User:ShawnDouglas/scripts

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cat foo | tr '\r' '\n' > bar
cat foo | tr '\r' '\n' > bar
mv bar foo
mv bar foo
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</pre>
 +
 +
*print first n chars of STDIN
 +
<pre>
 +
#!/usr/bin/python
 +
 +
import string
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import sys
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import fileinput
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 +
def nowhite(s):
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  return ''.join([c for c in s if c in string.letters])
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 +
seq = ''
 +
 +
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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for line in fileinput.input("-"):
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  seq = seq + nowhite(line)
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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]
</pre>
</pre>

Revision as of 10:26, 27 June 2006

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

Misc

  • replace mac return character ('\r') with unix return ('\n')
cat foo | tr '\r' '\n' > bar
mv bar foo
  • print first n chars of STDIN
#!/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)

# print last n chars
#print seq[-n:]

# print first n chars
print seq[:n]
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