[med-svn] [gwamar] branch master updated (ebe1def -> 900e976)
Andreas Tille
tille at debian.org
Tue Dec 8 15:49:33 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository gwamar.
from ebe1def Upstream confirmed GPL in e-mail
new bfa6d55 Adapt watch file to new directory layout
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
new b62e293 Merge tag 'upstream/1.15.1+dfsg'
new 3735039 Upstream applied patches
new 5f1c173 Try again Python 3
new ebf5ea2 Make sure the internal Python3 scripts will be found
new 900e976 Adapt usage hint to Debian invocation
The 9 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 +
debian/bin/gwamar | 10 +-
debian/changelog | 4 +-
debian/control | 6 +-
debian/patches/2to3.patch | 15 +
.../adapt_debian_locations_of_binaries.patch | 23 -
debian/patches/patch_usage.patch | 14 +
debian/patches/series | 3 +-
debian/rules | 2 +-
debian/watch | 4 +-
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
204 files changed, 1755 insertions(+), 17943 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
create mode 100644 debian/patches/2to3.patch
delete mode 100644 debian/patches/adapt_debian_locations_of_binaries.patch
create mode 100644 debian/patches/patch_usage.patch
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
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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
delete mode 100644 other/visR/drug_spec/data_drugs_sens_flq_Rv0006.R
delete mode 100644 other/visR/drug_spec/data_drugs_sens_iso_Rv1483.R
delete mode 100644 other/visR/drug_spec/data_drugs_sens_iso_Rv1484.R
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
delete mode 100644 other/visR/roc/roc_scores.R
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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