User:ShawnDouglas/scripts: Difference between revisions
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XhoI = 'ctcgag' | XhoI = 'ctcgag' | ||
BbvCIA = 'cctcagc' | BbvCIA = 'cctcagc' | ||
BbvCIB = | BbvCIB = comp(BbvCIA) | ||
result = False | result = False |
Revision as of 09:33, 12 December 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
complement = string.maketrans('ACGTacgt','TGCAtgca') def comp(s): return s.translate(complement)[::-1]
- 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]
- Check for restriction site
## # 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