User:ShawnDouglas/scripts: Difference between revisions
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'''Misc''' | '''Misc''' | ||
*reverse complement | |||
<pre> | |||
def rev(s): | |||
return s[::-1] | |||
complement = string.maketrans('ACGTacgt','TGCAtgca') | |||
def comp(s): | |||
return rev(s.translate(complement)) | |||
</pre> | |||
*replace mac return character ('\r') with unix return ('\n') | *replace mac return character ('\r') with unix return ('\n') | ||
<pre> | <pre> |
Revision as of 12:43, 5 July 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
- reverse complement
def rev(s): return s[::-1] complement = string.maketrans('ACGTacgt','TGCAtgca') def comp(s): return rev(s.translate(complement))
- 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) #seq = seq[offset:] + seq[:offset] # wrap around first offset bases # print last n chars #print seq[-n:] # print first n chars print seq[:n]