[med-svn] [graphlan] 13/14: Updated version 1.1 from 'upstream/1.1'

[Andreas Tille]

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tille pushed a commit to branch master
in repository graphlan.

commit 5e823e7fb5cd5c5ad1308d69c3140a45510bd9c3
Merge: 0951c5a 027e842
Author: Andreas Tille <tille at debian.org>
Date:   Wed Nov 15 11:28:33 2017 +0100

    Updated version 1.1 from 'upstream/1.1'
    
    with Debian dir 7271158a1e073998343b961a47ab49f43b2b2ec3

 .hg_archival.txt                                   |     4 +
 .hgignore                                          |     6 +
 .hgsub                                             |     2 +
 .hgsubstate                                        |     2 +
 .hgtags                                            |     7 +
 examples/DisappearingMicrobiome/DisMic.xml         | 26217 +++++++++++++++++++
 examples/DisappearingMicrobiome/annot.txt          | 18814 +++++++++++++
 examples/DisappearingMicrobiome/genomes.all.txt    |  3739 +++
 examples/DisappearingMicrobiome/run.sh             |    57 +
 examples/HMP_tree/annot.txt                        |  8866 +++++++
 examples/HMP_tree/hmptree.xml                      |  2694 ++
 examples/HMP_tree/run.sh                           |     3 +
 examples/HMP_tree_simple/annot.txt                 |   756 +
 examples/HMP_tree_simple/hmptree.xml               |  2694 ++
 examples/HMP_tree_simple/run.sh                    |     3 +
 examples/IBD_biogeography/IBDgeo.txt               |   220 +
 examples/IBD_biogeography/annotation.txt           |   174 +
 examples/IBD_biogeography/run.sh                   |     3 +
 examples/PhyloPhlAn/annot.txt                      | 22293 ++++++++++++++++
 examples/PhyloPhlAn/ppa_tol.xml                    | 26217 +++++++++++++++++++
 examples/PhyloPhlAn/run.sh                         |     3 +
 examples/archaea/annot.txt                         |   747 +
 examples/archaea/archaea.txt                       |   121 +
 examples/archaea/run.sh                            |     3 +
 examples/guide/annot_0.txt                         |     7 +
 examples/guide/annot_1.txt                         |    41 +
 examples/guide/annot_2.txt                         |    24 +
 examples/guide/annot_3.txt                         |   429 +
 examples/guide/guide.txt                           |    51 +
 examples/guide/step0.sh                            |     2 +
 examples/guide/step1.sh                            |     3 +
 examples/guide/step2.sh                            |     3 +
 examples/guide/step3.sh                            |     3 +
 examples/guide/step4.sh                            |     3 +
 examples/gut_microbiome/annot.txt                  |   570 +
 examples/gut_microbiome/gut_microbiome.txt         |   290 +
 examples/gut_microbiome/run.sh                     |     3 +
 examples/hmp_metahit/PIPELINE.sh                   |   106 +
 examples/hmp_metahit/merge-very-good.txt           |   891 +
 examples/hmp_metahit/merge-very-good.txt.out       |   890 +
 examples/hmp_metahit/metahit.txt                   |   264 +
 examples/hmp_metahit_functional/PIPELINE.sh        |    88 +
 examples/hmp_metahit_functional/hmp.txt            |   315 +
 examples/hmp_metahit_functional/merge-humann.py    |   163 +
 examples/hmp_metahit_functional/merge.txt          |   302 +
 examples/hmp_metahit_functional/merge.txt.out      |   344 +
 examples/hmp_metahit_functional/metahit.txt        |   268 +
 .../hmp_metahit_functional/metahit_download.txt    |   264 +
 examples/hmp_metahit_functional/metahit_map.txt    |   124 +
 examples/internal_labels/annot_0.txt               |    22 +
 examples/internal_labels/annot_1.txt               |    99 +
 examples/internal_labels/annot_2.txt               |    36 +
 examples/internal_labels/annot_3.txt               |   239 +
 examples/internal_labels/archaea.txt               |    86 +
 examples/internal_labels/readme.txt                |    27 +
 examples/internal_labels/step0.sh                  |     3 +
 examples/internal_labels/step1.sh                  |     4 +
 examples/internal_labels/step2.sh                  |     4 +
 examples/internal_labels/step3.sh                  |     4 +
 examples/internal_labels/step4.sh                  |     4 +
 examples/kegg/annot.txt                            | 20167 ++++++++++++++
 examples/kegg/ppa_kegg_raxml.names.nn.nwk          |  6873 +++++
 examples/kegg/run.sh                               |     3 +
 examples/metaref_fams/mr1.a.txt                    |   138 +
 examples/metaref_fams/mr1.txt                      |    94 +
 examples/metaref_fams/mr2.a.txt                    |    72 +
 examples/metaref_fams/run.sh                       |     8 +
 examples/phylo_small/annot.txt                     |   948 +
 examples/phylo_small/phylo_small.xml               |   274 +
 examples/phylo_small/run.sh                        |     3 +
 examples/readme.txt                                |     6 +
 examples/saliva_microbiome/PIPELINE.sh             |    14 +
 examples/saliva_microbiome/otu_table.biom          |     1 +
 examples/simple/annot.txt                          |    58 +
 examples/simple/core_genes.txt                     |   192 +
 examples/simple/run.sh                             |     3 +
 examples/vaginal_microbiota/PIPELINE.sh            |    14 +
 .../stm_otu_table_with_taxonomy.biom               |     1 +
 graphlan.py                                        |    70 +
 graphlan_annotate.py                               |    57 +
 license.txt                                        |     7 +
 readme.txt                                         |   468 +
 src/__init__.py                                    |     0
 src/graphlan_lib.py                                |  1079 +
 src/pyphlan.py                                     |   729 +
 85 files changed, 150900 insertions(+)

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