Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/PalsToAlign.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 import time |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 import os |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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4 class PalsToAlign(object): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 """ |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 Convert the output from PALS (GFF2 format) into the 'align' format. |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 """ |
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8 def __init__(self,inputPalsFileName="" , outputAlignFileName="", removeSameSequences=False): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 self._removeSameSequences = removeSameSequences |
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10 self._inputPalsFileName = inputPalsFileName |
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11 self._outputAlignFileName = outputAlignFileName |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 |
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13 def run (self): |
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14 file = open(self._inputPalsFileName, "r") |
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15 tmpFileName = "PalsToAlign%s"%str(os.getpid() ) |
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16 tmpFile = open(tmpFileName, "w") |
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17 |
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18 for line in file.readlines(): |
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19 |
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20 if line == "": |
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21 break |
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22 |
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23 data = line.split("\t") |
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24 |
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25 qryName = data[0] |
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26 source = data[1] |
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27 feature = data[2] |
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28 qryStart = data[3] |
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29 qryEnd = data[4] |
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30 score = data[5] |
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31 strand = data[6] |
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32 frame = data[7] |
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33 attributes = data[8][:-1].split() |
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34 |
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35 sbjName = attributes[1] |
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36 sbjStart = attributes[2] |
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37 sbjEnd = attributes[3][:-1] |
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38 percId = (1 - float(attributes[-1])) * 100.0 |
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39 |
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40 if strand != "+": |
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41 tmp = sbjStart |
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42 sbjStart = sbjEnd |
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43 sbjEnd = tmp |
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44 |
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45 if self._removeSameSequences \ |
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46 and "chunk" in qryName and "chunk" in sbjName \ |
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47 and min(int(qryStart), int(qryEnd)) == 1 \ |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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48 and min(int(sbjStart), int(sbjEnd)) == 1 \ |
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49 and percId == 100.0: |
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50 line = self.inFile.readline() |
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51 continue |
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52 |
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53 if qryStart < qryEnd: |
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54 alignLine = "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (qryName, qryStart, qryEnd, sbjName, sbjStart, sbjEnd, "0.0", score, percId) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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55 else: |
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56 alignLine = "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (qryName, qryEnd, qryStart, sbjName, sbjEnd, sbjStart, "0.0", score, percId) |
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57 |
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58 tmpFile.write(alignLine) |
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59 |
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60 file.close() |
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61 tmpFile.close() |
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62 |
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63 os.system("sort -k 1,1 -k 4,4 -k 2,2n -k 3,3n -k 5,5n -k 6,6n -k 8,8n %s > %s" % (tmpFileName, self._outputAlignFileName)) |
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64 os.remove(tmpFileName) |
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65 |
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66 |