Mercurial > repos > abims-sbr > mutcount

annotate scripts/functions.py @ 2:988467f963f0 draft

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planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
author abims-sbr
date Wed, 17 Jan 2018 08:57:49 -0500
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children f1e24200e5ae
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988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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1 def simplify_fasta_name(fasta_name,LT):
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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2 for abbreviation in LT:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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3 if abbreviation in fasta_name:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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4 new_fasta_name = abbreviation
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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6 return(new_fasta_name)
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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8 ## Generates bash, with key = fasta name; value = sequence (WITH GAP, IF ANY, REMOVED IN THIS FUNCTION)
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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9 def dico(fasta_file,LT):
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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11 count_fastaName=0
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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12 F1 = open(fasta_file, "r")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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14 bash1 = {}
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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15 while 1:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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16 nextline = F1.readline()
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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17 #print nextline
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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18 if not nextline :
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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19 break
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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21 if nextline[0] == ">":
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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22 count_fastaName = count_fastaName + 1
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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23 fasta_name = nextline[1:-1]
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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24 nextline = F1.readline()
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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25 sequence = nextline[:-1]
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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27 if fasta_name not in bash1.keys():
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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28 fasta_name = simplify_fasta_name(fasta_name,LT) ### DEF 0 ###
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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29 bash1[fasta_name] = sequence
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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30 else:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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31 print fasta_name
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33 # Find alignment length
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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34 kk = bash1.keys()
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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35 key0 = kk[0]
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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36 seq0 = bash1[key0]
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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37 ln_seq = len(seq0)
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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39 F1.close()
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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41 return(bash1)