User:ShawnDouglas/scripts

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Current revision (14:56, 12 February 2012) (view source)
(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
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'''Misc'''
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'''DNA sequence manipulation'''
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*replace mac return character ('\r') with unix return ('\n')
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<pre>
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cat foo | tr '\r' '\n' > bar
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mv bar foo
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</pre>
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*print first n chars of STDIN
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*reverse complement & remove whitespace
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<pre>
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#!/usr/bin/python
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import string
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<syntaxhighlight lang="python">
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import sys
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complement = string.maketrans('ACGTacgt','TGCAtgca')
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import fileinput
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def comp(s):
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  return s.translate(complement)[::-1]
def nowhite(s):
def nowhite(s):
   return ''.join([c for c in s if c in string.letters])
   return ''.join([c for c in s if c in string.letters])
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seq = ''
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</syntaxhighlight>
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if len(sys.argv) > 1:
 
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  n = int(sys.argv[1])
 
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else:
 
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  sys.exit("usage: " + sys.argv[0] + " [length]")
 
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# read in sequence
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*replace mac return character ('\r') with unix return ('\n')
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for line in fileinput.input("-"):
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<pre>
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  seq = seq + nowhite(line)
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cat foo | tr '\r' '\n' > bar
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mv bar foo
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# print last n chars
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#print seq[-n:]
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# print first n chars
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print seq[:n]
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</pre>
</pre>

Current revision

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
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])


  • replace mac return character ('\r') with unix return ('\n')
cat foo | tr '\r' '\n' > bar
mv bar foo
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