protk 1.2.6.pre1 → 1.2.6.pre2

data/bin/mascot2xml.rb

@@ -1,87 +0,0 @@
-#!/usr/bin/env ruby
-#
-# This file is part of protk
-# Created by Ira Cooke 12/4/2010
-#
-# Convert mascot dat files to pepxml without using TPP Mascot2XML 
-#
-
-
-require 'protk/constants'
-require 'protk/search_tool'
-require 'mascot/dat'
-require 'libxml'
-
-include LibXML
-
-
-
-
-# Environment with global constants
-#
-genv=Constants.new
-
-tool=SearchTool.new([:database,:explicit_output,:over_write])
-tool.option_parser.banner = "Convert mascot dat files to pep.xml files.\n\nUsage: mascot2xml.rb [options] file1.dat file2.dat ... "
-tool.option_parser.parse!
-
-throw "Only one file at a time is allowed when using explicit output" if (tool.explicit_output && ARGV.length > 1)
-
-def update_msms_pipeline_analysis(pepxml_doc,mascot_dat,outname)
-  pipeline_analysis_node=pepxml_doc.find("//#{$pepxml_ns_prefix}msms_pipeline_analysis", $pepxml_ns)[0]
-  pipeline_analysis_node.attributes['date']=Time.at(mascot_dat.header.date.to_i).to_s
-  pipeline_analysis_node.attributes['summary_xml']=outname
-end
-
-def update_enzyme(pepxml_doc,mascot_dat)
-  dat_enzyme=mascot_dat.enzyme
-  enzyme_node=pepxml_doc.find("//#{$pepxml_ns_prefix}sample_enzyme", $pepxml_ns)[0]
-  enzyme_node.attributes['name']=dat_enzyme.title
-  specificity=enzyme_node.find("./#{$pepxml_ns_prefix}specificity",$pepxml_ns)[0]
-#  p dat_enzyme.cleavages
-  # TODO: What does the spec say about multiple cut sites
-#  specificity.attributes['cut']=
-end
-
-
-
-ARGV.each do |file_name| 
-  name=file_name.chomp
-
-  dat = Mascot::DAT.open(name)
-  pepxml_template_parser=XML::Parser.file("#{genv.data_lib_dir}/pepxml_mascot_template.xml")
-  pepxml_doc = pepxml_template_parser.parse
-
-  outname = nil
-  if ( tool.explicit_output !=nil)
-    outname = tool.explicit_output
-  else
-    basename = Pathname.new(name).basename
-    outname = "#{basename}.pepXML"
-  end
-
-  $pepxml_ns_prefix="xmlns:"
-  $pepxml_ns="xmlns:http://regis-web.systemsbiology.net/pepXML"
-  if not pepxml_doc.root.namespaces.default
-    $pepxml_ns_prefix=""
-    $pepxml_ns=nil
-  end
-
-  update_msms_pipeline_analysis(pepxml_doc,dat,outname)
-  update_enzyme(pepxml_doc,dat)
-
-  spectrum_queries={}
-
-  dat.peptides.each do |psm|
-    # psm.score
-    qnum= psm.query
-    if qnum
-      qid=qnum.to_s
-      spectrum_queries[qid]=[] if ( spectrum_queries[qid]==nil) 
-      spectrum_queries[qid] << psm
-    end
-  end
-
-  spectrum_queries.each_pair { |name, val| p "#{name} #{val[0].pep}" }
-
-end

data/ext/protk/simplealign/simplealign.c

@@ -1,17 +0,0 @@
-
-
-static VALUE simplealign_align (VALUE self, VALUE pep_in, VALUE n_in, VALUE gene_in,VALUE m_in)
-{
-  unsigned int n = NUM2INT(n_in);
-  unsigned int m = NUM2INT(m_in);
-
-  char *peptide = RSTRING_PTR(pep_in);
-  char *gene = RSTRING_PTR(gene_in);
-}
-void Init_simplealign(void)
-{
-  VALUE klass = rb_define_class("SimpleAlign",rb_cObject);
-
-  rb_define_singleton_method(klass,
-    "align",simplealign_align , 9);
-}

data/lib/protk/data/pepxml_mascot_template.xml

@@ -1,29 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<?xml-stylesheet type="text/xsl" href="/home/iracooke/.protk/tools/tpp/schema/pepXML_std.xsl"?>
-<msms_pipeline_analysis date="2013-01-07T18:29:15" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://regis-web.systemsbiology.net/pepXML /home/iracooke/.protk/tools/tpp/schema/pepXML_v117.xsd" summary_xml="/home/iracooke/FionaHela/mr176/mr176-HeLa4hrx2_GC1_01_8136.d_mascot2xml.pep.xml">
-  <msms_run_summary base_name="/home/iracooke/FionaHela/mr176/mr176-HeLa4hrx2_GC1_01_8136.d_mascot2xml" raw_data_type="raw" raw_data="(null)">
-<sample_enzyme name="trypsin">
-<specificity cut="KR" no_cut="P" sense="C"/>
-</sample_enzyme>
-<search_summary base_name="/home/iracooke/FionaHela/mr176/mr176-HeLa4hrx2_GC1_01_8136.d_mascot2xml" search_engine="MASCOT" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1">
-<search_database local_path="/home/iracooke/.protk/Databases/sphuman/current.fasta" type="AA"/>
-<enzymatic_search_constraint enzyme="trypsin" max_num_internal_cleavages="2" min_number_termini="2"/>
-<aminoacid_modification aminoacid="C" massdiff="57.0215" mass="160.0306" variable="N"/>
-<parameter name="" value=""/>
-</search_summary>
-    <spectrum_query spectrum="" start_scan="" end_scan="" precursor_neutral_mass="" assumed_charge="" index="">
-    <search_result>
-      <search_hit hit_rank="" peptide="" peptide_prev_aa="" peptide_next_aa="" protein="" num_tot_proteins="" num_matched_ions="" tot_num_ions="" calc_neutral_pep_mass="" massdiff="" num_tol_term="" num_missed_cleavages="" is_rejected="">
-<modification_info>
-<mod_aminoacid_mass position="" mass=""/>
-</modification_info>
-        <search_score name="ionscore" value=""/>
-        <search_score name="identityscore" value=""/>
-        <search_score name="star" value="0"/>
-        <search_score name="homologyscore" value=""/>
-        <search_score name="expect" value=""/>
-      </search_hit>
-    </search_result>
-    </spectrum_query>
-  </msms_run_summary>
-</msms_pipeline_analysis>

data/lib/protk/data/predefined_db.trembl_annotation.yaml

@@ -1,20 +0,0 @@
-#
-# This is a predefined setup file for manage_db 
-#
-# Swissprot_uniprot annotation database (full entries for each protein)
-#
---- 
-:description: Swissprot Trembl annotation database (full entries for each protein)
-:archive_old: false
-:is_annotation_db: true
-:decoy_prefix: decoy_
-:include_filters: []
-
-:format: dat
-:id_regexes: []
-
-:make_blast_index: false
-:sources: 
-- - ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.dat.gz
-  - ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/reldate.txt
-:decoys: false