Scripts Details

This section detailed information about the scripts included

• blast2gff - Convert BLAST output to GFF
  • Overview
    • Uniprot
    • BlastDB
    • Changes
  • Options
    • blast2gff
• filter-gff - Filter GFF annotations
  • Overview
    • Value Filtering
    • Overlap Filtering
    • Per Sequence Values
    • Coverage Filtering
    • Changes
  • Options
    • filter-gff
• add-gff-info - Add informations to GFF annotations
  • Overview
    • 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
  • Options
    • add-gff-info
• get-gff-info - Extract informations to GFF annotations
  • Overview
    • sequence command
    • dbm command
    • mongodb command
    • gtf command
    • split command
    • cov command
    • Changes
  • Options
    • get-gff-info
• hmmer2gff - Convert HMMER output to GFF
  • Overview
    • Changes
  • Options
    • Named Arguments
    • File options
    • Filters
    • GFF
• snp_parser - SNPs analysis
  • Overview
  • Script Reference
    • Changes
  • Options
    • Named Arguments
• Download Taxonomy
• Download Accession/TaxonID
• taxon-utils - Taxonomy Utilities
  • Overview
    • Last Common Ancestor (lca and lca_line)
    • Filter by Taxon
    • Convert Taxa Tables to HDF5
    • Extract taxonomy
    • Import Taxonomy
    • Changes
  • Options
    • taxon-utils
• fasta-utils - Fasta Utilities
  • Overview
    • split command
    • translate command
    • uid command
    • filter
    • info
    • rename
    • Changes
  • Options
    • fasta-utils
• fastq-utils - Fastq Utilities
  • Overview
    • Commands
    • Changes
  • Options
    • fastq-utils
• json2gff - Convert JSON to GFF
  • Overview
    • mongodb command
  • Options
    • json2gff
• sampling-utils - Resampling Utilities
  • Overview
    • Resampling Utilities
  • Options
    • sampling-utils
• edit-gff - GFF Viewer and Editor
  • Overview
    • Print Attributes in a GFF file
    • View GFF
    • Change or Add Attributes
    • Remove Attributes
    • Table
    • Rename
    • Changes
  • Options
    • edit-gff
• pnps-gen - pN/pS Table Generation
  • Overview
    • Calculates pN/pS values
    • Parse VCF Files
    • Calculate Rank pN/pS
    • Calculate Gene/Rank pN/pS
    • Changes
  • Options
    • pnps-gen