Mercurial > repos > yating-l > rename_tracks

annotate rename_tracks.py @ 0:8b19a698d90e draft

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planemo upload commit b615ca3bfed9f2115f62d1af30d4726fe8ba08d8
author yating-l
date Mon, 25 Jun 2018 15:01:41 -0400
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children 72ccb2f848a0
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8b19a698d90e planemo upload commit b615ca3bfed9f2115f62d1af30d4726fe8ba08d8
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1 # -*- coding: utf8 -*-
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2
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3 """
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4 Rename the custom evidence tracks so that the tracks use the same sequence names as the renamed reference
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5 """
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6 import sys
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7 import csv
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8 import subprocess
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9 import tempfile
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10
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11 def rename_interval(inputFile, nameDict, renamedFile):
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12 writer = open(renamedFile, 'w')
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13 with open(inputFile, 'r') as f:
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14 lines = f.readlines()
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15 for l in lines:
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16 if not l.startswith("#"):
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17 scaffold_name = l.split()[0]
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18 if scaffold_name in nameDict:
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19 l = l.replace(scaffold_name, nameDict[scaffold_name])
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20 writer.write(l)
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21 writer.close()
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22
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23 def rename_bam(inputFile, nameDict, renamedFile):
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24 header = subprocess.Popen(['samtools', 'view', '-H', inputFile], stdout=subprocess.PIPE)
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25 array_call = ['sed']
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26 for k,v in nameDict.items():
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27 substitute = "s/%s/%s/" % (str(k), str(v))
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28 array_call.append('-e')
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29 array_call.append(substitute)
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30 reheader = subprocess.Popen(array_call, stdin=header.stdout, stdout=subprocess.PIPE)
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31 out = open(renamedFile, 'w')
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32 subprocess.Popen(['samtools', 'reheader', '-', inputFile], stdin=reheader.stdout, stdout=out)
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33
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34 def rename_bigwig(inputFile, renamedReference, nameDict, renamedFile):
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35 bedGraphFile = tempfile.NamedTemporaryFile(bufsize=0)
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36 chrom_sizes = tempfile.NamedTemporaryFile(bufsize=0)
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37 sorted_bedGraphFile = tempfile.NamedTemporaryFile(bufsize=0)
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38 renamed_sorted_bedGraphFile = tempfile.NamedTemporaryFile(bufsize=0)
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39
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40 subprocess.call(['bigWigToBedGraph', inputFile, bedGraphFile.name])
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41 subprocess.call(['faSize', '-detailed', '-tab', renamedReference], stdout=chrom_sizes)
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42 subprocess.call(['sort', '-k1,1', '-k2,2n', bedGraphFile.name], stdout=sorted_bedGraphFile)
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43 rename_interval(sorted_bedGraphFile.name, nameDict, renamed_sorted_bedGraphFile.name)
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44 subprocess.call(['bedGraphToBigWig', renamed_sorted_bedGraphFile.name, chrom_sizes.name, renamedFile])
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45
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46 def getNameDict(nameMapping):
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47 nameDict = {}
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48 with open(nameMapping, 'r') as f:
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49 reader = csv.reader(f)
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50 for row in reader:
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51 nameDict[row[0]] = row[1]
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52 return nameDict
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53
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54 def main():
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55 inputFile = sys.argv[1]
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56 nameMapping = sys.argv[2]
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57 inputFormat = sys.argv[3]
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58 outputfile = sys.argv[4]
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59 nameDict = getNameDict(nameMapping)
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60 if inputFormat == "bed" or inputFormat == "gff3" or inputFormat == "gtf":
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61 rename_interval(inputFile, nameDict, outputfile)
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62 elif inputFormat == "bam":
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63 rename_bam(inputFile, nameDict, outputfile)
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64 elif inputFormat == "bigwig":
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65 renamedReference = sys.argv[5]
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66 rename_bigwig(inputFile, renamedReference, nameDict, outputfile)
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67
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68 if __name__ == "__main__":
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69 main()