protk 1.2.6.pre5 → 1.3.0.pre1
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- checksums.yaml +4 -4
- data/README.md +84 -45
- data/bin/add_retention_times.rb +9 -5
- data/bin/augustus_to_proteindb.rb +7 -11
- data/bin/interprophet.rb +28 -46
- data/bin/make_decoy.rb +16 -48
- data/bin/mascot_search.rb +57 -71
- data/bin/mascot_to_pepxml.rb +13 -26
- data/bin/msgfplus_search.rb +70 -107
- data/bin/omssa_search.rb +52 -109
- data/bin/peptide_prophet.rb +44 -119
- data/bin/pepxml_to_table.rb +24 -27
- data/bin/protein_prophet.rb +22 -82
- data/bin/protxml_to_gff.rb +22 -519
- data/bin/protxml_to_table.rb +2 -16
- data/bin/sixframe.rb +10 -32
- data/bin/tandem_search.rb +30 -403
- data/bin/tandem_to_pepxml.rb +43 -0
- data/bin/unimod_to_loc.rb +1 -1
- data/ext/{protk/decoymaker → decoymaker}/decoymaker.c +74 -21
- data/ext/decoymaker/extconf.rb +3 -0
- data/lib/protk/constants.rb +16 -2
- data/lib/protk/data/default_config.yml +2 -1
- data/lib/protk/data/tandem_gpm_defaults.xml +175 -0
- data/lib/protk/data/tandem_isb_kscore_defaults.xml +123 -0
- data/lib/protk/data/tandem_isb_native_defaults.xml +123 -0
- data/lib/protk/data/tandem_params.xml +17 -54
- data/lib/protk/fastadb.rb +2 -2
- data/lib/protk/prophet_tool.rb +1 -1
- data/lib/protk/protxml_to_gff_tool.rb +474 -0
- data/lib/protk/search_tool.rb +58 -103
- data/lib/protk/setup_rakefile.rake +9 -5
- data/lib/protk/tandem_search_tool.rb +256 -0
- data/lib/protk/tool.rb +85 -104
- data/lib/protk.rb +1 -6
- metadata +24 -103
- data/bin/annotate_ids.rb +0 -59
- data/bin/asapratio.rb +0 -27
- data/bin/blastxml_to_table.rb +0 -119
- data/bin/correct_omssa_retention_times.rb +0 -27
- data/bin/feature_finder.rb +0 -95
- data/bin/file_convert.rb +0 -164
- data/bin/generate_omssa_loc.rb +0 -42
- data/bin/gffmerge.rb +0 -208
- data/bin/libra.rb +0 -70
- data/bin/toppas_pipeline.rb +0 -84
- data/bin/uniprot_annotation.rb +0 -141
- data/bin/xls_to_table.rb +0 -52
- data/bin/xpress.rb +0 -27
- data/ext/protk/decoymaker/extconf.rb +0 -3
- data/ext/protk/simplealign/extconf.rb +0 -3
- data/lib/protk/biotools_excel_converter.rb +0 -60
- data/lib/protk/eupathdb_gene_information_table.rb +0 -158
- data/lib/protk/gapped_aligner.rb +0 -264
- data/lib/protk/protein_annotator.rb +0 -646
- data/lib/protk/spreadsheet_extensions.rb +0 -79
- data/lib/protk/xtandem_defaults.rb +0 -11
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require 'spreadsheet'
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# Add a method to the Spreadsheet::Worksheet class to insert a column
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class Spreadsheet::Worksheet < Object
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def insert_column(col,index)
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# First check to see if the length of the column equals the number of rows
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if ( col.length!=self.rows.length && self.rows.length!=0)
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raise "The length of column #{col.length} does not equal the number of rows #{self.rows.length}"
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end
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if ( col.class!=Array || index.class!=Fixnum)
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raise "Wrong arguments. Requires a column array and an integer index"
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end
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# Check for special case where there are no rows yet and if so then insert as new rows
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if ( self.rows.length==0)
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col.each_index { |i|
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self.insert_row(i,[col[i]])
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}
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else
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# Insert the column row by row. Probably inefficient but it works
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rowi=0
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self.each {|row|
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row.insert(index,col[rowi])
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rowi+=1
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}
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end
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end
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end
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class Spreadsheet::Workbook < Object
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# creates an output excel file (returning the workbook object), transcribing all original content up to the given number of rows
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# Throws an error if the input contains more than 1 worksheet
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#
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def copyBook(numrows=0)
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if ( !numrows )
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numrows=0
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end
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# Create a new workbook from scratch for writing
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outputBook = Spreadsheet::Workbook.new
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outputSheet = outputBook.create_worksheet
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# There should only be one worksheet in the input workbook
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worksheets=self.worksheets
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if ( self.worksheets.length != 1 )
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puts "More than one worksheet in this excel file. This script only operates on single worksheets"
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end
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# Get the worksheet
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inputSheet=self.worksheet 0
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# Figure out how many rows to convert if not specified
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if ( numrows==0 || numrows > (inputSheet.row_count+1))
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numrows=inputSheet.row_count
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end
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# Transcribe everything from the old worksheet to the new one
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puts "Creating new spreadsheet with #{numrows} rows"
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(0...[numrows,inputSheet.row_count].min).each { |r|
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outputSheet.insert_row(r,inputSheet.row(r))
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newRow=outputSheet.row(r)
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# After inserting the row make sure it doesn't contain any nil values
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newRow.each_index { |ci|
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if ( newRow[ci]==nil)
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newRow[ci]=""
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end
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}
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}
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outputBook
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end
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end
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