Rearrange PAML test resource directory

biopython · Feb 22, 2012 · 3f61fc9 · 3f61fc9
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diff --git a/Tests/PAML/Resources/aa_alignment.phylip → Tests/PAML/Alignments/aa_alignment.phylip b/Tests/PAML/Resources/aa_alignment.phylip → Tests/PAML/Alignments/aa_alignment.phylip
diff --git a/Tests/PAML/Resources/alignment.phylip → Tests/PAML/Alignments/alignment.phylip b/Tests/PAML/Resources/alignment.phylip → Tests/PAML/Alignments/alignment.phylip
diff --git a/...Resources/codeml/lysinYangSwanson2002.nuc → .../PAML/Alignments/lysinYangSwanson2002.nuc b/...Resources/codeml/lysinYangSwanson2002.nuc → .../PAML/Alignments/lysinYangSwanson2002.nuc
diff --git a/Tests/PAML/Resources/README.txt → Tests/PAML/Control_files/README.txt b/Tests/PAML/Resources/README.txt → Tests/PAML/Control_files/README.txt
diff --git a/Tests/PAML/bad1.ctl → Tests/PAML/Control_files/bad1.ctl b/Tests/PAML/bad1.ctl → Tests/PAML/Control_files/bad1.ctl
diff --git a/Tests/PAML/bad2.ctl → Tests/PAML/Control_files/bad2.ctl b/Tests/PAML/bad2.ctl → Tests/PAML/Control_files/bad2.ctl
diff --git a/Tests/PAML/bad3.ctl → Tests/PAML/Control_files/bad3.ctl b/Tests/PAML/bad3.ctl → Tests/PAML/Control_files/bad3.ctl
diff --git a/Tests/PAML/Resources/baseml/baseml.ctl → Tests/PAML/Control_files/baseml.ctl b/Tests/PAML/Resources/baseml/baseml.ctl → Tests/PAML/Control_files/baseml.ctl
diff --git a/Tests/PAML/baseml.ctl → Tests/PAML/Control_files/baseml/baseml.ctl b/Tests/PAML/baseml.ctl → Tests/PAML/Control_files/baseml/baseml.ctl
diff --git a/Tests/PAML/Resources/codeml/SE.ctl → Tests/PAML/Control_files/codeml/SE.ctl b/Tests/PAML/Resources/codeml/SE.ctl → Tests/PAML/Control_files/codeml/SE.ctl
diff --git a/Tests/PAML/Resources/codeml/aa_model0.ctl → ...s/PAML/Control_files/codeml/aa_model0.ctl b/Tests/PAML/Resources/codeml/aa_model0.ctl → ...s/PAML/Control_files/codeml/aa_model0.ctl
diff --git a/Tests/PAML/Resources/codeml/aa_pairwise.ctl → ...PAML/Control_files/codeml/aa_pairwise.ctl b/Tests/PAML/Resources/codeml/aa_pairwise.ctl → ...PAML/Control_files/codeml/aa_pairwise.ctl
diff --git a/...ces/codeml/allNSSites_and_allVersions.ctl → ...PAML/Control_files/codeml/all_NSsites.ctl b/...ces/codeml/allNSSites_and_allVersions.ctl → ...PAML/Control_files/codeml/all_NSsites.ctl
diff --git a/Tests/PAML/Resources/codeml/branchsiteA.ctl → ...PAML/Control_files/codeml/branchsiteA.ctl b/Tests/PAML/Resources/codeml/branchsiteA.ctl → ...PAML/Control_files/codeml/branchsiteA.ctl
diff --git a/Tests/PAML/Resources/codeml/clademodelC.ctl → ...PAML/Control_files/codeml/clademodelC.ctl b/Tests/PAML/Resources/codeml/clademodelC.ctl → ...PAML/Control_files/codeml/clademodelC.ctl
diff --git a/Tests/PAML/codeml.ctl → Tests/PAML/Control_files/codeml/codeml.ctl b/Tests/PAML/codeml.ctl → Tests/PAML/Control_files/codeml/codeml.ctl
diff --git a/Tests/PAML/Resources/codeml/freebranch.ctl → ...s/PAML/Control_files/codeml/freeratio.ctl b/Tests/PAML/Resources/codeml/freebranch.ctl → ...s/PAML/Control_files/codeml/freeratio.ctl
diff --git a/...PAML/Resources/codeml/ngene2_mgene012.ctl → .../Control_files/codeml/ngene2_mgene012.ctl b/...PAML/Resources/codeml/ngene2_mgene012.ctl → .../Control_files/codeml/ngene2_mgene012.ctl
diff --git a/.../PAML/Resources/codeml/ngene2_mgene34.ctl → ...L/Control_files/codeml/ngene2_mgene34.ctl b/.../PAML/Resources/codeml/ngene2_mgene34.ctl → ...L/Control_files/codeml/ngene2_mgene34.ctl
diff --git a/Tests/PAML/Resources/codeml/pairwise.ctl → Tests/PAML/Control_files/codeml/pairwise.ctl b/Tests/PAML/Resources/codeml/pairwise.ctl → Tests/PAML/Control_files/codeml/pairwise.ctl
diff --git a/Tests/PAML/Resources/species.tree → Tests/PAML/Control_files/species.tree b/Tests/PAML/Resources/species.tree → Tests/PAML/Control_files/species.tree
diff --git a/Tests/PAML/Resources/yn00/yn00.ctl → Tests/PAML/Control_files/yn00.ctl b/Tests/PAML/Resources/yn00/yn00.ctl → Tests/PAML/Control_files/yn00.ctl
diff --git a/Tests/PAML/yn00.ctl → Tests/PAML/Control_files/yn00/yn00.ctl b/Tests/PAML/yn00.ctl → Tests/PAML/Control_files/yn00/yn00.ctl
diff --git a/Tests/PAML/bad_results.out → Tests/PAML/Results/bad_results.out b/Tests/PAML/bad_results.out → Tests/PAML/Results/bad_results.out
diff --git a/Tests/PAML/Results/codeml/codeml_SE.out → Tests/PAML/Results/codeml/SE/SE-4_3.out b/Tests/PAML/Results/codeml/codeml_SE.out → Tests/PAML/Results/codeml/SE/SE-4_3.out
diff --git a/.../PAML/Results/codeml/codeml_aa_model0.out → ...sults/codeml/aa_model0/aa_model0-4_4c.out b/.../PAML/Results/codeml/codeml_aa_model0.out → ...sults/codeml/aa_model0/aa_model0-4_4c.out
diff --git a/...AML/Results/codeml/codeml_aa_pairwise.out → ...s/codeml/aa_pairwise/aa_pairwise-4_4c.out b/...AML/Results/codeml/codeml_aa_pairwise.out → ...s/codeml/aa_pairwise/aa_pairwise-4_4c.out
diff --git a/...PAML/Results/codeml/versions/codeml41.out → ...ts/codeml/all_NSsites/all_NSsites-4_1.out b/...PAML/Results/codeml/versions/codeml41.out → ...ts/codeml/all_NSsites/all_NSsites-4_1.out
diff --git a/...PAML/Results/codeml/versions/codeml43.out → ...ts/codeml/all_NSsites/all_NSsites-4_3.out b/...PAML/Results/codeml/versions/codeml43.out → ...ts/codeml/all_NSsites/all_NSsites-4_3.out
diff --git a/...PAML/Results/codeml/versions/codeml44.out → ...ts/codeml/all_NSsites/all_NSsites-4_4.out b/...PAML/Results/codeml/versions/codeml44.out → ...ts/codeml/all_NSsites/all_NSsites-4_4.out
diff --git a/...AML/Results/codeml/versions/codeml44c.out → ...s/codeml/all_NSsites/all_NSsites-4_4c.out b/...AML/Results/codeml/versions/codeml44c.out → ...s/codeml/all_NSsites/all_NSsites-4_4c.out
diff --git a/...PAML/Results/codeml/versions/codeml45.out → ...ts/codeml/all_NSsites/all_NSsites-4_5.out b/...PAML/Results/codeml/versions/codeml45.out → ...ts/codeml/all_NSsites/all_NSsites-4_5.out
diff --git a/...AML/Results/codeml/codeml_branchsiteA.out → ...ts/codeml/branchsiteA/branchsiteA-4_3.out b/...AML/Results/codeml/codeml_branchsiteA.out → ...ts/codeml/branchsiteA/branchsiteA-4_3.out
diff --git a/...AML/Results/codeml/codeml_clademodelC.out → ...ts/codeml/clademodelC/clademodelC-4_3.out b/...AML/Results/codeml/codeml_clademodelC.out → ...ts/codeml/clademodelC/clademodelC-4_3.out
diff --git a/Tests/PAML/Results/codeml/codeml_NSsites_all.out b/Tests/PAML/Results/codeml/codeml_NSsites_all.out
diff --git a/...PAML/Results/codeml/codeml_freebranch.out → ...sults/codeml/freeratio/freeratio-4_4c.out b/...PAML/Results/codeml/codeml_freebranch.out → ...sults/codeml/freeratio/freeratio-4_4c.out
diff --git a/...Results/codeml/codeml_ngene2_mgene012.out → .../ngene2_mgene012/ngene2_mgene012-4_4c.out b/...Results/codeml/codeml_ngene2_mgene012.out → .../ngene2_mgene012/ngene2_mgene012-4_4c.out
diff --git a/.../Results/codeml/codeml_ngene2_mgene34.out → ...ml/ngene2_mgene34/ngene2_mgene34-4_4c.out b/.../Results/codeml/codeml_ngene2_mgene34.out → ...ml/ngene2_mgene34/ngene2_mgene34-4_4c.out
diff --git a/...s/PAML/Results/codeml/codeml_pairwise.out → ...Results/codeml/pairwise/pairwise-4_4c.out b/...s/PAML/Results/codeml/codeml_pairwise.out → ...Results/codeml/pairwise/pairwise-4_4c.out
diff --git a/Tests/PAML/bad.tree → Tests/PAML/Trees/bad.tree b/Tests/PAML/bad.tree → Tests/PAML/Trees/bad.tree
diff --git a/Tests/PAML/Resources/codeml/lysin.trees → Tests/PAML/Trees/lysin.trees b/Tests/PAML/Resources/codeml/lysin.trees → Tests/PAML/Trees/lysin.trees
diff --git a/Tests/PAML/species.tree → Tests/PAML/Trees/species.tree b/Tests/PAML/species.tree → Tests/PAML/Trees/species.tree
diff --git a/Tests/PAML/aa_alignment.phylip b/Tests/PAML/aa_alignment.phylip
diff --git a/Tests/PAML/alignment.phylip b/Tests/PAML/alignment.phylip