Mercurial > repos > davidvanzessen > argalaxy_tools

comparison gene_identification.py @ 57:16c7fc1c4bf8 draft

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author davidvanzessen
date Fri, 18 Mar 2016 07:50:34 -0400
parents 2eb94c08e550
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56:2eb94c08e550 57:16c7fc1c4bf8
38 else: 38 else:
39 dic[ID] = linesplt[seqIndex] 39 dic[ID] = linesplt[seqIndex]
40 40
41 print "Number of input sequences:", len(dic) 41 print "Number of input sequences:", len(dic)
42 42
43 #old cm sequence: gggagtgcatccgccccaacccttttccccctcgtctcctgtgagaattccc
44
43 #lambda/kappa reference sequence 45 #lambda/kappa reference sequence
44 searchstrings = {"ca": "catccccgaccagccccaaggtcttcccgctgagcctctgcagcacccagccagatgggaacgtggtcatcgcctgcctgg", 46 searchstrings = {"ca": "catccccgaccagccccaaggtcttcccgctgagcctctgcagcacccagccagatgggaacgtggtcatcgcctgcctgg",
45 "cg": "ctccaccaagggcccatcggtcttccccctggcaccctcctccaagagcacctctgggggcacagcggccctgggctgcctggtcaaggactacttccccgaaccggtgacggtgtcgtggaactcaggcgccctgaccag", 47 "cg": "ctccaccaagggcccatcggtcttccccctggcaccctcctccaagagcacctctgggggcacagcggccctgggctgcctggtcaaggactacttccccgaaccggtgacggtgtcgtggaactcaggcgccctgaccag",
46 "cm": "gggagtgcatccgccccaacc"} 48 "cm": "gggagtgcatccgccccaacc"} #new (shorter) cm sequence
47 #"cm": "gggagtgcatccgccccaacccttttccccctcgtctcctgtgagaattccc"}
48 49
49 compiledregex = {"ca": [], 50 compiledregex = {"ca": [],
50 "cg": [], 51 "cg": [],
51 "cm": []} 52 "cm": []}
52 53