[med-svn] [gwamar] 05/09: Merge tag 'upstream/1.15.1+dfsg'
Andreas Tille
tille at debian.org
Tue Dec 8 15:49:57 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository gwamar.
commit b62e29327be293c3fa951891861e8d0a18c08d42
Merge: bfa6d55 fd6d36a
Author: Andreas Tille <tille at debian.org>
Date: Mon Dec 7 12:27:11 2015 +0100
Merge tag 'upstream/1.15.1+dfsg'
Upstream version 1.15.1+dfsg
.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_simmat.R | 314 +++
195 files changed, 2022 insertions(+), 17909 deletions(-)
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