Difference between revisions of "User:ShawnDouglas/scripts"

From OpenWetWare
Jump to: navigation, search
m
(clean up some old python code)
 
Line 8: Line 8:
 
*[[/hexgui.py]] - Tk GUI for honeycomb lattice program
 
*[[/hexgui.py]] - Tk GUI for honeycomb lattice program
  
'''Misc'''
+
'''DNA sequence manipulation'''
*reverse complement
+
 
<pre>
+
*reverse complement & remove whitespace
 +
 
 +
<syntaxhighlight lang="python">
 
complement = string.maketrans('ACGTacgt','TGCAtgca')
 
complement = string.maketrans('ACGTacgt','TGCAtgca')
 
def comp(s):
 
def comp(s):
 
   return s.translate(complement)[::-1]
 
   return s.translate(complement)[::-1]
</pre>
+
 
 +
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')
 
*replace mac return character ('\r') with unix return ('\n')
Line 21: Line 28:
 
mv bar foo
 
mv bar foo
 
</pre>
 
</pre>
 
*print first n chars of STDIN
 
<syntax type="python">
 
#!/usr/bin/python
 
 
import string
 
import sys
 
import fileinput
 
 
def nowhite(s):
 
  return ''.join([c for c in s if c in string.letters])
 
 
seq = ''
 
 
if len(sys.argv) > 1:
 
  n = int(sys.argv[1])
 
else:
 
  sys.exit("usage: " + sys.argv[0] + " [length]")
 
 
# read in sequence
 
for line in fileinput.input("-"):
 
  seq = seq + nowhite(line)
 
 
#seq = seq[offset:] + seq[:offset]    # wrap around first offset bases
 
 
# print last n chars
 
#print seq[-n:]
 
 
# print first n chars
 
print seq[:n]
 
</syntax>
 
 
*Check for restriction site
 
<syntax type="python">
 
##
 
# return True if s DOES contain any restriction sites
 
# return False if s DOES NOT contain any restriction sites
 
##
 
def hasresite(s):
 
  BamHI = 'ggatcc'
 
  EcoRI = 'gaattc'
 
  FokI = 'ggatg'
 
  HindIII = 'aagctt'
 
  BglII = 'agatct'
 
  XbaI = 'tctaga'
 
  XhoI = 'ctcgag'
 
  BbvCIA = 'cctcagc'
 
  BbvCIB = comp(BbvCIA)
 
 
  result = False
 
 
  if s.count(BamHI) > 0:
 
    #print 'BamHI found'
 
    result = True
 
  elif s.count(EcoRI) > 0:
 
    #print 'EcoRI found'
 
    result = True
 
  elif s.count(FokI) > 0:
 
    #print 'FokI found'
 
    result = True
 
  elif s.count(HindIII) > 0:
 
    #print 'HindIII found'
 
    result = True
 
  elif s.count(BglII) > 0:
 
    #print 'BglII found'
 
    result = True
 
  elif s.count(XbaI) > 0:
 
    #print 'XbaI found'
 
    result = True
 
  elif s.count(XhoI) > 0:
 
    #print 'XhoI found'
 
    result = True
 
  elif s.count(BbvCIA) > 0:
 
    #print 'BbvCI.IA found'
 
    result = True
 
  elif s.count(BbvCIB) > 0:
 
    #print 'BbvCI.IB found'
 
    result = True
 
 
  return result
 
</syntax>
 

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