Mercurial > repos > yating-l > rename_scaffolds

annotate rename.py @ 4:e35a3509c160 draft

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planemo upload commit 3675b4447d11fb1cd75d505886e1bf693f9d07f5
author yating-l
date Thu, 26 Jul 2018 15:46:24 -0400
parents 9529a207d704
children 7c8b327f298c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 """
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2 Call rename to rename scaffolds in reference genome so that the sequence names are less than 31 characters. Rename all scaffolds to scaffold_1, scaffold_2, ..., scaffold_N and provide a name mapping file
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3 Call truncate to truncate the scaffold names that are more than 31 characters. Replace each invalid character (non-ASCII, '\t', '\n', '\x0b', '\x0c', '\r') with '_'
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4 """
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5 import sys
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6 import csv
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7 import codecs
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8 import string
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10 def rename(inputfile, outputfile, writer):
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11 with open(outputfile, 'w') as out:
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12 with codecs.open(inputfile, 'r', encoding='utf-8') as rf:
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13 lines = rf.readlines()
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14 i = 1
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15 for line in lines:
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16 if ">" in line:
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17 oldname = line[1:].rstrip()
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18 newname = "scaffold_" + str(i)
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19 line = ">" + newname + "\n"
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20 i = i+1
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21 writer.writerow([oldname.encode('utf-8'), newname])
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22 out.write(line)
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23
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24 def truncate(inputFile, outputFile, valid_characters):
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25 names = []
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26 with codecs.open(outputFile, 'w', encoding='utf-8') as out:
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27 with codecs.open(inputFile, 'r', encoding='utf-8') as rf:
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28 lines = rf.readlines()
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29 for l in lines:
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30 if ">" in l:
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31 print l.encode('utf-8')
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32 name = l[1:].rstrip()
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33 name = substituteNonAscii(name, valid_characters)
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34 if len(name) > 31:
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35 name = name[:31]
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36 print "\tTruncate the scaffold name to less than 31 characters: %s" % name
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37 if name in names:
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38 sys.exit("Name conflict! Name " + name + " already exist.")
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39 names.append(name)
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40 l = ">" + name + "\n"
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41 print "======================\n"
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42 out.write(l)
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43
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44 def substituteNonAscii(str, valid_charaters):
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45 l = []
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46 for c in str:
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47 if c not in valid_charaters:
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48 print "\tSubstitute invalid character %s with _" % c.encode('utf-8')
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49 c = '_'
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50 l.append(c)
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51 return "".join(l)
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52
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53 def main():
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54 inputfile = str(sys.argv[1])
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55 manipulate = str(sys.argv[2])
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56 outputfile = str(sys.argv[3])
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57 valid_characters = string.letters + string.punctuation + string.digits + ' '
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58 if manipulate == "rename":
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59 indexfile = str(sys.argv[4])
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60 csvfile = open(indexfile, 'w')
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61 writer = csv.writer(csvfile)
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62 rename(inputfile, outputfile, writer)
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63 elif manipulate == "truncate":
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64 truncate(inputfile, outputfile, valid_characters)
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66 if __name__ == "__main__":
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67 main()
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