contribs) (clean up some old python code) |
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*[[/toehold.py]] - given input sequence generate N-mers orthogonal (to seq and its complement) to be used as toeholds | *[[/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 | *[[/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') | |||
<pre> | |||
cat foo | tr '\r' '\n' > bar | |||
mv bar foo | |||
</pre> | |||
Latest revision as of 11:56, 12 February 2012
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
