GFFtk
  • Installation
    • Using pip
    • Using conda
    • From source
    • Dependencies
    • Verifying Installation
    • Updating GFFtk
  • Usage
    • Command-Line Interface
      • Basic Usage
      • Available Subcommands
      • Detailed Command Options
      • Examples
    • Python API
      • Core Modules
      • Basic Usage
      • GFF3 Data Structure
      • Examples
  • Tutorial
    • Installation
    • Basic GFF3 Operations
      • Parsing a GFF3 File
      • Modifying Gene Annotations
      • Filtering Genes
    • Format Conversion
      • Converting GFF3 to GTF
      • Converting GFF3 to BED
      • Converting GFF3 to TBL
      • Extracting Protein Sequences
      • Extracting Transcript Sequences
    • Consensus Gene Models
      • Generating Consensus Gene Models
      • Using Weights for Consensus Generation
    • Advanced Topics
      • Working with GenBank Files
    • Comparing GFF3 Files
      • Working with FASTA Files
      • Working with Combined GFF3+FASTA Files
      • GFF3 File Manipulation
  • Filtering Annotations
    • Basic Usage
      • Filter Syntax
      • Pattern Format
    • Common Examples
      • Filter by Gene Product
      • Filter by Annotation Source
      • Filter by Location
    • Advanced Filtering
      • Case-Insensitive Matching
      • Regular Expression Patterns
      • Multiple Filters
    • Filter Keys
      • Core Attributes
      • Annotation Details
    • Output Formats
    • Tips and Best Practices
    • Error Handling
  • Modules
    • gfftk.gff
      • dict2combined_gff_fasta()
      • dict2gff3()
      • dict2gff3alignments()
      • dict2gtf()
      • gff2dict()
      • gtf2dict()
      • is_combined_gff_fasta()
      • simplifyGO()
      • split_combined_gff_fasta()
      • start_end_gap()
      • validate_and_translate_models()
      • validate_models()
    • gfftk.consensus
      • add_evidence()
      • auto_score_threshold()
      • bed2interlap()
      • best_model_default()
      • calculate_gene_distance()
      • calculate_source_order()
      • check_intron_compatibility()
      • cluster_by_aed()
      • cluster_interlap()
      • cluster_interlap_original()
      • consensus()
      • contained()
      • de_novo_distance()
      • ensure_unique_names()
      • extend_utrs()
      • fasta_length()
      • filter4evidence()
      • filter_models_repeats()
      • generate_consensus()
      • getAED()
      • get_loci()
      • get_overlap()
      • gff2interlap()
      • gff_writer()
      • gffevidence2dict()
      • map_coords()
      • order_sources()
      • parse_data()
      • reasonable_model()
      • refine_cluster()
      • safe_extract_coordinates()
      • score_aggregator()
      • score_by_evidence()
      • score_evidence()
      • select_best_utrs()
      • solve_sub_loci()
      • src_scaling_factor()
      • sub_cluster()
    • gfftk.convert
      • convert()
      • gff2cdstranscripts()
      • gff2combined()
      • gff2gbff()
      • gff2gff3()
      • gff2gtf()
      • gff2proteins()
      • gff2tbl()
      • gff2transcripts()
      • gtf2cdstranscripts()
      • gtf2gbff()
      • gtf2gff()
      • gtf2proteins()
      • gtf2tbl()
      • gtf2transcripts()
      • tbl2cdstranscripts()
      • tbl2gbff()
      • tbl2gff3()
      • tbl2gtf()
      • tbl2proteins()
      • tbl2transcripts()
    • gfftk.genbank
      • dict2gbff()
      • dict2tbl()
      • drop_alt_coords()
      • duplicate_coords()
      • fetch_coords()
      • findUTRs()
      • reformatGO()
      • sbt_writer()
      • table2asn()
      • tbl2dict()
  • API
    • Convert
      • gff2cdstranscripts()
      • gff2combined()
      • gff2gbff()
      • gff2gff3()
      • gff2gtf()
      • gff2proteins()
      • gff2tbl()
      • gff2transcripts()
      • gtf2cdstranscripts()
      • gtf2gbff()
      • gtf2gff()
      • gtf2proteins()
      • gtf2tbl()
      • gtf2transcripts()
      • tbl2cdstranscripts()
      • tbl2gbff()
      • tbl2gff3()
      • tbl2gtf()
      • tbl2proteins()
      • tbl2transcripts()
    • GFF
      • dict2combined_gff_fasta()
      • dict2gff3()
      • dict2gff3alignments()
      • dict2gtf()
      • gff2dict()
      • gtf2dict()
      • is_combined_gff_fasta()
      • split_combined_gff_fasta()
    • Genbank
      • dict2tbl()
      • tbl2dict()
    • Fasta
      • FASTA
        • FASTA.get_seq()
      • fasta2dict()
      • fasta2headers()
      • fasta2lengths()
      • getSeqRegions()
      • translate()
    • Consensus
      • add_evidence()
      • bed2interlap()
      • best_model_default()
      • calculate_gene_distance()
      • calculate_source_order()
      • check_intron_compatibility()
      • cluster_by_aed()
      • cluster_interlap()
      • cluster_interlap_original()
      • contained()
      • de_novo_distance()
      • ensure_unique_names()
      • extend_utrs()
      • fasta_length()
      • filter4evidence()
      • filter_models_repeats()
      • generate_consensus()
      • getAED()
      • get_loci()
      • get_overlap()
      • gff2interlap()
      • gff_writer()
      • gffevidence2dict()
      • map_coords()
      • order_sources()
      • parse_data()
      • reasonable_model()
      • refine_cluster()
      • safe_extract_coordinates()
      • score_by_evidence()
      • score_evidence()
      • select_best_utrs()
      • src_scaling_factor()
      • sub_cluster()
    • Stats
      • annotation_stats()
    • Go
      • go_term_dict()
    • Utils
      • check_file_type()
      • filter_annotations()
      • is_gzipped()
      • is_text_file()
      • test_table2asn_functional()
      • zopen()
GFFtk
  • Welcome to GFFtk’s documentation!
  • View page source

Welcome to GFFtk’s documentation!

  • Installation
    • Using pip
    • Using conda
    • From source
    • Dependencies
    • Verifying Installation
    • Updating GFFtk
  • Usage
    • Command-Line Interface
    • Python API
  • Tutorial
    • Installation
    • Basic GFF3 Operations
    • Format Conversion
    • Consensus Gene Models
    • Advanced Topics
    • Comparing GFF3 Files
  • Filtering Annotations
    • Basic Usage
    • Common Examples
    • Advanced Filtering
    • Filter Keys
    • Output Formats
    • Tips and Best Practices
    • Error Handling
  • Modules
    • gfftk.gff
    • gfftk.consensus
    • gfftk.convert
    • gfftk.genbank
  • API
    • Convert
    • GFF
    • Genbank
    • Fasta
    • Consensus
    • Stats
    • Go
    • Utils

Indices and tables

  • Index

  • Module Index

  • Search Page

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