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1 '''
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2 Created on Jan 1, 2011
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3
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4 @author: John L. Herndon
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5 @contact: herndon@cs.colostate.edu
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6 @organization: Colorado State University
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7 @group: Computer Science Department, Asa Ben-Hur's laboratory
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8 '''
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9
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10 import utils
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11 import os
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12 import re
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13
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14 def parseCoordMatchLine( match ):
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15
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16 match = match.replace( '\t', ' ' )
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17 sections = match.split( '|', 4 )
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18
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19 #parse the first section, containing the start and end
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20 #locations of the match
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21 firstsection = sections[ 0 ].strip( )
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22 firstsectiontokens = re.split( ' +', firstsection )
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23 start = int( firstsectiontokens[ 0 ].strip( ) )
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24 end = int( firstsectiontokens[ 1 ].strip( ) )
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25
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26 #parse the last section, containing the sequenceID
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27 lastsection = sections[ -1 ].strip( )
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28 lastsectiontokens = re.split( " +", lastsection )
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29
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30 seqid = lastsectiontokens[ 0 ].strip( )
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31
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32 return utils.Match( start, end, seqid )
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33
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34 def parseCoordMatchFile( coordFileName ):
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35 '''
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36 A method to parse the coord file.
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37 returns a list of utils.match objects
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38 '''
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39 returnValue = [ ]
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40
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41 #throw if the file doesn't exist
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42 if os.path.exists( coordFileName ) == False:
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43 raise utils.NoFileFoundException( coordFileName )
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44
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45
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46 #read the nucmer file into memory
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47 lines = open( coordFileName ).readlines( )
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48
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49 #skip forward to the start of the matches.
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50 i = 0
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51 while lines[ i ] [ 0] != '=':
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52 i += 1
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53 matchLines = lines[ i+1 : ]
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54
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55 #parse each line for match start, end and sequenceID
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56 for matchLine in matchLines:
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57 returnValue.append( parseCoordMatchLine( matchLine ) )
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58
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59 utils.logMessage( "NucmerParser::parseCoordMatchFile( )", "Parse {0}, finding {1} matches".format( coordFileName, len( returnValue ) ) )
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60
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61 return returnValue
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62
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63
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64
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65
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66
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67
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68 |
