mspire 0.4.9 → 0.5.0
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- data/README +27 -17
- data/changelog.txt +31 -62
- data/lib/ms/calc.rb +32 -0
- data/lib/ms/data/interleaved.rb +60 -0
- data/lib/ms/data/lazy_io.rb +73 -0
- data/lib/ms/data/lazy_string.rb +15 -0
- data/lib/ms/data/simple.rb +59 -0
- data/lib/ms/data/transposed.rb +41 -0
- data/lib/ms/data.rb +57 -0
- data/lib/ms/format/format_error.rb +12 -0
- data/lib/ms/spectrum.rb +25 -384
- data/lib/ms/support/binary_search.rb +126 -0
- data/lib/ms.rb +10 -10
- metadata +38 -350
- data/INSTALL +0 -58
- data/README.rdoc +0 -18
- data/Rakefile +0 -330
- data/bin/aafreqs.rb +0 -23
- data/bin/bioworks2excel.rb +0 -14
- data/bin/bioworks_to_pepxml.rb +0 -148
- data/bin/bioworks_to_pepxml_gui.rb +0 -225
- data/bin/fasta_shaker.rb +0 -5
- data/bin/filter_and_validate.rb +0 -5
- data/bin/gi2annot.rb +0 -14
- data/bin/id_class_anal.rb +0 -112
- data/bin/id_precision.rb +0 -172
- data/bin/ms_to_lmat.rb +0 -67
- data/bin/pepproph_filter.rb +0 -16
- data/bin/prob_validate.rb +0 -6
- data/bin/protein_summary.rb +0 -6
- data/bin/protxml2prots_peps.rb +0 -32
- data/bin/raw_to_mzXML.rb +0 -55
- data/bin/run_percolator.rb +0 -122
- data/bin/sqt_group.rb +0 -26
- data/bin/srf_group.rb +0 -27
- data/bin/srf_to_sqt.rb +0 -40
- data/lib/align/chams.rb +0 -78
- data/lib/align.rb +0 -154
- data/lib/archive/targz.rb +0 -94
- data/lib/bsearch.rb +0 -120
- data/lib/core_extensions.rb +0 -16
- data/lib/fasta.rb +0 -626
- data/lib/gi.rb +0 -124
- data/lib/group_by.rb +0 -10
- data/lib/index_by.rb +0 -11
- data/lib/merge_deep.rb +0 -21
- data/lib/ms/converter/mzxml.rb +0 -77
- data/lib/ms/gradient_program.rb +0 -170
- data/lib/ms/msrun.rb +0 -244
- data/lib/ms/msrun_index.rb +0 -108
- data/lib/ms/parser/mzdata/axml.rb +0 -67
- data/lib/ms/parser/mzdata/dom.rb +0 -175
- data/lib/ms/parser/mzdata/libxml.rb +0 -7
- data/lib/ms/parser/mzdata.rb +0 -31
- data/lib/ms/parser/mzxml/axml.rb +0 -70
- data/lib/ms/parser/mzxml/dom.rb +0 -182
- data/lib/ms/parser/mzxml/hpricot.rb +0 -253
- data/lib/ms/parser/mzxml/libxml.rb +0 -19
- data/lib/ms/parser/mzxml/regexp.rb +0 -122
- data/lib/ms/parser/mzxml/rexml.rb +0 -72
- data/lib/ms/parser/mzxml/xmlparser.rb +0 -248
- data/lib/ms/parser/mzxml.rb +0 -282
- data/lib/ms/parser.rb +0 -108
- data/lib/ms/precursor.rb +0 -25
- data/lib/ms/scan.rb +0 -81
- data/lib/mspire.rb +0 -4
- data/lib/pi_zero.rb +0 -244
- data/lib/qvalue.rb +0 -161
- data/lib/roc.rb +0 -187
- data/lib/sample_enzyme.rb +0 -160
- data/lib/scan_i.rb +0 -21
- data/lib/spec_id/aa_freqs.rb +0 -170
- data/lib/spec_id/bioworks.rb +0 -497
- data/lib/spec_id/digestor.rb +0 -138
- data/lib/spec_id/mass.rb +0 -179
- data/lib/spec_id/parser/proph.rb +0 -335
- data/lib/spec_id/precision/filter/cmdline.rb +0 -218
- data/lib/spec_id/precision/filter/interactive.rb +0 -134
- data/lib/spec_id/precision/filter/output.rb +0 -148
- data/lib/spec_id/precision/filter.rb +0 -637
- data/lib/spec_id/precision/output.rb +0 -60
- data/lib/spec_id/precision/prob/cmdline.rb +0 -160
- data/lib/spec_id/precision/prob/output.rb +0 -94
- data/lib/spec_id/precision/prob.rb +0 -249
- data/lib/spec_id/proph/pep_summary.rb +0 -104
- data/lib/spec_id/proph/prot_summary.rb +0 -484
- data/lib/spec_id/proph.rb +0 -4
- data/lib/spec_id/protein_summary.rb +0 -489
- data/lib/spec_id/sequest/params.rb +0 -316
- data/lib/spec_id/sequest/pepxml.rb +0 -1458
- data/lib/spec_id/sequest.rb +0 -33
- data/lib/spec_id/sqt.rb +0 -349
- data/lib/spec_id/srf.rb +0 -973
- data/lib/spec_id.rb +0 -778
- data/lib/spec_id_xml.rb +0 -99
- data/lib/transmem/phobius.rb +0 -147
- data/lib/transmem/toppred.rb +0 -368
- data/lib/transmem.rb +0 -157
- data/lib/validator/aa.rb +0 -48
- data/lib/validator/aa_est.rb +0 -112
- data/lib/validator/background.rb +0 -77
- data/lib/validator/bias.rb +0 -95
- data/lib/validator/cmdline.rb +0 -431
- data/lib/validator/decoy.rb +0 -107
- data/lib/validator/digestion_based.rb +0 -70
- data/lib/validator/probability.rb +0 -51
- data/lib/validator/prot_from_pep.rb +0 -234
- data/lib/validator/q_value.rb +0 -32
- data/lib/validator/transmem.rb +0 -272
- data/lib/validator/true_pos.rb +0 -46
- data/lib/validator.rb +0 -197
- data/lib/xml.rb +0 -38
- data/lib/xml_style_parser.rb +0 -119
- data/lib/xmlparser_wrapper.rb +0 -19
- data/release_notes.txt +0 -2
- data/script/compile_and_plot_smriti_final.rb +0 -97
- data/script/create_little_pepxml.rb +0 -61
- data/script/degenerate_peptides.rb +0 -47
- data/script/estimate_fpr_by_cysteine.rb +0 -226
- data/script/extract_gradient_programs.rb +0 -56
- data/script/find_cysteine_background.rb +0 -137
- data/script/genuine_tps_and_probs.rb +0 -136
- data/script/get_apex_values_rexml.rb +0 -44
- data/script/histogram_probs.rb +0 -61
- data/script/mascot_fix_pepxml.rb +0 -123
- data/script/msvis.rb +0 -42
- data/script/mzXML2timeIndex.rb +0 -25
- data/script/peps_per_bin.rb +0 -67
- data/script/prep_dir.rb +0 -121
- data/script/simple_protein_digestion.rb +0 -27
- data/script/smriti_final_analysis.rb +0 -103
- data/script/sqt_to_meta.rb +0 -24
- data/script/top_hit_per_scan.rb +0 -67
- data/script/toppred_to_yaml.rb +0 -47
- data/script/tpp_installer.rb +0 -249
- data/specs/align_spec.rb +0 -79
- data/specs/bin/bioworks_to_pepxml_spec.rb +0 -79
- data/specs/bin/fasta_shaker_spec.rb +0 -259
- data/specs/bin/filter_and_validate__multiple_vals_helper.yaml +0 -199
- data/specs/bin/filter_and_validate_spec.rb +0 -180
- data/specs/bin/ms_to_lmat_spec.rb +0 -34
- data/specs/bin/prob_validate_spec.rb +0 -86
- data/specs/bin/protein_summary_spec.rb +0 -14
- data/specs/fasta_spec.rb +0 -354
- data/specs/gi_spec.rb +0 -22
- data/specs/load_bin_path.rb +0 -7
- data/specs/merge_deep_spec.rb +0 -13
- data/specs/ms/gradient_program_spec.rb +0 -77
- data/specs/ms/msrun_spec.rb +0 -498
- data/specs/ms/parser_spec.rb +0 -92
- data/specs/ms/spectrum_spec.rb +0 -87
- data/specs/pi_zero_spec.rb +0 -115
- data/specs/qvalue_spec.rb +0 -39
- data/specs/roc_spec.rb +0 -251
- data/specs/rspec_autotest.rb +0 -149
- data/specs/sample_enzyme_spec.rb +0 -126
- data/specs/spec_helper.rb +0 -135
- data/specs/spec_id/aa_freqs_spec.rb +0 -52
- data/specs/spec_id/bioworks_spec.rb +0 -148
- data/specs/spec_id/digestor_spec.rb +0 -75
- data/specs/spec_id/precision/filter/cmdline_spec.rb +0 -20
- data/specs/spec_id/precision/filter/output_spec.rb +0 -31
- data/specs/spec_id/precision/filter_spec.rb +0 -246
- data/specs/spec_id/precision/prob_spec.rb +0 -44
- data/specs/spec_id/precision/prob_spec_helper.rb +0 -0
- data/specs/spec_id/proph/pep_summary_spec.rb +0 -98
- data/specs/spec_id/proph/prot_summary_spec.rb +0 -128
- data/specs/spec_id/protein_summary_spec.rb +0 -189
- data/specs/spec_id/sequest/params_spec.rb +0 -68
- data/specs/spec_id/sequest/pepxml_spec.rb +0 -374
- data/specs/spec_id/sequest_spec.rb +0 -38
- data/specs/spec_id/sqt_spec.rb +0 -246
- data/specs/spec_id/srf_spec.rb +0 -172
- data/specs/spec_id/srf_spec_helper.rb +0 -139
- data/specs/spec_id_helper.rb +0 -33
- data/specs/spec_id_spec.rb +0 -366
- data/specs/spec_id_xml_spec.rb +0 -33
- data/specs/transmem/phobius_spec.rb +0 -425
- data/specs/transmem/toppred_spec.rb +0 -298
- data/specs/transmem_spec.rb +0 -60
- data/specs/transmem_spec_shared.rb +0 -64
- data/specs/validator/aa_est_spec.rb +0 -66
- data/specs/validator/aa_spec.rb +0 -40
- data/specs/validator/background_spec.rb +0 -67
- data/specs/validator/bias_spec.rb +0 -122
- data/specs/validator/decoy_spec.rb +0 -51
- data/specs/validator/fasta_helper.rb +0 -26
- data/specs/validator/prot_from_pep_spec.rb +0 -141
- data/specs/validator/transmem_spec.rb +0 -146
- data/specs/validator/true_pos_spec.rb +0 -58
- data/specs/validator_helper.rb +0 -33
- data/specs/xml_spec.rb +0 -12
- data/test_files/000_pepxml18_small.xml +0 -206
- data/test_files/020a.mzXML.timeIndex +0 -4710
- data/test_files/4-03-03_mzXML/000.mzXML.timeIndex +0 -3973
- data/test_files/4-03-03_mzXML/020.mzXML.timeIndex +0 -3872
- data/test_files/4-03-03_small-prot.xml +0 -321
- data/test_files/4-03-03_small.xml +0 -3876
- data/test_files/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
- data/test_files/bioworks-3.3_10prots.xml +0 -5999
- data/test_files/bioworks31.params +0 -77
- data/test_files/bioworks32.params +0 -62
- data/test_files/bioworks33.params +0 -63
- data/test_files/bioworks_single_run_small.xml +0 -7237
- data/test_files/bioworks_small.fasta +0 -212
- data/test_files/bioworks_small.params +0 -63
- data/test_files/bioworks_small.phobius +0 -109
- data/test_files/bioworks_small.toppred.out +0 -2847
- data/test_files/bioworks_small.xml +0 -5610
- data/test_files/bioworks_with_INV_small.xml +0 -3753
- data/test_files/bioworks_with_SHUFF_small.xml +0 -2503
- data/test_files/corrupted_900.srf +0 -0
- data/test_files/head_of_7MIX.srf +0 -0
- data/test_files/interact-opd1_mods_small-prot.xml +0 -304
- data/test_files/messups.fasta +0 -297
- data/test_files/opd1/000.my_answer.100lines.xml +0 -101
- data/test_files/opd1/000.tpp_1.2.3.first10.xml +0 -115
- data/test_files/opd1/000.tpp_2.9.2.first10.xml +0 -126
- data/test_files/opd1/000.v2.1.mzXML.timeIndex +0 -3748
- data/test_files/opd1/000_020-prot.png +0 -0
- data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml +0 -62
- data/test_files/opd1/000_020_3prots-prot.xml +0 -62
- data/test_files/opd1/opd1_cat_inv_small-prot.xml +0 -139
- data/test_files/opd1/sequest.3.1.params +0 -77
- data/test_files/opd1/sequest.3.2.params +0 -62
- data/test_files/opd1/twenty_scans.mzXML +0 -418
- data/test_files/opd1/twenty_scans.v2.1.mzXML +0 -382
- data/test_files/opd1/twenty_scans_answ.lmat +0 -0
- data/test_files/opd1/twenty_scans_answ.lmata +0 -9
- data/test_files/opd1_020_beginning.RAW +0 -0
- data/test_files/opd1_2runs_2mods/data/020.mzData.xml +0 -683
- data/test_files/opd1_2runs_2mods/data/020.readw.mzXML +0 -382
- data/test_files/opd1_2runs_2mods/data/040.mzData.xml +0 -683
- data/test_files/opd1_2runs_2mods/data/040.readw.mzXML +0 -382
- data/test_files/opd1_2runs_2mods/data/README.txt +0 -6
- data/test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml +0 -753
- data/test_files/orbitrap_mzData/000_cut.xml +0 -1920
- data/test_files/pepproph_small.xml +0 -4691
- data/test_files/phobius.small.noheader.txt +0 -50
- data/test_files/phobius.small.small.txt +0 -53
- data/test_files/s01_anC1_ld020mM.key.txt +0 -25
- data/test_files/s01_anC1_ld020mM.meth +0 -0
- data/test_files/small.fasta +0 -297
- data/test_files/small.sqt +0 -87
- data/test_files/smallraw.RAW +0 -0
- data/test_files/tf_bioworks2excel.bioXML +0 -14340
- data/test_files/tf_bioworks2excel.txt.actual +0 -1035
- data/test_files/toppred.small.out +0 -416
- data/test_files/toppred.xml.out +0 -318
- data/test_files/validator_hits_separate/bias_bioworks_small_HS.fasta +0 -7
- data/test_files/validator_hits_separate/bioworks_small_HS.xml +0 -5651
- data/test_files/yeast_gly_small-prot.xml +0 -265
- data/test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes +0 -6
- data/test_files/yeast_gly_small.xml +0 -3807
- data/test_files/yeast_gly_small2.parentTimes +0 -6
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div.file_info, div.software, div.fppr, div.num_proteins{
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"<a href=\"http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=#{gi}\" title=\"#{name}\">#{gi}</a>"
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end
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133
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# Takes the -prot.xml filename and grabs the png file (if available)
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def error_info(prot_file_name)
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img = prot_file_name.gsub('.xml', '.png')
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136
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img_bn = File.basename(img)
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137
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"<div id=\"error\"><img src=\"#{img_bn}\" alt=\"[ Optional: To view error/sensitivity image, put #{img_bn} in the same directory as #{File.basename(prot_file_name)} ]\"/>\n</div>"
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end
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139
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140
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# attempts to get the NCBI gi code
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def accession(name)
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if (name.include? '|') && (name[0,3] == 'gi|')
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name.split('|')[1]
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144
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else
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145
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name
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146
|
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end
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147
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end
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149
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def flag_to_regex(flag, prefix=false)
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if flag
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if prefix
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/^#{Regexp.escape(flag)}/
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else
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/#{Regexp.escape(flag)}/
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end
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else
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nil
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158
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end
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159
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end
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160
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161
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# given a list of proteins, output a tab delimited textfile with protein
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# name and the total number of peptides found
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163
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def output_peptide_counts_file(prots, filename)
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File.open(filename, "w") do |fh_out|
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prots.each do |prot|
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166
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fh_out.puts [prot._protein_name, prot._total_number_peptides].join("\t")
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167
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end
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168
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end
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end
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171
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# filters on the false positive regex and sorts by prot probability
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172
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def filter_and_sort(uniq_prots, flag=nil, prefix=false)
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173
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false_flag_re = flag_to_regex(flag, prefix)
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174
|
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sorted = uniq_prots.sort_by {|prt| [prt._probability, prt.parent._probability]}.reverse
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## filter on prefix
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if prefix
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177
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sorted = sorted.reject {|prot| prot._protein_name =~ false_flag_re }
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|
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end
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sorted
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180
|
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end
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181
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182
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# assumes that these are sorted on probability
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183
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# desired_fppr is a float
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184
|
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# returns [number_of_prots, actual_fppr]
|
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185
|
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def num_prots_above_fppr(prots, desired_fppr)
|
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186
|
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current_fppr_rate_percent = 0.0
|
|
187
|
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previous_fppr_rate_percent = 0.0
|
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188
|
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current_sum_one_minus_prob = 0.0
|
|
189
|
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proteins_within_fppr = 0
|
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190
|
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actual_fppr = nil
|
|
191
|
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already_found = false
|
|
192
|
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prot_cnt = 0
|
|
193
|
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prots.each do |prot|
|
|
194
|
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prot_cnt += 1
|
|
195
|
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# SUM(1-probX)/#prots
|
|
196
|
-
current_sum_one_minus_prob += 1.0 - prot._probability.to_f
|
|
197
|
-
current_fppr_rate_percent = (current_sum_one_minus_prob / prot_cnt) * 100
|
|
198
|
-
|
|
199
|
-
if current_fppr_rate_percent > desired_fppr && !already_found
|
|
200
|
-
actual_fppr = previous_fppr_rate_percent
|
|
201
|
-
proteins_within_fppr = prot_cnt
|
|
202
|
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already_found = true
|
|
203
|
-
end
|
|
204
|
-
previous_fppr_rate_percent = current_fppr_rate_percent
|
|
205
|
-
end
|
|
206
|
-
[proteins_within_fppr, actual_fppr]
|
|
207
|
-
end
|
|
208
|
-
|
|
209
|
-
#### #readable_previous_fppr_rate_percent = sprintf("%.2f", previous_fppr_rate_percent)
|
|
210
|
-
|
|
211
|
-
# returns a string of the table rows
|
|
212
|
-
# false_positive_rate (give as a %) is the cutoff mark
|
|
213
|
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# returns the number of proteins at the desired_fppr (if given)
|
|
214
|
-
def table_rows(uniq_prots, prefix, false_positive_rate_percent, num_cols, desired_fppr, actual_percent_fp, annotations=nil, peptide_count_filename=nil)
|
|
215
|
-
prot_cnt = 0
|
|
216
|
-
an_cnt = 0
|
|
217
|
-
|
|
218
|
-
uniq_prots.map do |prot|
|
|
219
|
-
tr do
|
|
220
|
-
prot_cnt += 1
|
|
221
|
-
gi = accession(prot._protein_name)
|
|
222
|
-
|
|
223
|
-
if annotations
|
|
224
|
-
protein_description = annotations[an_cnt]
|
|
225
|
-
an_cnt += 1
|
|
226
|
-
else
|
|
227
|
-
if prot.annotation.size > 0
|
|
228
|
-
protein_description = prot.annotation.first._protein_description
|
|
229
|
-
else
|
|
230
|
-
protein_description = 'NA'
|
|
231
|
-
end
|
|
232
|
-
end
|
|
233
|
-
tds([prot_cnt, prot._probability, ref_html(gi, prot._protein_name), protein_description, prot._percent_coverage, peptide_cell(prot_cnt, prot._unique_stripped_peptides.split('+')), prot._total_number_peptides, prot._pct_spectrum_ids])
|
|
234
|
-
end
|
|
235
|
-
end.join
|
|
236
|
-
end
|
|
237
|
-
|
|
238
|
-
def print_html_pieces(file, *pieces)
|
|
239
|
-
File.open(file, "w") do |out|
|
|
240
|
-
pieces.each do |piece|
|
|
241
|
-
out.print piece
|
|
242
|
-
end
|
|
243
|
-
end
|
|
244
|
-
end
|
|
245
|
-
|
|
246
|
-
def file_info(file)
|
|
247
|
-
"<div class=\"file_info\"><h3>Source File Information</h3>File: #{File.expand_path(file)}
|
|
248
|
-
<br/>Last Modified: #{File.mtime(file)}
|
|
249
|
-
<br/>Size: #{File.size(file)/1000} KB
|
|
250
|
-
</div>"
|
|
251
|
-
end
|
|
252
|
-
|
|
253
|
-
def bioworks_script_info(obj)
|
|
254
|
-
version = "3.2??"
|
|
255
|
-
if obj.version
|
|
256
|
-
version = obj.version
|
|
257
|
-
end
|
|
258
|
-
script_info{"Bioworks version #{version}"}
|
|
259
|
-
end
|
|
260
|
-
|
|
261
|
-
def protproph_script_info
|
|
262
|
-
begin
|
|
263
|
-
where = `which xinteract`
|
|
264
|
-
reply = `#{where}`
|
|
265
|
-
rescue Exception
|
|
266
|
-
reply = ""
|
|
267
|
-
end
|
|
268
|
-
prophet = "TPP (version unknown)" # put your version here if you can't get it dynamically
|
|
269
|
-
if reply =~ /xinteract.*?\((TPP .*)\)/
|
|
270
|
-
prophet = $1.dup
|
|
271
|
-
end
|
|
272
|
-
script_info { "ProteinProphet from: #{prophet}" }
|
|
273
|
-
end
|
|
274
|
-
|
|
275
|
-
def mspire_version
|
|
276
|
-
string = "mspire"
|
|
277
|
-
begin
|
|
278
|
-
if `gem list --local mspire` =~ /mspire \((.*?)\)/
|
|
279
|
-
string << (" v" + $1)
|
|
280
|
-
end
|
|
281
|
-
rescue Exception
|
|
282
|
-
end
|
|
283
|
-
string
|
|
284
|
-
end
|
|
285
|
-
|
|
286
|
-
def script_info
|
|
287
|
-
"<div class=\"software\"><h3>Software Information</h3>#{yield}<br/>Ruby package: #{mspire_version}<br/>Command: #{[File.basename(__FILE__), *@orig_argv].join(" ")}</div>"
|
|
288
|
-
end
|
|
289
|
-
|
|
290
|
-
def proph_output(file, outfn, opt, fppr_output_as_html)
|
|
291
|
-
header_anchors = [at('#', 'number'), at('prob','protein probability (for Prophet, higher is better)'), at('ref', 'gi number if available (or complete reference)'), at('annotation', 'annotation from the fasta file'), at('%cov', 'percent of protein sequence covered by corresponding peptides'), at('peps', 'unique peptides identified (includes non-contributing peptides). Click number to show/hide'), at('#peps', 'total number of corresponding peptides that contributed to protein probability'), at('%ids', 'fraction of correct dataset peptide identifications corresponding to protein')]
|
|
292
|
-
num_cols = header_anchors.size
|
|
293
|
-
theaders = ths(header_anchors)
|
|
294
|
-
|
|
295
|
-
root = AXML.parse_file(file)
|
|
296
|
-
prots = []
|
|
297
|
-
## find the min_prob at a fppr of XX
|
|
298
|
-
min_prob_redline = 1.01 # if no fppr is less than what they give, then all are redlined!
|
|
299
|
-
|
|
300
|
-
if opt.c
|
|
301
|
-
actual_percent_fp = opt.c.to_f
|
|
302
|
-
elsif opt.cut_at
|
|
303
|
-
actual_percent_fp = opt.cut_at.to_f
|
|
304
|
-
else
|
|
305
|
-
actual_percent_fp = nil
|
|
306
|
-
end
|
|
307
|
-
root.protein_group.each do |group|
|
|
308
|
-
group.protein.each do |prt|
|
|
309
|
-
prots << prt
|
|
310
|
-
end
|
|
311
|
-
end
|
|
312
|
-
uniq_prots = prots.hash_by(:_protein_name).map{|name,prot_arr| prot_arr.first }
|
|
313
|
-
filtered_sorted_prots = filter_and_sort(uniq_prots, opt.f, opt.prefix)
|
|
314
|
-
|
|
315
|
-
## num proteins above cutoff (if opt.c)
|
|
316
|
-
num_prots_html = ''
|
|
317
|
-
if opt.c || opt.cut_at
|
|
318
|
-
(num_prots, actual_fppr) = num_prots_above_fppr(filtered_sorted_prots, actual_percent_fp)
|
|
319
|
-
num_prots_html = num_prots_to_html(actual_percent_fp, actual_fppr, num_prots)
|
|
320
|
-
end
|
|
321
|
-
if opt.cut_at
|
|
322
|
-
filtered_sorted_prots = filtered_sorted_prots[0,num_prots]
|
|
323
|
-
end
|
|
324
|
-
|
|
325
|
-
output_peptide_counts_file(filtered_sorted_prots, opt.peptide_count) if opt.peptide_count
|
|
326
|
-
|
|
327
|
-
# get an array of annotations (or nil if no option)
|
|
328
|
-
annotations =
|
|
329
|
-
if opt.get_annotation
|
|
330
|
-
gis = filtered_sorted_prots.map {|prot| accession(prot._protein_name) }
|
|
331
|
-
GI.gi2annot(gis)
|
|
332
|
-
end
|
|
333
|
-
|
|
334
|
-
table_string = table do
|
|
335
|
-
tr{theaders} + table_rows(filtered_sorted_prots, opt.f, actual_percent_fp, num_cols, opt.c.to_f, actual_percent_fp, annotations, opt.peptide_count)
|
|
336
|
-
end
|
|
337
|
-
er_info = opt.precision ? error_info(file) : ""
|
|
338
|
-
html_pieces = [outfn, header, fppr_output_as_html, er_info, file_info(file), protproph_script_info, num_prots_html, table_string, trailer]
|
|
339
|
-
print_html_pieces(*html_pieces)
|
|
340
|
-
end # proph_output
|
|
341
|
-
|
|
342
|
-
# given a list of peptide sequences creates javascript to hide/show them
|
|
343
|
-
def peptide_cell(prot_num, peptide_sequences)
|
|
344
|
-
"<a href=\"#prot#{prot_num}\" onclick=\"toggle_vis('#{prot_num}');\">#{peptide_sequences.size}</a><div id=\"#{prot_num}\" style=\"display:none;\">#{peptide_sequences.join(', ')}</div>"
|
|
345
|
-
end
|
|
346
|
-
|
|
347
|
-
# takes spec_id object
|
|
348
|
-
# the outfn is the output filename
|
|
349
|
-
# opt is an OpenStruct that holds opt.f = the false prefix
|
|
350
|
-
def bioworks_output(spec_id, outfn, file=nil, false_flag_re=nil, fppr_output_as_html=nil)
|
|
351
|
-
fppr_output_as_html ||= ''
|
|
352
|
-
header_anchors = [at('#', 'number'), at('prob','protein probability (for Bioworks, lower is better)'), at('ref', 'gi number if available (or complete reference)'), at('annotation', 'annotation from the fasta file'), at('%cov', 'percent of protein sequence covered by corresponding peptides'), at('peps', 'unique peptides identified (at any confidence) Click number to show/hide.'), at('#peps', 'total number of peptides seen (not unique)')]
|
|
353
|
-
num_cols = header_anchors.size
|
|
354
|
-
theaders = ths(header_anchors)
|
|
355
|
-
proteins = spec_id.prots
|
|
356
|
-
protein_num = 0
|
|
357
|
-
rows = ""
|
|
358
|
-
proteins.each do |prot|
|
|
359
|
-
if false_flag_re && prot.reference =~ false_flag_re
|
|
360
|
-
next
|
|
361
|
-
end
|
|
362
|
-
uniq_peps = Hash.new {|h,k| h[k] = true; }
|
|
363
|
-
protein_num += 1
|
|
364
|
-
prot.peps.each do |pep|
|
|
365
|
-
uniq_peps[pep.sequence.split('.')[1]] = true
|
|
366
|
-
end
|
|
367
|
-
pieces = prot.reference.split(' ')
|
|
368
|
-
long_prot_name = pieces.shift
|
|
369
|
-
annotation = pieces.join(' ')
|
|
370
|
-
accession = prot.accession
|
|
371
|
-
if accession == '0' ; accession = long_prot_name end
|
|
372
|
-
rows << tr{ tds([protein_num, prot.protein_probability, ref_html(accession, long_prot_name), annotation, prot.coverage, peptide_cell(protein_num, uniq_peps.keys), prot.peps.size]) }
|
|
373
|
-
end
|
|
374
|
-
table_string = table do
|
|
375
|
-
tr{theaders} + rows
|
|
376
|
-
end
|
|
377
|
-
print_html_pieces(outfn, header, fppr_output_as_html, file_info(file), bioworks_script_info(spec_id), table_string, trailer)
|
|
378
|
-
end # bioworks_output
|
|
379
|
-
|
|
380
|
-
def num_prots_to_html(desired_cutoff, actual_cutoff, num_proteins)
|
|
381
|
-
actual_cutoff = sprintf("%.3f", actual_cutoff)
|
|
382
|
-
desired_cutoff = sprintf("%.3f", desired_cutoff)
|
|
383
|
-
"<div class=\"num_proteins\"><h3>False Positive Predictive Rate [ FP/(TP+FP) ]</h3>
|
|
384
|
-
Desired FPPR: #{desired_cutoff} %<br/>
|
|
385
|
-
Actual FPPR: #{actual_cutoff} %<br/>
|
|
386
|
-
Number of Proteins at Actual FPPR: #{num_proteins}
|
|
387
|
-
</div>"
|
|
388
|
-
end
|
|
389
|
-
|
|
390
|
-
# transforms the output string of file_as_decoy into html
|
|
391
|
-
def file_as_decoy_to_html(string)
|
|
392
|
-
lines = string.split("\n")
|
|
393
|
-
#puts lines ?? is this supposed to be commented out?
|
|
394
|
-
lines = lines.reject do |obj| obj =~ /\*{10}/ end
|
|
395
|
-
lines.map! do |line| "#{line}<br/>" end
|
|
396
|
-
"<div class=\"fppr\">
|
|
397
|
-
<h3>Classification Analysis</h3>
|
|
398
|
-
#{lines.join("\n")}
|
|
399
|
-
</div>"
|
|
400
|
-
end
|
|
401
|
-
|
|
402
|
-
# transforms the output string of file_as_decoy into html
|
|
403
|
-
def prefix_as_decoy_to_html(string)
|
|
404
|
-
"<div class=\"fppr\">
|
|
405
|
-
<h3>Classification Analysis</h3>
|
|
406
|
-
</div>" +
|
|
407
|
-
string
|
|
408
|
-
end
|
|
409
|
-
|
|
410
|
-
def create_from_command_line_args(argv)
|
|
411
|
-
@orig_argv = argv.dup
|
|
412
|
-
|
|
413
|
-
opt = OpenStruct.new
|
|
414
|
-
opt.f = DEF_PREFIX
|
|
415
|
-
opts = OptionParser.new do |op|
|
|
416
|
-
op.banner = "usage: #{File.basename(__FILE__)} [options] <file>.xml ..."
|
|
417
|
-
op.separator " where file = bioworks -or- <run>-prot (prophet output)"
|
|
418
|
-
op.separator " outputs: <file>.summary.html"
|
|
419
|
-
op.separator ""
|
|
420
|
-
op.on("-f", "--false <prefix>", "ignore proteins with flag (def: #{DEF_PREFIX})") {|v| opt.f = v }
|
|
421
|
-
op.on("--prefix", "false flag for prefixes only") {|v| opt.prefix = v }
|
|
422
|
-
op.on("-p", "--precision", "include the output from precision.rb") {|v| opt.p = v }
|
|
423
|
-
op.separator(" if --precision then -f is used to specify a file or prefix")
|
|
424
|
-
op.separator(" that indicates the false positives.")
|
|
425
|
-
op.on("--peptide_count <filename>", "outputs text file with # peptides per protein") {|v| opt.peptide_count = v}
|
|
426
|
-
op.separator ""
|
|
427
|
-
op.separator "Options for #{PRECISION_PROGRAM_BASE}.rb :"
|
|
428
|
-
op.on("--#{PRECISION_PROGRAM_BASE}", "include output of #{PRECISION_PROGRAM_BASE}.rb,") {|v| opt.precision = v}
|
|
429
|
-
op.separator(" type '#{PRECISION_PROGRAM_BASE}.rb' for details")
|
|
430
|
-
op.separator ""
|
|
431
|
-
op.separator "specific to ProteinProphet (with no concatenated DB):"
|
|
432
|
-
op.on("-c", "--cutoff percent", "false positive predictive rate (FPPR)% for given cutoff") {|v| opt.c = v }
|
|
433
|
-
op.on("--cut_at percent", "only reports proteins within FPPR %") {|v| opt.cut_at = v }
|
|
434
|
-
op.on("--get_annotation", "retrieves annotation by gi code") {|v| opt.get_annotation = v}
|
|
435
|
-
op.separator " (use if your proteins have gi's but no annotation) "
|
|
436
|
-
end
|
|
437
|
-
|
|
438
|
-
opts.parse!(argv)
|
|
439
|
-
|
|
440
|
-
if argv.size < 1
|
|
441
|
-
puts opts
|
|
442
|
-
return
|
|
443
|
-
end
|
|
444
|
-
|
|
445
|
-
fppr_output_as_html = ''
|
|
446
|
-
files = argv.to_a
|
|
447
|
-
files.each do |file|
|
|
448
|
-
outfn = file.sub(/\.xml$/, '.summary.html')
|
|
449
|
-
outfn = outfn.sub(/\.srg$/, '.summary.html')
|
|
450
|
-
## False Positive Rate Calculation:
|
|
451
|
-
if opt.precision
|
|
452
|
-
opt.o = outfn # won't actually be written over, but used
|
|
453
|
-
to_use_argv = create_precision_argv(file, opt)
|
|
454
|
-
(out_string, opt) = Prec.new.precision(to_use_argv)
|
|
455
|
-
fppr_output_as_html = prefix_as_decoy_to_html(out_string)
|
|
456
|
-
end
|
|
457
|
-
|
|
458
|
-
case SpecID.file_type(file)
|
|
459
|
-
when "protproph"
|
|
460
|
-
#spec_id = SpecID.new(file)
|
|
461
|
-
proph_output(file, outfn, opt, fppr_output_as_html)
|
|
462
|
-
when "bioworks"
|
|
463
|
-
spec_id = SpecID.new(file)
|
|
464
|
-
|
|
465
|
-
false_regex = flag_to_regex(opt.f, opt.prefix)
|
|
466
|
-
bioworks_output(spec_id, outfn, file, false_regex, fppr_output_as_html)
|
|
467
|
-
else
|
|
468
|
-
abort "filetype for #{file} not recognized!"
|
|
469
|
-
end
|
|
470
|
-
end
|
|
471
|
-
|
|
472
|
-
end # method create_from_command_line
|
|
473
|
-
|
|
474
|
-
def create_precision_argv(file, opt)
|
|
475
|
-
# include only those options specific
|
|
476
|
-
new_argv = [file]
|
|
477
|
-
if opt.prefix ; new_argv << '--prefix' end
|
|
478
|
-
if opt.f ; new_argv << '-f' << opt.f end
|
|
479
|
-
if opt.o ; new_argv << '-o' << opt.o end
|
|
480
|
-
new_argv
|
|
481
|
-
end
|
|
482
|
-
|
|
483
|
-
end # ProteinSummary
|
|
484
|
-
|
|
485
|
-
##################################################################
|
|
486
|
-
# MAIN
|
|
487
|
-
##################################################################
|
|
488
|
-
|
|
489
|
-
|