MANIFEST.in
README.rst
setup.cfg
setup.py
bin/snp_analysis.py
docs/Makefile
docs/convert_ipy.sh
docs/create-apidoc.sh
docs/download-tutorial-data.sh
docs/make.bat
docs/source/changes.rst
docs/source/conf.py
docs/source/gff.rst
docs/source/index.rst
docs/source/install.rst
docs/source/introduction.rst
docs/source/library.rst
docs/source/api/mgkit.align.rst
docs/source/api/mgkit.consts.rst
docs/source/api/mgkit.counts.func.rst
docs/source/api/mgkit.counts.rst
docs/source/api/mgkit.counts.scaling.rst
docs/source/api/mgkit.db.dbm.rst
docs/source/api/mgkit.db.mongo.rst
docs/source/api/mgkit.db.rst
docs/source/api/mgkit.filter.common.rst
docs/source/api/mgkit.filter.gff.rst
docs/source/api/mgkit.filter.gff_old.rst
docs/source/api/mgkit.filter.lists.rst
docs/source/api/mgkit.filter.reads.rst
docs/source/api/mgkit.filter.rst
docs/source/api/mgkit.filter.taxon.rst
docs/source/api/mgkit.graphs.rst
docs/source/api/mgkit.io.blast.rst
docs/source/api/mgkit.io.fasta.rst
docs/source/api/mgkit.io.fastq.rst
docs/source/api/mgkit.io.gff.rst
docs/source/api/mgkit.io.glimmer.rst
docs/source/api/mgkit.io.rst
docs/source/api/mgkit.io.snpdat.rst
docs/source/api/mgkit.io.uniprot.rst
docs/source/api/mgkit.kegg.rst
docs/source/api/mgkit.logger.rst
docs/source/api/mgkit.mappings.cazy.rst
docs/source/api/mgkit.mappings.eggnog.rst
docs/source/api/mgkit.mappings.enzyme.rst
docs/source/api/mgkit.mappings.go.rst
docs/source/api/mgkit.mappings.pandas_map.rst
docs/source/api/mgkit.mappings.rst
docs/source/api/mgkit.mappings.taxon.rst
docs/source/api/mgkit.mappings.utils.rst
docs/source/api/mgkit.net.embl.rst
docs/source/api/mgkit.net.rst
docs/source/api/mgkit.net.uniprot.rst
docs/source/api/mgkit.net.utils.rst
docs/source/api/mgkit.plots.abund.rst
docs/source/api/mgkit.plots.boxplot.rst
docs/source/api/mgkit.plots.colors.rst
docs/source/api/mgkit.plots.heatmap.rst
docs/source/api/mgkit.plots.rst
docs/source/api/mgkit.plots.unused.rst
docs/source/api/mgkit.plots.utils.rst
docs/source/api/mgkit.rst
docs/source/api/mgkit.simple_cache.rst
docs/source/api/mgkit.snps.classes.rst
docs/source/api/mgkit.snps.conv_func.rst
docs/source/api/mgkit.snps.filter.rst
docs/source/api/mgkit.snps.funcs.rst
docs/source/api/mgkit.snps.mapper.rst
docs/source/api/mgkit.snps.rst
docs/source/api/mgkit.taxon.rst
docs/source/api/mgkit.utils.common.rst
docs/source/api/mgkit.utils.dictionary.rst
docs/source/api/mgkit.utils.pandas.rst
docs/source/api/mgkit.utils.r_func.rst
docs/source/api/mgkit.utils.rst
docs/source/api/mgkit.utils.sequence.rst
docs/source/api/mgkit.utils.trans_tables.rst
docs/source/api/mgkit.workflow.add_coverage.rst
docs/source/api/mgkit.workflow.add_gff_info.rst
docs/source/api/mgkit.workflow.assembly.rst
docs/source/api/mgkit.workflow.blast2gff.rst
docs/source/api/mgkit.workflow.download_data.rst
docs/source/api/mgkit.workflow.download_profiles.rst
docs/source/api/mgkit.workflow.extract_gff_info.rst
docs/source/api/mgkit.workflow.fastq_utils.rst
docs/source/api/mgkit.workflow.filter_gff.rst
docs/source/api/mgkit.workflow.hmmer2gff.rst
docs/source/api/mgkit.workflow.nuc2aa.rst
docs/source/api/mgkit.workflow.rst
docs/source/api/mgkit.workflow.snp_parser.rst
docs/source/api/mgkit.workflow.utils.rst
docs/source/api/modules.rst
docs/source/examples/index.rst
docs/source/examples/tutorial-blast.sh
docs/source/examples/tutorial-hmmer.sh
docs/source/examples/db/example-annotation-db-package.ipynb
docs/source/examples/db/example-annotation-db-package.py
docs/source/examples/db/example-annotation-db-package.rst
docs/source/examples/db/.ipynb_checkpoints/example-annotation-db-package-checkpoint.ipynb
docs/source/examples/plots/abund.ipynb
docs/source/examples/plots/abund.py
docs/source/examples/plots/abund.rst
docs/source/examples/plots/boxplot.ipynb
docs/source/examples/plots/boxplot.py
docs/source/examples/plots/boxplot.rst
docs/source/examples/plots/heatmap.ipynb
docs/source/examples/plots/heatmap.py
docs/source/examples/plots/heatmap.rst
docs/source/examples/plots/misc-plots.ipynb
docs/source/examples/plots/misc-plots.py
docs/source/examples/plots/misc-plots.rst
docs/source/examples/plots/test-trim-tight.pdf
docs/source/examples/plots/test-trim.pdf
docs/source/examples/plots/.ipynb_checkpoints/abund-checkpoint.ipynb
docs/source/examples/plots/.ipynb_checkpoints/heatmap-checkpoint.ipynb
docs/source/examples/plots/.ipynb_checkpoints/misc-plots-checkpoint.ipynb
docs/source/examples/plots/.ipynb_checkpoints/abund-checkpoint_files/abund-checkpoint_10_1.png
docs/source/examples/plots/.ipynb_checkpoints/abund-checkpoint_files/abund-checkpoint_11_1.png
docs/source/examples/plots/.ipynb_checkpoints/abund-checkpoint_files/abund-checkpoint_12_1.png
docs/source/examples/plots/.ipynb_checkpoints/abund-checkpoint_files/abund-checkpoint_13_1.png
docs/source/examples/plots/.ipynb_checkpoints/abund-checkpoint_files/abund-checkpoint_14_1.png
docs/source/examples/plots/.ipynb_checkpoints/abund-checkpoint_files/abund-checkpoint_15_2.png
docs/source/examples/plots/.ipynb_checkpoints/abund-checkpoint_files/abund-checkpoint_16_2.png
docs/source/examples/plots/.ipynb_checkpoints/abund-checkpoint_files/abund-checkpoint_17_2.png
docs/source/examples/plots/.ipynb_checkpoints/abund-checkpoint_files/abund-checkpoint_20_0.png
docs/source/examples/plots/.ipynb_checkpoints/abund-checkpoint_files/abund-checkpoint_21_2.png
docs/source/examples/plots/.ipynb_checkpoints/abund-checkpoint_files/abund-checkpoint_6_0.png
docs/source/examples/plots/.ipynb_checkpoints/abund-checkpoint_files/abund-checkpoint_7_0.png
docs/source/examples/plots/.ipynb_checkpoints/abund-checkpoint_files/abund-checkpoint_8_0.png
docs/source/examples/plots/.ipynb_checkpoints/heatmap-checkpoint_files/heatmap-checkpoint_11_1.png
docs/source/examples/plots/.ipynb_checkpoints/heatmap-checkpoint_files/heatmap-checkpoint_13_0.png
docs/source/examples/plots/.ipynb_checkpoints/heatmap-checkpoint_files/heatmap-checkpoint_15_0.png
docs/source/examples/plots/.ipynb_checkpoints/heatmap-checkpoint_files/heatmap-checkpoint_18_0.png
docs/source/examples/plots/.ipynb_checkpoints/heatmap-checkpoint_files/heatmap-checkpoint_20_0.png
docs/source/examples/plots/.ipynb_checkpoints/heatmap-checkpoint_files/heatmap-checkpoint_22_0.png
docs/source/examples/plots/.ipynb_checkpoints/heatmap-checkpoint_files/heatmap-checkpoint_4_0.png
docs/source/examples/plots/.ipynb_checkpoints/heatmap-checkpoint_files/heatmap-checkpoint_7_1.png
docs/source/examples/plots/.ipynb_checkpoints/heatmap-checkpoint_files/heatmap-checkpoint_9_1.png
docs/source/examples/plots/.ipynb_checkpoints/misc-plots-checkpoint_files/misc-plots-checkpoint_2_0.png
docs/source/examples/plots/.ipynb_checkpoints/misc-plots-checkpoint_files/misc-plots-checkpoint_2_1.png
docs/source/examples/plots/abund_files/abund_10_1.png
docs/source/examples/plots/abund_files/abund_11_1.png
docs/source/examples/plots/abund_files/abund_12_1.png
docs/source/examples/plots/abund_files/abund_13_1.png
docs/source/examples/plots/abund_files/abund_14_1.png
docs/source/examples/plots/abund_files/abund_15_1.png
docs/source/examples/plots/abund_files/abund_15_2.png
docs/source/examples/plots/abund_files/abund_16_1.png
docs/source/examples/plots/abund_files/abund_16_2.png
docs/source/examples/plots/abund_files/abund_17_1.png
docs/source/examples/plots/abund_files/abund_17_2.png
docs/source/examples/plots/abund_files/abund_20_0.png
docs/source/examples/plots/abund_files/abund_21_1.png
docs/source/examples/plots/abund_files/abund_21_2.png
docs/source/examples/plots/abund_files/abund_6_0.png
docs/source/examples/plots/abund_files/abund_7_0.png
docs/source/examples/plots/abund_files/abund_8_0.png
docs/source/examples/plots/boxplot_files/boxplot_10_0.png
docs/source/examples/plots/boxplot_files/boxplot_12_0.png
docs/source/examples/plots/boxplot_files/boxplot_14_0.png
docs/source/examples/plots/boxplot_files/boxplot_16_0.png
docs/source/examples/plots/boxplot_files/boxplot_18_0.png
docs/source/examples/plots/boxplot_files/boxplot_20_0.png
docs/source/examples/plots/boxplot_files/boxplot_22_0.png
docs/source/examples/plots/boxplot_files/boxplot_24_0.png
docs/source/examples/plots/boxplot_files/boxplot_4_0.png
docs/source/examples/plots/boxplot_files/boxplot_6_0.png
docs/source/examples/plots/boxplot_files/boxplot_8_0.png
docs/source/examples/plots/heatmap_files/heatmap_11_1.png
docs/source/examples/plots/heatmap_files/heatmap_13_0.png
docs/source/examples/plots/heatmap_files/heatmap_15_0.png
docs/source/examples/plots/heatmap_files/heatmap_18_0.png
docs/source/examples/plots/heatmap_files/heatmap_20_0.png
docs/source/examples/plots/heatmap_files/heatmap_22_0.png
docs/source/examples/plots/heatmap_files/heatmap_4_0.png
docs/source/examples/plots/heatmap_files/heatmap_7_1.png
docs/source/examples/plots/heatmap_files/heatmap_9_1.png
docs/source/examples/plots/misc-plots_files/misc-plots_2_0.png
docs/source/examples/plots/misc-plots_files/misc-plots_2_1.png
docs/source/images/uniprot_taxonomy-figure.png
docs/source/pipeline/Exploring-Metagenomic-Data.ipynb
docs/source/pipeline/Exploring-Metagenomic-Data.py
docs/source/pipeline/Exploring-Metagenomic-Data.rst
docs/source/pipeline/blast-pred.rst
docs/source/pipeline/gene_prediction.rst
docs/source/pipeline/hmmer-tutorial-explore-data.ipynb
docs/source/pipeline/hmmer-tutorial-explore-data.py
docs/source/pipeline/hmmer-tutorial-explore-data.rst
docs/source/pipeline/hmmer-tutorial-notebook.rst
docs/source/pipeline/index.rst
docs/source/pipeline/pipeline-hmmer.rst
docs/source/pipeline/simple-tutorial-notebook.rst
docs/source/pipeline/tutorial.rst
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint.ipynb
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint.py
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint.rst
docs/source/pipeline/.ipynb_checkpoints/hmmer-tutorial-explore-data-checkpoint.ipynb
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint_files/Exploring-Metagenomic-Data-checkpoint_28_1.png
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint_files/Exploring-Metagenomic-Data-checkpoint_29_1.png
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint_files/Exploring-Metagenomic-Data-checkpoint_31_0.png
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint_files/Exploring-Metagenomic-Data-checkpoint_32_0.png
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint_files/Exploring-Metagenomic-Data-checkpoint_33_0.png
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint_files/Exploring-Metagenomic-Data-checkpoint_34_0.png
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint_files/Exploring-Metagenomic-Data-checkpoint_49_0.png
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint_files/Exploring-Metagenomic-Data-checkpoint_50_0.png
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint_files/Exploring-Metagenomic-Data-checkpoint_60_0.png
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint_files/Exploring-Metagenomic-Data-checkpoint_61_0.png
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint_files/Exploring-Metagenomic-Data-checkpoint_70_0.png
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint_files/Exploring-Metagenomic-Data-checkpoint_71_0.png
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint_files/Exploring-Metagenomic-Data-checkpoint_77_0.png
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint_files/Exploring-Metagenomic-Data-checkpoint_78_0.png
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint_files/Exploring-Metagenomic-Data-checkpoint_85_0.png
docs/source/pipeline/.ipynb_checkpoints/Exploring-Metagenomic-Data-checkpoint_files/Exploring-Metagenomic-Data-checkpoint_86_0.png
docs/source/pipeline/Exploring-Metagenomic-Data_files/Exploring-Metagenomic-Data_28_1.png
docs/source/pipeline/Exploring-Metagenomic-Data_files/Exploring-Metagenomic-Data_29_1.png
docs/source/pipeline/Exploring-Metagenomic-Data_files/Exploring-Metagenomic-Data_31_0.png
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docs/source/pipeline/Exploring-Metagenomic-Data_files/Exploring-Metagenomic-Data_52_0.png
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docs/source/pipeline/Exploring-Metagenomic-Data_files/Exploring-Metagenomic-Data_88_1.png
docs/source/pipeline/diagrams/count-data-analysis.blockdiag.txt
docs/source/pipeline/diagrams/diversity-analysis.blockdiag.txt
docs/source/pipeline/diagrams/gene_prediction-flowchart-general.blockdiag.txt
docs/source/pipeline/diagrams/quantification.blockdiag.txt
docs/source/pipeline/diagrams/snp_parser.blockdiag.txt
docs/source/pipeline/hmmer-tutorial-explore-data_files/hmmer-tutorial-explore-data_18_0.png
docs/source/pipeline/hmmer-tutorial-explore-data_files/hmmer-tutorial-explore-data_20_1.png
docs/source/pipeline/hmmer-tutorial-explore-data_files/hmmer-tutorial-explore-data_43_0.png
docs/source/pipeline/hmmer-tutorial-explore-data_files/hmmer-tutorial-explore-data_45_0.png
docs/source/pipeline/hmmer-tutorial-explore-data_files/hmmer-tutorial-explore-data_53_0.png
docs/source/pipeline/hmmer-tutorial-explore-data_files/hmmer-tutorial-explore-data_54_0.png
docs/source/pipeline/hmmer-tutorial-explore-data_files/hmmer-tutorial-explore-data_58_0.png
docs/source/pipeline/hmmer-tutorial-explore-data_files/hmmer-tutorial-explore-data_74_0.png
docs/source/scripts/add-gff-info.rst
docs/source/scripts/assembly_stats.rst
docs/source/scripts/blast2gff.rst
docs/source/scripts/download_data.rst
docs/source/scripts/download_profiles.rst
docs/source/scripts/filter-gff.rst
docs/source/scripts/get-gff-info.rst
docs/source/scripts/hmmer2gff.rst
docs/source/scripts/index.rst
docs/source/scripts/snp_analysis.rst
mgkit/__init__.py
mgkit/align.py
mgkit/consts.py
mgkit/graphs.py
mgkit/kegg.py
mgkit/logger.py
mgkit/simple_cache.py
mgkit/taxon.py
mgkit.egg-info/PKG-INFO
mgkit.egg-info/SOURCES.txt
mgkit.egg-info/dependency_links.txt
mgkit.egg-info/entry_points.txt
mgkit.egg-info/requires.txt
mgkit.egg-info/top_level.txt
mgkit/counts/__init__.py
mgkit/counts/func.py
mgkit/counts/scaling.py
mgkit/db/__init__.py
mgkit/db/dbm.py
mgkit/db/mongo.py
mgkit/filter/__init__.py
mgkit/filter/common.py
mgkit/filter/gff.py
mgkit/filter/gff_old.py
mgkit/filter/lists.py
mgkit/filter/reads.py
mgkit/filter/taxon.py
mgkit/io/__init__.py
mgkit/io/blast.py
mgkit/io/fasta.py
mgkit/io/fastq.py
mgkit/io/gff.py
mgkit/io/glimmer.py
mgkit/io/snpdat.py
mgkit/io/uniprot.py
mgkit/mappings/__init__.py
mgkit/mappings/cazy.py
mgkit/mappings/eggnog.py
mgkit/mappings/enzyme.py
mgkit/mappings/go.py
mgkit/mappings/pandas_map.py
mgkit/mappings/taxon.py
mgkit/mappings/utils.py
mgkit/net/__init__.py
mgkit/net/embl.py
mgkit/net/uniprot.py
mgkit/net/utils.py
mgkit/plots/__init__.py
mgkit/plots/abund.py
mgkit/plots/boxplot.py
mgkit/plots/colors.py
mgkit/plots/heatmap.py
mgkit/plots/unused.py
mgkit/plots/utils.py
mgkit/snps/__init__.py
mgkit/snps/classes.py
mgkit/snps/conv_func.py
mgkit/snps/filter.py
mgkit/snps/funcs.py
mgkit/snps/mapper.py
mgkit/utils/__init__.py
mgkit/utils/common.py
mgkit/utils/dictionary.py
mgkit/utils/pandas.py
mgkit/utils/r_func.py
mgkit/utils/sequence.py
mgkit/utils/trans_tables.py
mgkit/workflow/__init__.py
mgkit/workflow/add_coverage.py
mgkit/workflow/add_gff_info.py
mgkit/workflow/assembly.py
mgkit/workflow/blast2gff.py
mgkit/workflow/download_data.py
mgkit/workflow/download_profiles.py
mgkit/workflow/extract_gff_info.py
mgkit/workflow/fastq_utils.py
mgkit/workflow/filter_gff.py
mgkit/workflow/hmmer2gff.py
mgkit/workflow/nuc2aa.py
mgkit/workflow/snp_parser.py
mgkit/workflow/utils.py
tests/_utils.py
tests/misc_data.py
tests/taxon_data.py
tests/test_filter_gff.py
tests/test_filters_snps.py
tests/test_filters_taxon.py
tests/test_gff.py
tests/test_kegg.py
tests/test_mappings.py
tests/test_misc.py
tests/test_r_utils.py
tests/test_seq_utils.py
tests/test_snps.py
tests/test_taxon.py
tests/misc_data/test-seq-aa.fa
tests/misc_data/test-seq-nuc.fa
tests/misc_data/test.gff