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Migrated tool version 0.1 from old tool shed archive to new tool shed repository
author louise
date Tue, 07 Jun 2011 17:21:49 -0400
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97792524cc9c Migrated tool version 0.1 from old tool shed archive to new tool shed repository
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1 Here is the needed class to handle Solexa Export file type.
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2
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3 The tool and class were written by Nicolas Delhomme (delhomme@embl.de).
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4 Released under the GNU GPL: http://www.opensource.org/licenses/gpl-3.0.html
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5
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6 The threshold parameter was commented but it can very well be used. Just uncomment the commented code and comment the current command tag in the XML file.
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7
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8 If you want to apply this file as a patch, just run:
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9 patch <path_to_galaxy>/lib/galaxy/datatypes/tabular.py README
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10 ---
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11
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12 diff -r 50e249442c5a lib/galaxy/datatypes/tabular.py
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13 --- a/lib/galaxy/datatypes/tabular.py Thu Apr 07 08:39:07 2011 -0400
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14 +++ b/lib/galaxy/datatypes/tabular.py Tue May 24 14:16:12 2011 +0200
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15 @@ -504,3 +504,95 @@
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16
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17 def get_track_type( self ):
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18 return "FeatureTrack", {"data": "interval_index", "index": "summary_tree"}
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19 +
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20 +class Export( Tabular ):
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21 + file_ext = 'export'
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22 + def __init__(self, **kwd):
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23 + """Initialize export datatype"""
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24 + Tabular.__init__( self, **kwd )
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25 + self.column_names = ['MACHINE', 'RUN', 'LANE', 'TILE',
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26 + 'X', 'Y', 'MULTIPLEX', 'PAIRID',
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27 + 'READ', 'QUALITY', 'CHROMOSOME', 'CONTIG',
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28 + 'POSITION','STRAND','ALN_QUAL','CHASTITY'
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29 + ]
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30 +
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31 + def make_html_table( self, dataset, skipchars=[] ):
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32 + """Create HTML table, used for displaying peek"""
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33 + out = ['<table cellspacing="0" cellpadding="3">']
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34 + try:
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35 + # Generate column header
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36 + out.append( '<tr>' )
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37 + for i, name in enumerate( self.column_names ):
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38 + out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) )
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39 + # This data type requires at least 16 columns in the data
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40 + if dataset.metadata.columns - len( self.column_names ) > 0:
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41 + for i in range( len( self.column_names ), dataset.metadata.columns ):
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42 + out.append( '<th>%s</th>' % str( i+1 ) )
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43 + out.append( '</tr>' )
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44 + out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) )
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45 + out.append( '</table>' )
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46 + out = "".join( out )
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47 + except Exception, exc:
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48 + out = "Can't create peek %s" % exc
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49 + return out
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50 +
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51 + def set_meta( self, dataset, overwrite = True, **kwd ):
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52 +
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53 + #we'll arbitrarily only use the first 100 data lines in the export file to calculate tabular attributes (column types)
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54 + #optional metadata values set in Tabular class will be 'None'
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55 + Tabular.set_meta( self, dataset, overwrite = overwrite, max_data_lines = 100 )
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56 +
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57 + def sniff( self, filename ):
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58 + """
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59 + Determines whether the file is in Export format
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60 +
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61 + A file in Export format consists of lines of tab-separated data.
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62 + It does not have any header
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63 +
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64 + Rules for sniffing as True:
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65 + There must be 16 columns of data on each line
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66 + Columns 2 to 8 must be numbers
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67 + Column 16 should be either Y or N
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68 + We will only check that up to the first 5 alignments are correctly formatted.
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69 +
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70 + """
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71 + try:
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72 + fh = open( filename )
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73 + count = 0
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74 + while True:
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75 + line = fh.readline()
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76 + line = line.strip()
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77 + if not line:
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78 + break #EOF
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79 + if line:
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80 + if line[0] != '@':
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81 + linePieces = line.split('\t')
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82 + if len(linePieces) != 22:
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83 + return False
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84 + try:
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85 + check = int(linePieces[1])
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86 + check = int(linePieces[2])
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87 + check = int(linePieces[3])
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88 + check = int(linePieces[4])
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89 + check = int(linePieces[5])
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90 + check = int(linePieces[6])
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91 + check = int(linePieces[7])
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92 + assert linePieces[21] in [ 'Y', 'N' ]
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93 + except ValueError:
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94 + return False
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95 + count += 1
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96 + if count == 5:
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97 + return True
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98 + fh.close()
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99 + if count < 5 and count > 0:
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100 + return True
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101 + except:
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102 + pass
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103 + return False
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104 +
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105 +class BarcodeSet( Tabular ):
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106 + file_ext = 'bs'
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107 + column_names = ['SAMPLE', 'BARCODE']
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108 +
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109 + def sniff( self, filename ):
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110 + return False
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111
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