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annotate Group.py @ 0:57299471d6c1 draft default tip

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planemo upload commit 402a746f69e9f1dbb57007536fc36dc6ce3180de
author yating-l
date Wed, 12 Apr 2017 17:37:47 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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57299471d6c1 planemo upload commit 402a746f69e9f1dbb57007536fc36dc6ce3180de
yating-l
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1 from operator import itemgetter
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2
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3 # Input: A group: a list that contains lines belonging to the same gene
57299471d6c1 planemo upload commit 402a746f69e9f1dbb57007536fc36dc6ce3180de
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4 class Group:
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5 # Modify "type" column and "attributes" colunm, initialize id, gene, source, stream
57299471d6c1 planemo upload commit 402a746f69e9f1dbb57007536fc36dc6ce3180de
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6 def __init__(self, group):
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7 self.group = group
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8 self.id = str(group[0][0])
57299471d6c1 planemo upload commit 402a746f69e9f1dbb57007536fc36dc6ce3180de
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9 self.source = str(group[0][1])
57299471d6c1 planemo upload commit 402a746f69e9f1dbb57007536fc36dc6ce3180de
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10 self.stream = str(group[0][6])
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11 self.gene = str(group[0][8])
57299471d6c1 planemo upload commit 402a746f69e9f1dbb57007536fc36dc6ce3180de
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12 for x in range(0, len(group)):
57299471d6c1 planemo upload commit 402a746f69e9f1dbb57007536fc36dc6ce3180de
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13 self.group[x][2] = "CDS"
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14 self.group[x][8] = "Parent=mRNA_" + self.gene
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15 self.group[x][3] = int(self.group[x][3])
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16 self.group[x][4] = int(self.group[x][4])
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17
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18 # Order the group elements accoriding to Stream, +: ascanding order, -: descanding order
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19 def order(self):
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20 self.num = len(self.group)
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21 if self.stream == "+":
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22 self.group = sorted(self.group, key=itemgetter(3))
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23 self.min_item = self.group[0][3]
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24 self.max_item = self.group[self.num-1][4]
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25 elif self.stream == "-":
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26 self.group = sorted(self.group, key=itemgetter(3), reverse=True)
57299471d6c1 planemo upload commit 402a746f69e9f1dbb57007536fc36dc6ce3180de
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27 self.min_item = self.group[self.num-1][3]
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28 self.max_item = self.group[0][4]
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29 else:
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30 print("Stream in invalid!\n")
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31
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32 def phaseCalculator(self, i, donor = 0):
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33 if i >= self.num:
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34 pass
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35 else:
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36 self.type = self.group[i][2]
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37 self.size = self.group[i][4] - self.group[i][3] + 1
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38 if self.num == 1:
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39 if self.type == "Eterm":
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40 self.group[i][7] = str(self.size % 3)
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41 else:
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42 self.group[i][7] = "0"
57299471d6c1 planemo upload commit 402a746f69e9f1dbb57007536fc36dc6ce3180de
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43 elif self.num > 1 and i < self.num:
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44 accept = (3 - donor) % 3
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45 self.group[i][7] = str(accept)
57299471d6c1 planemo upload commit 402a746f69e9f1dbb57007536fc36dc6ce3180de
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46 donor = (self.size - accept) % 3
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47 i = i + 1
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48 self.phaseCalculator(i, donor)
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49
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50
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51 def writer(self, gff3):
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52 self.order()
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53 self.phaseCalculator(0)
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54 gff3.write(self.id + "\t" + self.source + "\tgene\t" + str(self.min_item) + "\t" + str(self.max_item) + "\t.\t" + self.stream + "\t.\t" + "ID=" + self.gene + "\n")
57299471d6c1 planemo upload commit 402a746f69e9f1dbb57007536fc36dc6ce3180de
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55 gff3.write(self.id + "\t" + self.source + "\tmRNA\t" + str(self.min_item) + "\t" + str(self.max_item) + "\t.\t" + self.stream + "\t.\t" + "ID=mRNA_" + self.gene + ";Parent=" + self.gene + "\n")
57299471d6c1 planemo upload commit 402a746f69e9f1dbb57007536fc36dc6ce3180de
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56 for x in range(0, len(self.group)):
57299471d6c1 planemo upload commit 402a746f69e9f1dbb57007536fc36dc6ce3180de
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57 self.group[x][3] = str(self.group[x][3])
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58 self.group[x][4] = str(self.group[x][4])
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59 gff3.write("\t".join(self.group[x]) + "\n")