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annotate orthologs/ucsb_hamster/unbuild.py @ 0:5b9a38ec4a39 draft default tip

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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/usr/bin/env python
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2 '''
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3 Usage: unbuild.py outputDirectoryName hmmFileWithTabs
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4 This script takes a tab sperated, newline escaped HMM models file then splits the models up and makes a file list.
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5 The output files are put into the directory outputDirectoryName.
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6 '''
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 from sys import argv, exit
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 import os
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9
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10
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11 def parse(line):
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12 line = line.partition('\t')
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13 name = line[0] + ".hmm"
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14 data = line[2].replace("\\n", "\n")
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15 return name, data
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16
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17
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18 def writeFile(location, data):
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19 try:
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20 with open(location, 'w') as f:
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21 f.write(data)
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22 except:
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23 pass
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24
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25
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26 def createDir(dir):
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27 if not os.path.exists(dir):
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28 os.makedirs(dir)
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29
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30
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31 if __name__ == "__main__":
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32 if len(argv) != 3:
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33 print "Usage: unbuild.py outputDirectoryName hmmFileWithTabs"
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34 exit()
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35 dir = argv[1]
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36 createDir(dir)
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37
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38 name_list = [] # Stores new file names
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39
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40 # Read data and seperate into files.
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41 with open(argv[2], 'r') as f:
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42 for line in f:
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43 name, data = parse(line)
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44 if data.strip() == "": # no data? skip it.
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45 continue
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46 name_list.append(name)
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47 name = dir + os.sep + name
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48 writeFile(name, data)
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49
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50 # Write new file names to a file.
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51 name_list_location = dir + os.sep + "hmmlist.txt"
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52 with open(name_list_location, 'w') as f:
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53 for name in name_list:
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54 f.write(name + "\n")