Mercurial > repos > edward-kirton > phrap

annotate phrap/jgi_assembly.py @ 0:f9e4e6fe0e73 default tip

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author edward-kirton
date Tue, 07 Jun 2011 17:41:56 -0400
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f9e4e6fe0e73 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 """
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2 Assembly classes
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3 """
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4
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5 import data
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6 import logging
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7 import re
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8 import string
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9 from cgi import escape
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10 from galaxy.datatypes.metadata import MetadataElement
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11 from galaxy.datatypes import metadata
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12 import galaxy.model
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13 from galaxy import util
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14 from sniff import *
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15
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16 log = logging.getLogger(__name__)
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17
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18 class Assembly( data.Text ):
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19 """Class describing an assembly"""
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20
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21 """Add metadata elements"""
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22 MetadataElement( name="contigs", default=0, desc="Number of contigs", readonly=True, visible=False, optional=True, no_value=0 )
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23 MetadataElement( name="reads", default=0, desc="Number of reads", readonly=True, visible=False, optional=True, no_value=0 )
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24
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25
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26 class Ace(Assembly):
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27 """Class describing an assembly Ace file"""
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28
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29 file_ext = "ace"
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30
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31 # def init_meta( self, dataset, copy_from=None ):
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32 # Assembly.init_meta( self, dataset, copy_from=copy_from )
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33
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34 def set_meta( self, dataset, overwrite=True, **kwd ):
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35 """
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36 Set the number of assembled contigs and read sequences and the number of data lines in dataset.
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37 """
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38 contigs = 0
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39 reads = 0
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40 for line in file( dataset.file_name ):
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41 line = line.strip()
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42 if line and line.startswith( '#' ):
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43 # Don't count comment lines
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44 continue
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45 if line and line.startswith( 'CO' ):
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46 contigs += 1
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47 if line and line.startswith( 'RD' ):
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48 reads += 1
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49 dataset.metadata.contigs = contigs
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50 dataset.metadata.reads = reads
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51
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52 def set_peek( self, dataset, is_multi_byte=False ):
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53 if not dataset.dataset.purged:
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54 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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55 if dataset.metadata.contigs:
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56 dataset.blurb = "%s contigs" % util.commaify( str( dataset.metadata.contigs ) )
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57 else:
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58 dataset.blurb = data.nice_size( dataset.get_size() )
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59 else:
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60 dataset.peek = 'file does not exist'
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61 dataset.blurb = 'file purged from disk'
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62
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63 def sniff( self, filename ):
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64 """
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65 Determines whether the file is in ace format
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66
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67 An ace file contains these sections
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68 AS \d+ \d+
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69
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70 CO \S+ \d+ \d+ \d+ \w
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71 [atcgATCGN\*]+
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72
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73 BQ
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74 [\d\s]+
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75
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76 AF \S+ [CU] \-?\d+
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77
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78 BS \d+ \d+ \S+
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79
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80 RD \S+ \d+ \d+ \d+
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81 [ATCGN\*]+
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82
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83 QA \d+ \d+ \d+ \d+
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84 DS .*
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85
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86 Currently we only check if file begins with AS
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87
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88 >>> fname = get_test_fname( 'genome.ace' )
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89 >>> Ace().sniff( fname )
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90 True
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91 >>> fname = get_test_fname( 'genome.fasta' )
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92 >>> Ace().sniff( fname )
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93 False
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94 """
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95
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96 try:
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97 fh = open( filename )
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98 line = fh.readline()
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99 line = line.strip()
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100 if line:
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101 if line.startswith( 'AS ' ):
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102 fh.close()
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103 return True
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104 fh.close()
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105 return False
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106 except:
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107 pass
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108 return False
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109
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110 class Velveth(Assembly):
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111 composite_type='basic'
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112 file_ext = "txt"
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113
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114 def __init__(self,**kwd):
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115 Assembly.__init__(self,**kwd)
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116 self.add_composite_file('Roadmap')
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117 self.add_composite_file('Sequences')