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[Nelsonlab-cmts] dev-boconnor/project_logic_analysis/conf classification_with_profiles.xml,1.1,1.2 original_glioma_classification_with_vgl.xml,1.1,1.2 original_glioma_expanded_phenotypes_pipe.xml,1.7,1.8 original_glioma_vgl_parsing_pipe.xml,1.1,1.2 p53_breast_cancer_data_Miller_et_al_2005.xml,1.1,1.2 t-cell_leukemia_data_Soulier_et_al_2005.xml,1.1,1.2
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From: <boc...@su...> - 2006-02-23 22:12:13
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Update of /cvsroot/dev-boconnor/project_logic_analysis/conf In directory sumo.genetics.ucla.edu:/tmp/cvs-serv7391/conf Modified Files: classification_with_profiles.xml original_glioma_classification_with_vgl.xml original_glioma_expanded_phenotypes_pipe.xml original_glioma_vgl_parsing_pipe.xml p53_breast_cancer_data_Miller_et_al_2005.xml t-cell_leukemia_data_Soulier_et_al_2005.xml Log Message: Updates Index: t-cell_leukemia_data_Soulier_et_al_2005.xml =================================================================== RCS file: /cvsroot/dev-boconnor/project_logic_analysis/conf/t-cell_leukemia_data_Soulier_et_al_2005.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** t-cell_leukemia_data_Soulier_et_al_2005.xml 22 Feb 2006 09:12:24 -0000 1.1 --- t-cell_leukemia_data_Soulier_et_al_2005.xml 23 Feb 2006 22:11:58 -0000 1.2 *************** *** 1,5 **** <!-- Variables that are used throughout --> [% datadir = "t-cell_leukemia_data_Soulier_et_al_2005" %] ! [% cutoff_for_stability_percent = 10 %] [% dirs = ['90'] %] [% dir_str = '90' %] --- 1,5 ---- <!-- Variables that are used throughout --> [% datadir = "t-cell_leukemia_data_Soulier_et_al_2005" %] ! [% cutoff_for_stability_percent = 6 %] [% dirs = ['90'] %] [% dir_str = '90' %] *************** *** 71,75 **** <!-- FIXME: need to find all the profiles otherwise there won't be much to classify with --> [% index = index + 100 %] <!-- FIXME: scoping issues with this variable!! --> ! <step id="[% index %]" active="0" type="module" processor="Nelson::Pipe::Container::Job::PickTopProfiles"> <input> <item id="parsed_output_stashname" value="summary_of_ppla_output"/> --- 71,75 ---- <!-- FIXME: need to find all the profiles otherwise there won't be much to classify with --> [% index = index + 100 %] <!-- FIXME: scoping issues with this variable!! --> ! <step id="[% index %]" active="1" type="module" processor="Nelson::Pipe::Container::Job::PickTopProfiles"> <input> <item id="parsed_output_stashname" value="summary_of_ppla_output"/> *************** *** 112,116 **** [% FOREACH dir = dirs %] <!-- FIXME: does this sort the profiles? I don't do that elsewhere. Maybe I should in PickTopProfiles --> ! <step id="[% index %]" active="0" type="shell_command" processor="perl scripts/exportTriplets.pl"> <processor_args> <arg id="1" name="" value="data/[% datadir %]/top_profiles/[% dir %]/top_[% cutoff_for_stability_percent %]_percent.profiles"/> --- 112,116 ---- [% FOREACH dir = dirs %] <!-- FIXME: does this sort the profiles? I don't do that elsewhere. Maybe I should in PickTopProfiles --> ! <step id="[% index %]" active="1" type="shell_command" processor="perl scripts/exportTriplets.pl"> <processor_args> <arg id="1" name="" value="data/[% datadir %]/top_profiles/[% dir %]/top_[% cutoff_for_stability_percent %]_percent.profiles"/> *************** *** 124,128 **** </step> [% index = index + 1 %] ! <step id="[% index %]" active="0" type="shell_command" processor="perl scripts/hypergeometric.pl"> <processor_args> <arg id="1" name="" value="data/[% datadir %]/top_profiles/[% dir %]/[% dir %]_percent_top_[% cutoff_for_stability_percent %]_percent.txt"/> --- 124,128 ---- </step> [% index = index + 1 %] ! <step id="[% index %]" active="1" type="shell_command" processor="perl scripts/hypergeometric.pl"> <processor_args> <arg id="1" name="" value="data/[% datadir %]/top_profiles/[% dir %]/[% dir %]_percent_top_[% cutoff_for_stability_percent %]_percent.txt"/> *************** *** 140,144 **** visualiseTriplet.pl output.--> [% index = index + 1 %] ! <step id="[% index %]" active="0" type="module" processor="Nelson::Pipe::Container::Job::AppendPValuesToExportOutput"> <input> <item id="profile_output" value="data/[% datadir %]/top_profiles/[% dir %]/[% dir %]_percent_top_[% cutoff_for_stability_percent %]_percent.txt"/> --- 140,144 ---- visualiseTriplet.pl output.--> [% index = index + 1 %] ! <step id="[% index %]" active="1" type="module" processor="Nelson::Pipe::Container::Job::AppendPValuesToExportOutput"> <input> <item id="profile_output" value="data/[% datadir %]/top_profiles/[% dir %]/[% dir %]_percent_top_[% cutoff_for_stability_percent %]_percent.txt"/> *************** *** 158,162 **** <!-- FIXME: this is redundant with what's below! --> [% index = index + 1 %] ! <step id="[% index %]" active="0" type="module" processor="Nelson::Pipe::Container::Job::ReadPPLAOutputProfiles"> <input> <item id="ppla_output_profiles_dir" value="data/[% datadir %]/top_profiles"/> --- 158,162 ---- <!-- FIXME: this is redundant with what's below! --> [% index = index + 1 %] ! <step id="[% index %]" active="1" type="module" processor="Nelson::Pipe::Container::Job::ReadPPLAOutputProfiles"> <input> <item id="ppla_output_profiles_dir" value="data/[% datadir %]/top_profiles"/> Index: classification_with_profiles.xml =================================================================== RCS file: /cvsroot/dev-boconnor/project_logic_analysis/conf/classification_with_profiles.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** classification_with_profiles.xml 22 Feb 2006 09:12:23 -0000 1.1 --- classification_with_profiles.xml 23 Feb 2006 22:11:58 -0000 1.2 *************** *** 9,13 **** <!-- FIXME: all PPLA input files must contain /^sample/ on the first row --> [% index = index + 1 %] ! <step id="[% index %]" active="0" type="module" processor="Nelson::Pipe::Container::Job::ReadPPLAInputFile"> <input> <item id="ppla_input_file" value="data/[% datadir %]/profiles/100/file_list_0.profile"/> --- 9,13 ---- <!-- FIXME: all PPLA input files must contain /^sample/ on the first row --> [% index = index + 1 %] ! <step id="[% index %]" active="1" type="module" processor="Nelson::Pipe::Container::Job::ReadPPLAInputFile"> <input> <item id="ppla_input_file" value="data/[% datadir %]/profiles/100/file_list_0.profile"/> *************** *** 48,52 **** [% index = index + 1 %] <!-- FIXME: this needs to loop and only use the top 10,20,30,40...100 top profiles for each HC --> ! <step id="[% index %]" active="0" type="module" processor="Nelson::Pipe::Container::Job::ScoreSamplesViaProfiles"> <input> <!-- FIXME: these phenotypes are hard coded, may need to change with different datasets --> --- 48,52 ---- [% index = index + 1 %] <!-- FIXME: this needs to loop and only use the top 10,20,30,40...100 top profiles for each HC --> ! <step id="[% index %]" active="1" type="module" processor="Nelson::Pipe::Container::Job::ScoreSamplesViaProfiles"> <input> <!-- FIXME: these phenotypes are hard coded, may need to change with different datasets --> *************** *** 66,70 **** </step> [% index = index + 1 %] ! <step id="[% index %]" active="0" type="module" processor="Nelson::Pipe::Container::Job::SummarizeClassification"> <input> <item id="stash_input" value="scores_for_samples"/> --- 66,70 ---- </step> [% index = index + 1 %] ! <step id="[% index %]" active="1" type="module" processor="Nelson::Pipe::Container::Job::SummarizeClassification"> <input> <item id="stash_input" value="scores_for_samples"/> *************** *** 80,84 **** </step> [% index = index + 1 %] ! <step id="[% index %]" active="0" type="shell_command" processor="R"> <processor_args> <arg id="1" name="" value="--vanilla"/> --- 80,84 ---- </step> [% index = index + 1 %] ! <step id="[% index %]" active="1" type="shell_command" processor="R"> <processor_args> <arg id="1" name="" value="--vanilla"/> Index: original_glioma_expanded_phenotypes_pipe.xml =================================================================== RCS file: /cvsroot/dev-boconnor/project_logic_analysis/conf/original_glioma_expanded_phenotypes_pipe.xml,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** original_glioma_expanded_phenotypes_pipe.xml 16 Feb 2006 08:19:59 -0000 1.7 --- original_glioma_expanded_phenotypes_pipe.xml 23 Feb 2006 22:11:58 -0000 1.8 *************** *** 55,59 **** <!-- Code that parses the Voting Gene List output --> ! [%# INCLUDE original_glioma_vgl_parsing_pipe.xml %] <!-- --- 55,59 ---- <!-- Code that parses the Voting Gene List output --> ! [% INCLUDE original_glioma_vgl_parsing_pipe.xml %] <!-- *************** *** 237,241 **** (maybe I can work with Barry on a statistical technique that doesnât require random sampling) --> ! [% INCLUDE search_for_tf_binding_sites.xml %] --- 237,241 ---- (maybe I can work with Barry on a statistical technique that doesnât require random sampling) --> ! [%# INCLUDE search_for_tf_binding_sites.xml %] *************** *** 248,252 **** <!-- Perform the classification based on the vgl from Marc --> ! [%# INCLUDE original_glioma_classification_with_vgl.xml %] <!-- Collect some statistics on stability and U score --> --- 248,252 ---- <!-- Perform the classification based on the vgl from Marc --> ! [% INCLUDE original_glioma_classification_with_vgl.xml %] <!-- Collect some statistics on stability and U score --> Index: original_glioma_classification_with_vgl.xml =================================================================== RCS file: /cvsroot/dev-boconnor/project_logic_analysis/conf/original_glioma_classification_with_vgl.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** original_glioma_classification_with_vgl.xml 8 Nov 2005 02:13:47 -0000 1.1 --- original_glioma_classification_with_vgl.xml 23 Feb 2006 22:11:58 -0000 1.2 *************** *** 5,9 **** [% i = 1 %] [% FOREACH dir = dirs %] ! <step id="48" active="0" type="module" processor="Nelson::Pipe::Container::Job::ScoreSamplesViaVGL"> <input> <item id="list_of_files" value="data/[% datadir %]/111_glioma_classification/to_classify_file_list.txt"/> --- 5,9 ---- [% i = 1 %] [% FOREACH dir = dirs %] ! <step id="48" active="1" type="module" processor="Nelson::Pipe::Container::Job::ScoreSamplesViaVGL"> <input> <item id="list_of_files" value="data/[% datadir %]/111_glioma_classification/to_classify_file_list.txt"/> *************** *** 20,24 **** </output> </step> ! <step id="48.2" active="0" type="module" processor="Nelson::Pipe::Container::Job::SummarizeClassification"> <input> <item id="stash_input" value="vgl_scores_for_samples"/> --- 20,24 ---- </output> </step> ! <step id="48.2" active="1" type="module" processor="Nelson::Pipe::Container::Job::SummarizeClassification"> <input> <item id="stash_input" value="vgl_scores_for_samples"/> Index: p53_breast_cancer_data_Miller_et_al_2005.xml =================================================================== RCS file: /cvsroot/dev-boconnor/project_logic_analysis/conf/p53_breast_cancer_data_Miller_et_al_2005.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** p53_breast_cancer_data_Miller_et_al_2005.xml 22 Feb 2006 09:12:24 -0000 1.1 --- p53_breast_cancer_data_Miller_et_al_2005.xml 23 Feb 2006 22:11:58 -0000 1.2 *************** *** 1,5 **** <!-- Variables that are used throughout --> [% datadir = "p53_breast_cancer_data_Miller_et_al_2005" %] ! [% cutoff_for_stability_percent = 10 %] [% dirs = ['75'] %] [% dir_str = '75' %] --- 1,5 ---- <!-- Variables that are used throughout --> [% datadir = "p53_breast_cancer_data_Miller_et_al_2005" %] ! [% cutoff_for_stability_percent = 6 %] [% dirs = ['75'] %] [% dir_str = '75' %] *************** *** 74,78 **** <!-- FIXME: need to find all the profiles otherwise there won't be much to classify with --> [% index = index + 29 %] <!-- FIXME: scoping issues with this variable!! --> ! <step id="[% index %]" active="0" type="module" processor="Nelson::Pipe::Container::Job::PickTopProfiles"> <input> <item id="parsed_output_stashname" value="summary_of_ppla_output"/> --- 74,78 ---- <!-- FIXME: need to find all the profiles otherwise there won't be much to classify with --> [% index = index + 29 %] <!-- FIXME: scoping issues with this variable!! --> ! <step id="[% index %]" active="1" type="module" processor="Nelson::Pipe::Container::Job::PickTopProfiles"> <input> <item id="parsed_output_stashname" value="summary_of_ppla_output"/> *************** *** 115,119 **** [% FOREACH dir = dirs %] <!-- FIXME: does this sort the profiles? I don't do that elsewhere. Maybe I should in PickTopProfiles --> ! <step id="[% index %]" active="0" type="shell_command" processor="perl scripts/exportTriplets.pl"> <processor_args> <arg id="1" name="" value="data/[% datadir %]/top_profiles/[% dir %]/top_[% cutoff_for_stability_percent %]_percent.profiles"/> --- 115,119 ---- [% FOREACH dir = dirs %] <!-- FIXME: does this sort the profiles? I don't do that elsewhere. Maybe I should in PickTopProfiles --> ! <step id="[% index %]" active="1" type="shell_command" processor="perl scripts/exportTriplets.pl"> <processor_args> <arg id="1" name="" value="data/[% datadir %]/top_profiles/[% dir %]/top_[% cutoff_for_stability_percent %]_percent.profiles"/> *************** *** 127,131 **** </step> [% index = index + 1 %] ! <step id="[% index %]" active="0" type="shell_command" processor="perl scripts/hypergeometric.pl"> <processor_args> <arg id="1" name="" value="data/[% datadir %]/top_profiles/[% dir %]/[% dir %]_percent_top_[% cutoff_for_stability_percent %]_percent.txt"/> --- 127,131 ---- </step> [% index = index + 1 %] ! <step id="[% index %]" active="1" type="shell_command" processor="perl scripts/hypergeometric.pl"> <processor_args> <arg id="1" name="" value="data/[% datadir %]/top_profiles/[% dir %]/[% dir %]_percent_top_[% cutoff_for_stability_percent %]_percent.txt"/> *************** *** 143,147 **** visualiseTriplet.pl output.--> [% index = index + 1 %] ! <step id="[% index %]" active="0" type="module" processor="Nelson::Pipe::Container::Job::AppendPValuesToExportOutput"> <input> <item id="profile_output" value="data/[% datadir %]/top_profiles/[% dir %]/[% dir %]_percent_top_[% cutoff_for_stability_percent %]_percent.txt"/> --- 143,147 ---- visualiseTriplet.pl output.--> [% index = index + 1 %] ! <step id="[% index %]" active="1" type="module" processor="Nelson::Pipe::Container::Job::AppendPValuesToExportOutput"> <input> <item id="profile_output" value="data/[% datadir %]/top_profiles/[% dir %]/[% dir %]_percent_top_[% cutoff_for_stability_percent %]_percent.txt"/> *************** *** 161,165 **** <!-- FIXME: this is redundant with what's below! --> [% index = index + 1 %] ! <step id="[% index %]" active="0" type="module" processor="Nelson::Pipe::Container::Job::ReadPPLAOutputProfiles"> <input> <item id="ppla_output_profiles_dir" value="data/[% datadir %]/top_profiles"/> --- 161,165 ---- <!-- FIXME: this is redundant with what's below! --> [% index = index + 1 %] ! <step id="[% index %]" active="1" type="module" processor="Nelson::Pipe::Container::Job::ReadPPLAOutputProfiles"> <input> <item id="ppla_output_profiles_dir" value="data/[% datadir %]/top_profiles"/> Index: original_glioma_vgl_parsing_pipe.xml =================================================================== RCS file: /cvsroot/dev-boconnor/project_logic_analysis/conf/original_glioma_vgl_parsing_pipe.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** original_glioma_vgl_parsing_pipe.xml 8 Nov 2005 02:13:48 -0000 1.1 --- original_glioma_vgl_parsing_pipe.xml 23 Feb 2006 22:11:58 -0000 1.2 *************** *** 13,16 **** --- 13,18 ---- <item id="col_offset" value="19"/> <!-- was 12 before, was that wrong? --> <item id="reference_profile" value="data/[% datadir %]/vgl/100/All_DChip_expression_vals_longNames_groupTtest.xls"/> + <item id="parser_type" value="4_columns"/> + <item id="input_file_name" value="All_DChip_expression_vals_longNames_groupTtest.xls"/> </input> <output> *************** *** 25,28 **** --- 27,31 ---- <item id="col_offset" value="32"/> <item id="reference_profile" value="data/[% datadir %]/vgl/100/All_DChip_expression_vals_longNames_groupTtest.xls"/> + <item id="parser_type" value="2_phenotypes"/> </input> <output> *************** *** 37,40 **** --- 40,44 ---- <item id="col_offset" value="52"/> <item id="reference_profile" value="data/[% datadir %]/vgl/100/All_DChip_expression_vals_longNames_groupTtest.xls"/> + <item id="parser_type" value="2_phenotypes"/> </input> <output> |
