Difference between revisions of "User:ShawnDouglas/scripts"

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(clean up some old python code)
 
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*[[/hexgui.py]] - Tk GUI for honeycomb lattice program
 
*[[/hexgui.py]] - Tk GUI for honeycomb lattice program
  
'''Misc'''
+
'''DNA sequence manipulation'''
*replace mac return character (\015) with unix return (\015\012)
+
 
<pre>cat file | tr '\r' '\n'</pre>
+
*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 10:56, 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