[med-svn] [gwamar] branch upstream updated (d0e35c7 -> fd6d36a)
Andreas Tille
tille at debian.org
Tue Dec 8 15:50:30 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository gwamar.
from d0e35c7 Imported Upstream version 1.14+dfsg
new 953c551 Imported Upstream version 1.15.1+dfsg
new 52e8bc8 Imported Upstream version 1.15.1+dfsg
new fd6d36a Imported Upstream version 1.15.1+dfsg
The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.project | 24 +
.pydevproject | 5 +
config/config_params.txt | 11 +-
config/config_tools.txt | 8 +
.../input/point_mutations.txt.REMOVED.git-id | 1 +
.../input/point_mutations.txt.REMOVED.git-id | 1 +
gwamar.py | 605 +++--
other/cctsweep/bm.sh | 104 -
other/cctsweep/cct.sh | 114 -
other/cctsweep/init.sh | 29 -
other/cctsweep/wm.sh | 63 -
other/comp_data/Rifampicin/tmp_tab_mtu173.aux | 1 -
other/comp_data/Rifampicin/tmp_tab_mtu173.log | 480 ----
other/comp_data/Rifampicin/tmp_tab_mtu_broad.aux | 1 -
other/comp_data/Rifampicin/tmp_tab_mtu_broad.log | 480 ----
other/comp_data/comp_rpoB_figure.aux | 1 -
other/comp_data/comp_rpoB_figure.log | 456 ----
other/comp_data/comp_rpoB_table.aux | 1 -
other/comp_data/comp_rpoB_table.log | 455 ----
other/comp_data/tmp_comp_rpoB_figure.aux | 1 -
other/comp_data/tmp_comp_rpoB_figure.log | 452 ----
other/comp_data/tmp_comp_rpoB_table.aux | 1 -
other/comp_data/tmp_comp_rpoB_table.log | 481 ----
other/comp_data/tmp_comp_rpoB_table2.aux | 1 -
other/comp_data/tmp_comp_rpoB_table2.log | 481 ----
other/res_data/spn/portable.xls.REMOVED.git-id | 1 +
other/res_data/spn/portable2.xls.REMOVED.git-id | 1 +
other/visR/backup/Xtr.png | Bin 2243 -> 0 bytes
other/visR/backup/chimp.png | Bin 2243 -> 0 bytes
other/visR/backup/colored-predictions.py | 198 --
other/visR/backup/dog.png | Bin 2243 -> 0 bytes
other/visR/backup/ete_test.py | 140 -
other/visR/backup/fish.png | Bin 2243 -> 0 bytes
other/visR/backup/fly.png | Bin 2243 -> 0 bytes
.../backup/generate-excel-tables-scored-genes.py | 232 --
other/visR/backup/img_faces.png | Bin 24277 -> 0 bytes
other/visR/backup/mouse.png | Bin 2243 -> 0 bytes
other/visR/backup/out.pdf | Bin 14327 -> 0 bytes
other/visR/backup/save-tree-mutations_old.py | 433 ----
other/visR/backup/score-subset-mutations.py | 518 ----
other/visR/backup/show-dates.py | 261 --
other/visR/backup/show-mutations.py | 259 --
other/visR/backup/show-tree-mutations.py | 209 --
other/visR/backup/show-tree-mutations_new.py | 206 --
other/visR/backup/test.svg | 2666 --------------------
other/visR/backup/where-located.py | 96 -
other/visR/curves/.fuse_hidden000185b700000003 | 116 -
other/visR/curves/pr_bars.R | 80 -
other/visR/curves/pr_scores_paper.R | 151 --
other/visR/curves/pr_scores_rand.R | 151 --
other/visR/curves/roc_scores_rand.R | 108 -
other/visR/data_stats/data_abailable.R | 30 -
other/visR/data_stats/data_abailable_corr.R | 33 -
other/visR/data_stats/data_corr.R | 37 -
other/visR/data_stats/data_ranks.R | 29 -
other/visR/data_stats/panels_res_stats.R | 60 -
other/visR/data_stats/res_stats.R | 46 -
other/visR/drug_spec/data_drugs_sens_ami_Rv3919c.R | 53 -
other/visR/drug_spec/data_drugs_sens_ami_Rvnr01.R | 53 -
other/visR/drug_spec/data_drugs_sens_ami_Rvnr02.R | 53 -
other/visR/drug_spec/data_drugs_sens_emb_Rv3795.R | 52 -
other/visR/drug_spec/data_drugs_sens_flq_Rv0005.R | 52 -
other/visR/drug_spec/data_drugs_sens_flq_Rv0006.R | 53 -
other/visR/drug_spec/data_drugs_sens_iso_Rv1483.R | 53 -
other/visR/drug_spec/data_drugs_sens_iso_Rv1484.R | 53 -
other/visR/drug_spec/data_drugs_sens_iso_Rv1908c.R | 54 -
other/visR/drug_spec/data_drugs_sens_pza_Rv2043c.R | 51 -
other/visR/drug_spec/data_drugs_sens_rif_Rv0667.R | 52 -
other/visR/drug_spec/data_scores_variants_fig.R | 57 -
other/visR/genome/gene_positions.R | 22 -
other/visR/genome/gene_positions_em59.R | 35 -
other/visR/genome/gene_positions_str238.R | 23 -
other/visR/genome/genome_positions.R | 43 -
other/visR/genome/genome_positions_full.R | 43 -
other/visR/prec_recall/data_prec_recall.R | 121 -
other/visR/prec_recall/data_prec_recall_diff.R | 88 -
.../prec_recall/data_prec_recall_norm_scores.R | 71 -
other/visR/prec_recall/data_prec_recall_pvalues.R | 69 -
other/visR/prec_recall/data_prec_recall_scores.R | 57 -
.../prec_recall/data_prec_recall_spec_pvalues.R | 72 -
.../prec_recall/data_prec_recall_spec_scores.R | 48 -
other/visR/pvalues/data_hist_pvalues.R | 106 -
other/visR/roc/roc_pvalues.R | 108 -
other/visR/roc/roc_scores.R | 123 -
other/visR/roc/roc_scores_all.R | 102 -
other/visR/scores_cmp/data_scores_comp.R | 32 -
other/visR/scores_cmp/data_scores_comp_fig.R | 40 -
other/visR/scores_cmp/data_scores_comp_fig2_all.R | 48 -
other/visR/scores_cmp/data_scores_comp_fig2_high.R | 47 -
other/visR/scores_corr/data_rank_corr.R | 21 -
other/visR/scores_corr/data_ranks_simple.R | 24 -
other/visR/scores_corr/score_correlations.R | 35 -
other/visR/test.R | 26 -
src/drsoft/analysis/a1_save_details_scores_all.py | 50 +-
src/drsoft/analysis/a2_save_details_scores_sel.py | 58 +-
src/drsoft/analysis/a3_save_associations_all.py | 55 +-
src/drsoft/analysis/a4_save_associations_sel.py | 65 +-
src/drsoft/comparison/cmp0_save_associations.py | 61 +-
...c-recall_stats.py => cmp1_prec_recall_stats.py} | 44 +-
src/drsoft/comparison/cmp2_auc_stats.py | 17 +-
src/drsoft/comparison/cmp3_draw_figures.py | 67 +-
src/drsoft/comparison/show0_gold_associations.py | 43 +-
.../backup => src/drsoft/compensatory}/__init__.py | 0
.../compensatory/show0_save_putative_muts.py | 44 +-
src/drsoft/compensatory/show1_latex_rpoB_figure.py | 23 +-
src/drsoft/compensatory/show2_latex_rpoB_table.py | 26 +-
.../compensatory/show2_latex_rpoB_table_sel.py | 26 +-
src/drsoft/compensatory/show3_latex_rpoB_table2.py | 65 +-
src/drsoft/compensatory/show4_rpoB_rels.py | 82 +-
src/drsoft/compensatory/show5_rpoB_pvalues.py | 26 +-
src/drsoft/format_comp/a0_mutations_latex_sel.py | 43 +-
src/drsoft/format_comp/a1_mutation_types.py | 47 +-
src/drsoft/format_comp/a2_mutation_patterns.py | 45 +-
src/drsoft/format_comp/a3_mutation_rel1.py | 47 +-
src/drsoft/format_comp/a4_mutation_rel2.py | 48 +-
src/drsoft/format_comp/a5_mutation_rel3.py | 47 +-
src/drsoft/format_comp/a7_graphvis.py | 82 +-
src/drsoft/format_comp/a8_graphvis_pvalue.py | 58 +-
src/drsoft/format_comp/a9_graphviz_new.py | 58 +-
src/drsoft/format_input/generate_geo_trees.py | 21 +-
src/drsoft/format_input/generate_latex_data.py | 27 +-
src/drsoft/format_input/generate_res_data.py | 83 +-
src/drsoft/format_input/generate_res_trees.py | 15 +-
src/drsoft/format_input/show1_save_mutatinos.py | 146 --
src/drsoft/format_input/show2_mutations_tree.py | 211 --
src/drsoft/format_input/show3_resistance_tree.py | 102 -
src/drsoft/format_input/show4_latex_mutations.py | 364 ---
src/drsoft/format_input/show5_res_tree_graphviz.py | 99 -
.../format_input/show6_res_mut_tree_graphviz.py | 198 --
src/drsoft/format_input/show7_latex_rpoB.py | 198 --
.../drsoft/format_results}/__init__.py | 0
.../format_results/a1_mutations_latex_sel.py | 42 +-
src/drsoft/modelling/cct.py | 51 +-
src/drsoft/modelling/fcct.py | 355 ---
src/drsoft/modelling/habib.py | 27 +-
src/drsoft/modelling/model_logic.py | 23 +-
src/drsoft/modelling/oldhabib.py | 233 --
src/drsoft/modelling/snew.py | 157 --
src/drsoft/modelling/stgh.py | 18 +-
src/drsoft/modelling/tgh.py | 70 +-
src/drsoft/modelling/tgh2.py | 353 ---
src/drsoft/modelling/treeutils.py | 731 ------
src/drsoft/modelling/xcct.py | 339 ---
.../visR/backup => src/drsoft/other}/__init__.py | 0
src/drsoft/other/show0_gold_associations.py | 41 +-
src/drsoft/permtest/perm1_generate_res_profiles.py | 42 +-
.../permtest/perm2_compute_perm_rep_scores.py | 45 +-
.../permtest/perm3_save_perm_rep_rankings.py | 49 +-
.../permtest/perm4_compute_perm_comb_scores.py | 42 +-
.../permtest/perm5_combine_perm_rep_scores.py | 33 +-
src/drsoft/permtest/perm6_calc_pvalues.py | 36 +-
src/drsoft/prepare/p0_convert_gold_associations.py | 36 +-
src/drsoft/prepare/p0_save_strains_ordered.py | 96 +-
src/drsoft/prepare/p1_prepare_experiments.py | 120 +-
src/drsoft/prepare/p2_convert_profiles_genes.py | 210 +-
src/drsoft/prepare/p3_convert_profiles_muts.py | 271 +-
src/drsoft/prepare/p4_gen_binary_trees.py | 148 +-
src/drsoft/prepare/p5_cmp_resistance_profiles.py | 125 +-
src/drsoft/scoring/sc1_compute_std_scores.py | 43 +-
src/drsoft/scoring/sc2_save_std_rankings.py | 50 +-
src/drsoft/scoring/sc3_compute_perm_scores.py | 24 +-
src/drsoft/scoring/sc4_save_perm_rankings.py | 46 +-
src/drsoft/scoring/sc5_compute_norm_scores.py | 48 +-
src/drsoft/structs/rel_graph.py | 2 -
src/drsoft/structs/res_tree.py | 1 -
src/drsoft/utils/gwamar_ann_utils.py | 4 +-
src/drsoft/utils/gwamar_bin_utils.py | 12 +-
src/drsoft/utils/gwamar_comp_utils.py | 6 -
src/drsoft/utils/gwamar_generator_utils.py | 19 -
src/drsoft/utils/gwamar_muts_io_utils.py | 8 +-
src/drsoft/utils/gwamar_muts_utils.py | 2 -
src/drsoft/utils/gwamar_params_utils.py | 12 +-
src/drsoft/utils/gwamar_pws.py | 9 +-
src/drsoft/utils/gwamar_res_io_utils.py | 71 +-
src/drsoft/utils/gwamar_res_utils.py | 6 +-
src/drsoft/utils/gwamar_scoring.py | 71 +-
src/drsoft/utils/gwamar_scoring_flat_utils.py | 28 +-
src/drsoft/utils/gwamar_scoring_tree_utils.py | 101 +-
src/drsoft/utils/gwamar_stat_utils.py | 20 -
src/drsoft/utils/gwamar_strains_io_utils.py | 6 +-
src/drsoft/utils/gwamar_tree_io_utils.py | 13 +-
src/drsoft/utils/gwamar_utils.py | 2 +-
{other/visR/backup => src/prebroad}/__init__.py | 0
.../backup => src/prebroad/prepare}/__init__.py | 0
src/prebroad/prepare/p1_download_files.py | 31 +-
src/prebroad/prepare/p2_save_strains.py | 21 +-
src/prebroad/prepare/p3_save_resdata.py | 26 +-
.../prepare/p4_combine_resistance_profiles.py | 25 +-
src/prebroad/prepare/p5_save_point_mutations_aa.py | 23 +-
src/prebroad/tree/t0_save_point_mutations_nt.py | 25 +-
src/prebroad/tree/t1_prepare_alignments.py | 31 +-
src/prebroad/tree/t2_compute_subset_tree.py | 35 +-
src/prebroad/tree/t3_resolve_clusters.py | 31 +-
src/prebroad/tree/t4_save_strains_ordered.py | 23 +-
src/visR/accuracy/{auc_vioplots.R => auc_simmat.R} | 0
195 files changed, 1708 insertions(+), 17909 deletions(-)
create mode 100644 .project
create mode 100644 .pydevproject
create mode 100644 config/config_tools.txt
create mode 100644 datasets/mtu173/input/point_mutations.txt.REMOVED.git-id
create mode 100644 datasets/sau461/input/point_mutations.txt.REMOVED.git-id
delete mode 100644 other/cctsweep/bm.sh
delete mode 100644 other/cctsweep/cct.sh
delete mode 100644 other/cctsweep/init.sh
delete mode 100644 other/cctsweep/wm.sh
delete mode 100644 other/comp_data/Rifampicin/tmp_tab_mtu173.aux
delete mode 100644 other/comp_data/Rifampicin/tmp_tab_mtu173.log
delete mode 100644 other/comp_data/Rifampicin/tmp_tab_mtu_broad.aux
delete mode 100644 other/comp_data/Rifampicin/tmp_tab_mtu_broad.log
delete mode 100644 other/comp_data/comp_rpoB_figure.aux
delete mode 100644 other/comp_data/comp_rpoB_figure.log
delete mode 100644 other/comp_data/comp_rpoB_table.aux
delete mode 100644 other/comp_data/comp_rpoB_table.log
delete mode 100644 other/comp_data/tmp_comp_rpoB_figure.aux
delete mode 100644 other/comp_data/tmp_comp_rpoB_figure.log
delete mode 100644 other/comp_data/tmp_comp_rpoB_table.aux
delete mode 100644 other/comp_data/tmp_comp_rpoB_table.log
delete mode 100644 other/comp_data/tmp_comp_rpoB_table2.aux
delete mode 100644 other/comp_data/tmp_comp_rpoB_table2.log
create mode 100644 other/res_data/spn/portable.xls.REMOVED.git-id
create mode 100644 other/res_data/spn/portable2.xls.REMOVED.git-id
delete mode 100644 other/visR/backup/Xtr.png
delete mode 100644 other/visR/backup/chimp.png
delete mode 100644 other/visR/backup/colored-predictions.py
delete mode 100644 other/visR/backup/dog.png
delete mode 100644 other/visR/backup/ete_test.py
delete mode 100644 other/visR/backup/fish.png
delete mode 100644 other/visR/backup/fly.png
delete mode 100644 other/visR/backup/generate-excel-tables-scored-genes.py
delete mode 100644 other/visR/backup/img_faces.png
delete mode 100644 other/visR/backup/mouse.png
delete mode 100644 other/visR/backup/out.pdf
delete mode 100644 other/visR/backup/save-tree-mutations_old.py
delete mode 100644 other/visR/backup/score-subset-mutations.py
delete mode 100644 other/visR/backup/show-dates.py
delete mode 100644 other/visR/backup/show-mutations.py
delete mode 100644 other/visR/backup/show-tree-mutations.py
delete mode 100644 other/visR/backup/show-tree-mutations_new.py
delete mode 100644 other/visR/backup/test.svg
delete mode 100644 other/visR/backup/where-located.py
delete mode 100644 other/visR/curves/.fuse_hidden000185b700000003
delete mode 100644 other/visR/curves/pr_bars.R
delete mode 100644 other/visR/curves/pr_scores_paper.R
delete mode 100644 other/visR/curves/pr_scores_rand.R
delete mode 100644 other/visR/curves/roc_scores_rand.R
delete mode 100644 other/visR/data_stats/data_abailable.R
delete mode 100644 other/visR/data_stats/data_abailable_corr.R
delete mode 100644 other/visR/data_stats/data_corr.R
delete mode 100644 other/visR/data_stats/data_ranks.R
delete mode 100644 other/visR/data_stats/panels_res_stats.R
delete mode 100644 other/visR/data_stats/res_stats.R
delete mode 100644 other/visR/drug_spec/data_drugs_sens_ami_Rv3919c.R
delete mode 100644 other/visR/drug_spec/data_drugs_sens_ami_Rvnr01.R
delete mode 100644 other/visR/drug_spec/data_drugs_sens_ami_Rvnr02.R
delete mode 100644 other/visR/drug_spec/data_drugs_sens_emb_Rv3795.R
delete mode 100644 other/visR/drug_spec/data_drugs_sens_flq_Rv0005.R
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delete mode 100644 other/visR/drug_spec/data_drugs_sens_iso_Rv1483.R
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delete mode 100644 other/visR/drug_spec/data_drugs_sens_iso_Rv1908c.R
delete mode 100644 other/visR/drug_spec/data_drugs_sens_pza_Rv2043c.R
delete mode 100644 other/visR/drug_spec/data_drugs_sens_rif_Rv0667.R
delete mode 100644 other/visR/drug_spec/data_scores_variants_fig.R
delete mode 100644 other/visR/genome/gene_positions.R
delete mode 100644 other/visR/genome/gene_positions_em59.R
delete mode 100644 other/visR/genome/gene_positions_str238.R
delete mode 100644 other/visR/genome/genome_positions.R
delete mode 100644 other/visR/genome/genome_positions_full.R
delete mode 100644 other/visR/prec_recall/data_prec_recall.R
delete mode 100644 other/visR/prec_recall/data_prec_recall_diff.R
delete mode 100644 other/visR/prec_recall/data_prec_recall_norm_scores.R
delete mode 100644 other/visR/prec_recall/data_prec_recall_pvalues.R
delete mode 100644 other/visR/prec_recall/data_prec_recall_scores.R
delete mode 100644 other/visR/prec_recall/data_prec_recall_spec_pvalues.R
delete mode 100644 other/visR/prec_recall/data_prec_recall_spec_scores.R
delete mode 100644 other/visR/pvalues/data_hist_pvalues.R
delete mode 100644 other/visR/roc/roc_pvalues.R
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delete mode 100644 other/visR/roc/roc_scores_all.R
delete mode 100644 other/visR/scores_cmp/data_scores_comp.R
delete mode 100644 other/visR/scores_cmp/data_scores_comp_fig.R
delete mode 100644 other/visR/scores_cmp/data_scores_comp_fig2_all.R
delete mode 100644 other/visR/scores_cmp/data_scores_comp_fig2_high.R
delete mode 100644 other/visR/scores_corr/data_rank_corr.R
delete mode 100644 other/visR/scores_corr/data_ranks_simple.R
delete mode 100644 other/visR/scores_corr/score_correlations.R
delete mode 100644 other/visR/test.R
rename src/drsoft/comparison/{cmp1_prec-recall_stats.py => cmp1_prec_recall_stats.py} (90%)
copy {other/visR/backup => src/drsoft/compensatory}/__init__.py (100%)
delete mode 100644 src/drsoft/format_input/show1_save_mutatinos.py
delete mode 100644 src/drsoft/format_input/show2_mutations_tree.py
delete mode 100644 src/drsoft/format_input/show3_resistance_tree.py
delete mode 100644 src/drsoft/format_input/show4_latex_mutations.py
delete mode 100644 src/drsoft/format_input/show5_res_tree_graphviz.py
delete mode 100644 src/drsoft/format_input/show6_res_mut_tree_graphviz.py
delete mode 100644 src/drsoft/format_input/show7_latex_rpoB.py
copy {other/visR/backup => src/drsoft/format_results}/__init__.py (100%)
delete mode 100644 src/drsoft/modelling/fcct.py
delete mode 100644 src/drsoft/modelling/oldhabib.py
delete mode 100644 src/drsoft/modelling/snew.py
delete mode 100644 src/drsoft/modelling/tgh2.py
delete mode 100644 src/drsoft/modelling/treeutils.py
delete mode 100644 src/drsoft/modelling/xcct.py
copy {other/visR/backup => src/drsoft/other}/__init__.py (100%)
copy {other/visR/backup => src/prebroad}/__init__.py (100%)
rename {other/visR/backup => src/prebroad/prepare}/__init__.py (100%)
copy src/visR/accuracy/{auc_vioplots.R => auc_simmat.R} (100%)
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