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Resolving conflict between V1.1.0 and v1.1.1
2 parents 587854c + dd764bd commit 1555889

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‎HotSpot3D-1.1.0.tar.gz‎

8.33 MB
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‎README.md‎

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Original file line numberDiff line numberDiff line change
@@ -7,31 +7,34 @@ Usage
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-----
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Program: HotSpot3D - 3D mutation proximity analysis program.
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<<<<<<< HEAD
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Version: V1.1.1
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=======
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Version: V1.1.0
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>>>>>>> dd764bdacc29bfc6ce40fb1cdfdbe3615cd0563f
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Author: Beifang Niu, John Wallis, Adam D Scott, Sohini Sengupta, & Amila Weerasinghe
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Usage: hotspot3d <command> [options]
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Preprocessing
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prep -- Run preprocessing steps 2-7
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drugport -- 0) Parse drugport database (OPTIONAL)
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uppro -- 1) Update proximity files
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calroi -- 2) Generate region of interest (ROI) information
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statis -- 3) Calculate p_values for pairs of mutations
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anno -- 4) Add region of interest (ROI) annotation
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trans -- 5) Add transcript annotation
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cosmic -- 6) Add COSMIC annotation to proximity file
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prior -- 7) Prioritization
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prep -- 2) Run preprocessing steps 2-7
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calroi -- 2a) Generate region of interest (ROI) information
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statis -- 2b) Calculate p_values for pairs of mutations
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anno -- 2c) Add region of interest (ROI) annotation
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trans -- 2d) Add transcript annotation
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cosmic -- 2e) Add COSMIC annotation to proximity file
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prior -- 2f) Prioritization
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Analysis
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search -- 0) 3D mutation proximity searching
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post -- 1) Post-processing of 3D proximity searching output
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cluster -- 2) Determine mutation-mutation and mutation-drug clusters
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sigclus -- 3) Determine significance of clusters (BETA/OPTIONAL)
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summary -- 4) Summarize clusters (OPTIONAL)
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visual -- 5) Visulization of 3D proximity (OPTIONAL)
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main -- Run analysis steps a-f (beta)
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search -- a) 3D mutation proximity searching
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post -- b) Post-processing of 3D proximity searching output
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cluster -- c) Determine mutation-mutation and mutation-drug clusters
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sigclus -- d) Determine significance of clusters (BETA/OPTIONAL)
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summary -- e) Summarize clusters (OPTIONAL)
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visual -- f) Visulization of 3D proximity (OPTIONAL)
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Support
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-------
@@ -113,6 +116,15 @@ Configure Environment
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export PATH=$PATH:~/perl5/bin/
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Add cosmic v67 information to 3D proximity results :
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mkdir preprocessing_dir/cosmic
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cp COSMIC/cosmic_67_for_HotSpot3D_missense_only.tsv.bz2 ./preprocessing_dir/cosmic/
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cd ./preprocessing_dir/cosmic/
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bzip2 -d cosmic_67_for_HotSpot3D_missense_only.tsv.bz2
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Example - Preprocessing
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hotspot3d uppro --output-dir=preprocessing_dir --pdb-file-dir=pdb_files_dir --drugport-file=drugport_parsing_results_file 1>hotspot3d.uppro.err 2>hotspot3d.uppro.out
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3. Calculate protein domain information for each UniProt ID (make sure all uppro jobs have finished!) :
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hotspot3d calroi --output-dir=preprocessing_dir
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4. Significance determination calculation :
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hotspot3d statis --output-dir=preprocessing_dir
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5. Add protein domain annotation information to 3D proximity information :
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hotspot3d anno --output-dir=preprocessing_dir
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6. Choose transcripts based on the alignment between Uniprot sequence and human peptides sequences :
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hotspot3d trans --output-dir=preprocessing_dir
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7. Add cosmic v67 information to 3D proximity results :
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mkdir preprocessing_dir/cosmic
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cp COSMIC/cosmic_67_for_HotSpot3D_missense_only.tsv.bz2 ./preprocessing_dir/cosmic/
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cd ./preprocessing_dir/cosmic/
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bzip2 -d cosmic_67_for_HotSpot3D_missense_only.tsv.bz2
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hotspot3d cosmic --output-dir=preprocessing_dir
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8. Prioritization :
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3. Run automated preprocessing for other measurments and annotations (can alternatively run steps 2a-2f individually) :
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hotspot3d prior --output-dir=preprocessing_dir --p-value-cutoff=0.1 --3d-distance-cutoff=20 --linear-distance-cutoff=0.5
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hotspot3d prep --output-dir=preprocessing_dir
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Example - Analysis

‎bin/hotspot3d‎

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use strict;
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use warnings;
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<<<<<<< HEAD
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our $VERSION = 'V1.1.1';
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=======
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our $VERSION = 'V1.1.0';
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>>>>>>> dd764bdacc29bfc6ce40fb1cdfdbe3615cd0563f
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use Carp;
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use FileHandle;
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use TGI::Mutpro::Main::Significance;
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use TGI::Mutpro::Main::Summary;
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use TGI::Mutpro::Main::Visual;
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use TGI::Mutpro::Main::AllMain;
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use TGI::Mutpro::Preprocess::Drugport;
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use TGI::Mutpro::Preprocess::Uppro;
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use TGI::Mutpro::Preprocess::Calpro;
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my $subCmd = shift;
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## Add module option here
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my %cmds = map{ ($_, 1) } qw( search post visual cluster sigclus summary drugport uppro calpro calroi statis anno trans homo cosmic prior prep density help );
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my %cmds = map{ ($_, 1) } qw( search post visual cluster sigclus summary drugport uppro calpro calroi statis anno trans homo cosmic prior prep main density help );
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unless (defined $subCmd) { die help_text(); };
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unless (exists $cmds{$subCmd}) {
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warn ' Please give valid sub command ! ', "\n";
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$subCmd eq 'cosmic' && do { TGI::Mutpro::Preprocess::Cosmic->new(); last SWITCH; };
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$subCmd eq 'prior' && do { TGI::Mutpro::Preprocess::Prior->new(); last SWITCH; };
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$subCmd eq 'prep' && do { TGI::Mutpro::Preprocess::AllPreprocess->new(); last SWITCH; };
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$subCmd eq 'main' && do { TGI::Mutpro::Main::AllMain->new(); last SWITCH; };
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$subCmd eq 'help' && do { die help_text(); last SWITCH; };
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}
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sub help_text {
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Usage: hotspot3d <command> [options]
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Preprocessing
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prep -- Run steps 2-7 of preprocessing
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drugport -- 0) Parse drugport database (OPTIONAL)
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uppro -- 1) Update proximity files
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calroi -- 2) Generate region of interest (ROI) information
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statis -- 3) Calculate p_values for pairs of mutations
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anno -- 4) Add region of interest (ROI) annotation
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trans -- 5) Add transcript annotation
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cosmic -- 6) Add COSMIC annotation to proximity file
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prior -- 7) Prioritization
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prep -- 2) Run steps 2a-2f of preprocessing
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calroi -- 2a) Generate region of interest (ROI) information
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statis -- 2b) Calculate p_values for pairs of mutations
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anno -- 2c) Add region of interest (ROI) annotation
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trans -- 2d) Add transcript annotation
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cosmic -- 2e) Add COSMIC annotation to proximity file
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prior -- 2f) Prioritization
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Analysis
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search -- 0) 3D mutation proximity searching
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post -- 1) Post-processing of 3D proximity searching output
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cluster -- 2) Determine mutation-mutation and mutation-drug clusters
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sigclus -- 3) Determine significance of clusters
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summary -- 4) Summarize clusters
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visual -- 5) Visulization of 3D proximity
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main -- 0) Run steps a-f of analysis (BETA)
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search -- a) 3D mutation proximity searching
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post -- b) Post-processing of 3D proximity searching output
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cluster -- c) Determine mutation-mutation and mutation-drug clusters
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sigclus -- d) Determine significance of clusters (BETA)
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summary -- e) Summarize clusters
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visual -- f) Visulization of 3D proximity
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help -- this message
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‎dist.ini‎

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name = HotSpot3D
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<<<<<<< HEAD
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author = Beifang Niu, John Wallis, Adam D Scott, Sohini Sengupta , & Amila Weerasinghe from McDonnell Genome Institute of Washington University at St. Louis
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version = 1.1.1
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=======
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author = Beifang Niu, John Wallis, Adam D Scott, Sohini Sengupta, & Amila Weerasinghe from McDonnell Genome Institute of Washington University at St. Louis
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version = 1.1.0
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>>>>>>> dd764bdacc29bfc6ce40fb1cdfdbe3615cd0563f
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license = Perl_5
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copyright_holder = McDonnell Genome Institute at Washington University
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copyright_year = 2013

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