diff options
Diffstat (limited to 'biology/pycogent/pkg-plist')
| -rw-r--r-- | biology/pycogent/pkg-plist | 45 |
1 files changed, 38 insertions, 7 deletions
diff --git a/biology/pycogent/pkg-plist b/biology/pycogent/pkg-plist index 81d4bebc9bd..addc2b2622d 100644 --- a/biology/pycogent/pkg-plist +++ b/biology/pycogent/pkg-plist @@ -145,6 +145,9 @@ %%PYTHON_SITELIBDIR%%/cogent/app/rdp_classifier.py %%PYTHON_SITELIBDIR%%/cogent/app/rdp_classifier.pyc %%PYTHON_SITELIBDIR%%/cogent/app/rdp_classifier.pyo +%%PYTHON_SITELIBDIR%%/cogent/app/rdp_classifier20.py +%%PYTHON_SITELIBDIR%%/cogent/app/rdp_classifier20.pyc +%%PYTHON_SITELIBDIR%%/cogent/app/rdp_classifier20.pyo %%PYTHON_SITELIBDIR%%/cogent/app/rnaalifold.py %%PYTHON_SITELIBDIR%%/cogent/app/rnaalifold.pyc %%PYTHON_SITELIBDIR%%/cogent/app/rnaalifold.pyo @@ -325,6 +328,9 @@ %%PYTHON_SITELIBDIR%%/cogent/draw/codon_usage.py %%PYTHON_SITELIBDIR%%/cogent/draw/codon_usage.pyc %%PYTHON_SITELIBDIR%%/cogent/draw/codon_usage.pyo +%%PYTHON_SITELIBDIR%%/cogent/draw/compatibility.py +%%PYTHON_SITELIBDIR%%/cogent/draw/compatibility.pyc +%%PYTHON_SITELIBDIR%%/cogent/draw/compatibility.pyo %%PYTHON_SITELIBDIR%%/cogent/draw/dendrogram.py %%PYTHON_SITELIBDIR%%/cogent/draw/dendrogram.pyc %%PYTHON_SITELIBDIR%%/cogent/draw/dendrogram.pyo @@ -356,6 +362,8 @@ %%PYTHON_SITELIBDIR%%/cogent/evolve/__init__.pyc %%PYTHON_SITELIBDIR%%/cogent/evolve/__init__.pyo %%PYTHON_SITELIBDIR%%/cogent/evolve/_likelihood_tree.so +%%PYTHON_SITELIBDIR%%/cogent/evolve/_pairwise_distance.so +%%PYTHON_SITELIBDIR%%/cogent/evolve/_solved_models.so %%PYTHON_SITELIBDIR%%/cogent/evolve/best_likelihood.py %%PYTHON_SITELIBDIR%%/cogent/evolve/best_likelihood.pyc %%PYTHON_SITELIBDIR%%/cogent/evolve/best_likelihood.pyo @@ -383,12 +391,18 @@ %%PYTHON_SITELIBDIR%%/cogent/evolve/motif_prob_model.py %%PYTHON_SITELIBDIR%%/cogent/evolve/motif_prob_model.pyc %%PYTHON_SITELIBDIR%%/cogent/evolve/motif_prob_model.pyo +%%PYTHON_SITELIBDIR%%/cogent/evolve/pairwise_distance.py +%%PYTHON_SITELIBDIR%%/cogent/evolve/pairwise_distance.pyc +%%PYTHON_SITELIBDIR%%/cogent/evolve/pairwise_distance.pyo %%PYTHON_SITELIBDIR%%/cogent/evolve/parameter_controller.py %%PYTHON_SITELIBDIR%%/cogent/evolve/parameter_controller.pyc %%PYTHON_SITELIBDIR%%/cogent/evolve/parameter_controller.pyo %%PYTHON_SITELIBDIR%%/cogent/evolve/predicate.py %%PYTHON_SITELIBDIR%%/cogent/evolve/predicate.pyc %%PYTHON_SITELIBDIR%%/cogent/evolve/predicate.pyo +%%PYTHON_SITELIBDIR%%/cogent/evolve/solved_models.py +%%PYTHON_SITELIBDIR%%/cogent/evolve/solved_models.pyc +%%PYTHON_SITELIBDIR%%/cogent/evolve/solved_models.pyo %%PYTHON_SITELIBDIR%%/cogent/evolve/simulate.py %%PYTHON_SITELIBDIR%%/cogent/evolve/simulate.pyc %%PYTHON_SITELIBDIR%%/cogent/evolve/simulate.pyo @@ -449,10 +463,12 @@ %%PYTHON_SITELIBDIR%%/cogent/maths/__init__.py %%PYTHON_SITELIBDIR%%/cogent/maths/__init__.pyc %%PYTHON_SITELIBDIR%%/cogent/maths/__init__.pyo -%%PYTHON_SITELIBDIR%%/cogent/maths/_matrix_exponentiation.so %%PYTHON_SITELIBDIR%%/cogent/maths/distance_transform.py %%PYTHON_SITELIBDIR%%/cogent/maths/distance_transform.pyc %%PYTHON_SITELIBDIR%%/cogent/maths/distance_transform.pyo +%%PYTHON_SITELIBDIR%%/cogent/maths/fit_function.py +%%PYTHON_SITELIBDIR%%/cogent/maths/fit_function.pyc +%%PYTHON_SITELIBDIR%%/cogent/maths/fit_function.pyo %%PYTHON_SITELIBDIR%%/cogent/maths/function_optimisation.py %%PYTHON_SITELIBDIR%%/cogent/maths/function_optimisation.pyc %%PYTHON_SITELIBDIR%%/cogent/maths/function_optimisation.pyo @@ -474,9 +490,6 @@ %%PYTHON_SITELIBDIR%%/cogent/maths/matrix_logarithm.py %%PYTHON_SITELIBDIR%%/cogent/maths/matrix_logarithm.pyc %%PYTHON_SITELIBDIR%%/cogent/maths/matrix_logarithm.pyo -%%PYTHON_SITELIBDIR%%/cogent/maths/optimiser.py -%%PYTHON_SITELIBDIR%%/cogent/maths/optimiser.pyc -%%PYTHON_SITELIBDIR%%/cogent/maths/optimiser.pyo %%PYTHON_SITELIBDIR%%/cogent/maths/optimisers.py %%PYTHON_SITELIBDIR%%/cogent/maths/optimisers.pyc %%PYTHON_SITELIBDIR%%/cogent/maths/optimisers.pyo @@ -515,6 +528,9 @@ %%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/get_by_cai.py %%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/get_by_cai.pyc %%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/get_by_cai.pyo +%%PYTHON_SITELIBDIR%%/cogent/maths/stats/jackknife.py +%%PYTHON_SITELIBDIR%%/cogent/maths/stats/jackknife.pyc +%%PYTHON_SITELIBDIR%%/cogent/maths/stats/jackknife.pyo %%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/util.py %%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/util.pyc %%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/util.pyo @@ -587,6 +603,9 @@ %%PYTHON_SITELIBDIR%%/cogent/parse/blast_xml.py %%PYTHON_SITELIBDIR%%/cogent/parse/blast_xml.pyc %%PYTHON_SITELIBDIR%%/cogent/parse/blast_xml.pyo +%%PYTHON_SITELIBDIR%%/cogent/parse/bowtie.py +%%PYTHON_SITELIBDIR%%/cogent/parse/bowtie.pyc +%%PYTHON_SITELIBDIR%%/cogent/parse/bowtie.pyo %%PYTHON_SITELIBDIR%%/cogent/parse/bpseq.py %%PYTHON_SITELIBDIR%%/cogent/parse/bpseq.pyc %%PYTHON_SITELIBDIR%%/cogent/parse/bpseq.pyo @@ -662,6 +681,9 @@ %%PYTHON_SITELIBDIR%%/cogent/parse/gibbs.py %%PYTHON_SITELIBDIR%%/cogent/parse/gibbs.pyc %%PYTHON_SITELIBDIR%%/cogent/parse/gibbs.pyo +%%PYTHON_SITELIBDIR%%/cogent/parse/greengenes.py +%%PYTHON_SITELIBDIR%%/cogent/parse/greengenes.pyc +%%PYTHON_SITELIBDIR%%/cogent/parse/greengenes.pyo %%PYTHON_SITELIBDIR%%/cogent/parse/flowgram.py %%PYTHON_SITELIBDIR%%/cogent/parse/flowgram.pyc %%PYTHON_SITELIBDIR%%/cogent/parse/flowgram.pyo @@ -680,6 +702,9 @@ %%PYTHON_SITELIBDIR%%/cogent/parse/infernal.py %%PYTHON_SITELIBDIR%%/cogent/parse/infernal.pyc %%PYTHON_SITELIBDIR%%/cogent/parse/infernal.pyo +%%PYTHON_SITELIBDIR%%/cogent/parse/kegg_fasta.py +%%PYTHON_SITELIBDIR%%/cogent/parse/kegg_fasta.pyc +%%PYTHON_SITELIBDIR%%/cogent/parse/kegg_fasta.pyo %%PYTHON_SITELIBDIR%%/cogent/parse/kegg_ko.py %%PYTHON_SITELIBDIR%%/cogent/parse/kegg_ko.pyc %%PYTHON_SITELIBDIR%%/cogent/parse/kegg_ko.pyo @@ -743,6 +768,9 @@ %%PYTHON_SITELIBDIR%%/cogent/parse/pknotsrg.py %%PYTHON_SITELIBDIR%%/cogent/parse/pknotsrg.pyc %%PYTHON_SITELIBDIR%%/cogent/parse/pknotsrg.pyo +%%PYTHON_SITELIBDIR%%/cogent/parse/psl.py +%%PYTHON_SITELIBDIR%%/cogent/parse/psl.pyc +%%PYTHON_SITELIBDIR%%/cogent/parse/psl.pyo %%PYTHON_SITELIBDIR%%/cogent/parse/rdb.py %%PYTHON_SITELIBDIR%%/cogent/parse/rdb.pyc %%PYTHON_SITELIBDIR%%/cogent/parse/rdb.pyo @@ -779,6 +807,9 @@ %%PYTHON_SITELIBDIR%%/cogent/parse/sfold.py %%PYTHON_SITELIBDIR%%/cogent/parse/sfold.pyc %%PYTHON_SITELIBDIR%%/cogent/parse/sfold.pyo +%%PYTHON_SITELIBDIR%%/cogent/parse/stockholm.py +%%PYTHON_SITELIBDIR%%/cogent/parse/stockholm.pyc +%%PYTHON_SITELIBDIR%%/cogent/parse/stockholm.pyo %%PYTHON_SITELIBDIR%%/cogent/parse/sprinzl.py %%PYTHON_SITELIBDIR%%/cogent/parse/sprinzl.pyc %%PYTHON_SITELIBDIR%%/cogent/parse/sprinzl.pyo @@ -809,9 +840,6 @@ %%PYTHON_SITELIBDIR%%/cogent/phylo/__init__.py %%PYTHON_SITELIBDIR%%/cogent/phylo/__init__.pyc %%PYTHON_SITELIBDIR%%/cogent/phylo/__init__.pyo -%%PYTHON_SITELIBDIR%%/cogent/phylo/compatibility.py -%%PYTHON_SITELIBDIR%%/cogent/phylo/compatibility.pyc -%%PYTHON_SITELIBDIR%%/cogent/phylo/compatibility.pyo %%PYTHON_SITELIBDIR%%/cogent/phylo/consensus.py %%PYTHON_SITELIBDIR%%/cogent/phylo/consensus.pyc %%PYTHON_SITELIBDIR%%/cogent/phylo/consensus.pyo @@ -940,6 +968,9 @@ %%PYTHON_SITELIBDIR%%/cogent/util/modules.py %%PYTHON_SITELIBDIR%%/cogent/util/modules.pyc %%PYTHON_SITELIBDIR%%/cogent/util/modules.pyo +%%PYTHON_SITELIBDIR%%/cogent/util/option_parsing.py +%%PYTHON_SITELIBDIR%%/cogent/util/option_parsing.pyc +%%PYTHON_SITELIBDIR%%/cogent/util/option_parsing.pyo %%PYTHON_SITELIBDIR%%/cogent/util/organizer.py %%PYTHON_SITELIBDIR%%/cogent/util/organizer.pyc %%PYTHON_SITELIBDIR%%/cogent/util/organizer.pyo |