Mercurial > repos > charles_s_test > seqsero2

annotate libs/Initial_functions.py @ 16:ed79f56d2184 draft default tip

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planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
author charles_s_test
date Thu, 30 Nov 2017 16:58:25 -0500
parents 6895de35a263
children
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1 #!/usr/bin/env python
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4 def To_list(L):
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5 import string
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6 New_list=[]
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7 for x in L:
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8 x1=x[:-1]
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9 x1=string.atoi(x1)
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10 New_list.append(x1)
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11 return New_list
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14 def Uniq(L): #return the uniq list and the count number
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15 Old=L
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16 L.sort()
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17 L = [L[i] for i in range(len(L)) if L[i] not in L[:i]]
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18 count=[]
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19 for j in range(len(L)):
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20 y=0
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21 for x in Old:
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22 if L[j]==x:
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23 y+=1
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24 count.append(y)
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25 return (L,count)
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28 def Parse_seros_in_genome_trakr(L): #return the sero names in the sra_result.xlsx, the next step is usually "Uniq" in above
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29 names2=[]
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30 for x in L:
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31 if "serovar" in x:
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32 key_word=x.split("serovar")[1].split("_")[1] #the seronames
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33 if key_word!="str." and key_word!="group": #to eliminate some "serovar_str." and "serovar_group"
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34 if key_word in ["I","II","III","IIIa","IIIb","IV","VI","B"]: #the serovar is behind those letters
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35 if x.split("serovar")[1].split("_")[2]!="str.":
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36 names2.append(x.split("serovar")[1].split("_")[2])
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37 else:
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38 names2.append(x.split("serovar")[1].split("_")[1])
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39 return names2
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