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
  • Adding information about Bins
  • Changes
• mgkit.workflow.alg_utils module
• mgkit.workflow.blast2gff module
  • Uniprot
  • BlastDB
  • Changes
• mgkit.workflow.count_utils module
  • Map Count Table to Genes
  • Concatenate Parquet Files
  • Convert Parquet into CSV
  • Changes
• mgkit.workflow.dict_utils module
  • Dictionary Utilities
  • Split
  • Reverse Dictionary
  • Changes
• mgkit.workflow.edit_gff module
  • Print Attributes in a GFF file
  • View GFF
  • Change or Add Attributes
  • Remove Attributes
  • Table
  • Rename
  • 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
  • filter
  • info
  • rename
  • 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.pnps_gen module
  • Calculates pN/pS values
  • Parse VCF Files
  • Calculate Rank pN/pS
  • Calculate Gene/Rank pN/pS
  • Changes
• 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
  • Extract taxonomy
    • Match names
  • Import Taxonomy
    • PhyloPhlan
  • Changes
• mgkit.workflow.utils module

Module contents

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