MGKit: Metagenomic framework
0.3.4
  • Introduction
  • Installation
  • Metagenomic Pipeline
  • Scripts Details
  • Example Notebooks
  • MGKit GFF Specifications
  • Library Reference
    • mgkit package
    • mgkit.align module
    • mgkit.consts module
    • mgkit.counts package
    • mgkit.counts.func module
    • mgkit.counts.glm module
    • mgkit.counts.scaling module
    • mgkit.db package
    • mgkit.db.dbm module
    • mgkit.db.mongo module
    • mgkit.filter package
    • mgkit.filter.common module
    • mgkit.filter.gff module
    • mgkit.filter.lists module
    • mgkit.filter.reads module
    • mgkit.filter.taxon module
    • mgkit.graphs module
    • mgkit.io package
    • mgkit.io.blast module
    • mgkit.io.fasta module
    • mgkit.io.fastq module
    • mgkit.io.gff module
    • mgkit.io.glimmer module
    • mgkit.io.snpdat module
    • mgkit.io.uniprot module
    • mgkit.io.utils module
    • mgkit.kegg module
    • mgkit.logger module
    • mgkit.mappings package
    • mgkit.mappings.cazy module
    • mgkit.mappings.eggnog module
    • mgkit.mappings.enzyme module
    • mgkit.mappings.go module
    • mgkit.mappings.pandas_map module
    • mgkit.mappings.taxon module
    • mgkit.mappings.utils module
    • mgkit.net package
    • mgkit.net.embl module
    • mgkit.net.pfam module
    • mgkit.net.uniprot module
    • mgkit.net.utils module
    • mgkit.plots package
    • mgkit.plots.abund module
    • mgkit.plots.boxplot module
    • mgkit.plots.colors module
    • mgkit.plots.heatmap module
    • mgkit.plots.utils module
    • mgkit.simple_cache module
    • mgkit.snps package
    • mgkit.snps.classes module
    • mgkit.snps.conv_func module
    • mgkit.snps.filter module
    • mgkit.snps.funcs module
    • mgkit.snps.mapper module
    • mgkit.taxon module
    • mgkit.utils package
    • mgkit.utils.common module
    • mgkit.utils.dictionary module
    • mgkit.utils.sequence module
    • mgkit.utils.trans_tables module
    • mgkit.workflow package
      • Submodules
        • mgkit.workflow.add_gff_info module
        • mgkit.workflow.blast2gff module
        • mgkit.workflow.extract_gff_info module
        • mgkit.workflow.fasta_utils module
        • mgkit.workflow.fastq_utils module
        • mgkit.workflow.filter_gff module
        • mgkit.workflow.hmmer2gff module
        • mgkit.workflow.json2gff module
        • mgkit.workflow.sampling_utils module
        • mgkit.workflow.snp_parser module
        • mgkit.workflow.taxon_utils module
        • mgkit.workflow.utils module
      • Module contents
    • mgkit.workflow.add_gff_info module
    • mgkit.workflow.blast2gff module
    • mgkit.workflow.extract_gff_info module
    • mgkit.workflow.fasta_utils module
    • mgkit.workflow.fastq_utils module
    • mgkit.workflow.filter_gff module
    • mgkit.workflow.hmmer2gff module
    • mgkit.workflow.json2gff module
    • mgkit.workflow.sampling_utils module
    • mgkit.workflow.snp_parser module
    • mgkit.workflow.taxon_utils module
    • mgkit.workflow.utils module
    • mgkit
  • Changes
MGKit: Metagenomic framework
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  • Library Reference »
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  • mgkit.workflow package
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mgkit.workflow package¶

Submodules¶

  • mgkit.workflow.add_gff_info module
    • Uniprot Command
    • Coverage Command
    • Adding Coverage from samtools depth
    • Uniprot Offline Mappings
    • Kegg Information
    • Expected Aminoacidic Changes
    • Adding Count Data
    • Adding Taxonomy from a Table
    • Adding information from Pfam
    • Changes
  • mgkit.workflow.blast2gff module
    • Uniprot
    • BlastDB
    • Changes
  • mgkit.workflow.extract_gff_info module
    • sequence command
    • dbm command
    • mongodb command
    • gtf command
    • split command
    • cov command
    • Changes
  • mgkit.workflow.fasta_utils module
    • split command
    • translate command
    • uid command
    • Changes
  • mgkit.workflow.fastq_utils module
    • Commands
    • Changes
  • mgkit.workflow.filter_gff module
    • Value Filtering
    • Overlap Filtering
    • Per Sequence Values
    • Coverage Filtering
    • Changes
  • mgkit.workflow.hmmer2gff module
    • Changes
  • mgkit.workflow.json2gff module
    • mongodb command
  • mgkit.workflow.sampling_utils module
    • Resampling Utilities
      • sample command
      • sample_stream command
      • sync command
      • rand_seq command
      • Changes
  • mgkit.workflow.snp_parser module
    • Changes
  • mgkit.workflow.taxon_utils module
    • Last Common Ancestor (lca and lca_line)
      • Krona Output
    • Filter by Taxon
    • Convert Taxa Tables to HDF5
    • Changes
  • mgkit.workflow.utils module

Module contents¶

Workflows used to script the library - execute bits of the pipelines supported

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© Copyright 2013-2015, Francesco Rubino.

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