User:ShawnDouglas/scripts: Difference between revisions
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cat foo | tr '\r' '\n' > bar | cat foo | tr '\r' '\n' > bar | ||
mv bar foo | mv bar foo | ||
</pre> | |||
*print first n chars of STDIN | |||
<pre> | |||
#!/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] | |||
</pre> | </pre> |
Revision as of 08:26, 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]