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gff3-merge.py

Usage

gff3-merge.py [-h] [-g1 GFF_FILE1] [-g2 GFF_FILE2] [-f FASTA] [-og OUTPUT_GFF] [-r REPORT_FILE] [-noAuto] [-v]

Testing environment

  1. Python 2.7
  2. Perl v5.16.3

Inputs

  1. GFF3 file with new or modified annotations, to be merged into GFF3 file 2. Specify the file name with the -g1 or --gff_file1 argument. Please note that this program requires gene/pseudogene and mRNA/pseudogenic_transcript to have an ID attribute in column 9. If replace tags are present (see below), these tags must refer to transcript/mRNA model IDs in the reference GFF3 file, specified by -g2.
  2. Reference models in GFF3 format: Specify the file name with the -g2 or --gff_file2 argument. The models from -g1 will be merged into this file, replacing models in -g2. Please note that this program requires gene/pseudogene and mRNA/pseudogenic_transcript to have an ID attribute in column 9. If the reference GFF3 file contains gene models with multiple isoforms, please review the section "Odd use cases" below prior to running the program.
  3. Fasta file: Specify the file name with the -f or --fasta argument. This file must be the Fasta file that the GFF3 seqids and coordinates in both GFF3 files refer to. For more information, refer to the GFF3 specification.

Outputs

  1. .gff: A merged gff3 file
  2. .txt: Merge log file

Quick start

  • Merge the two files with auto-assignment of replace tags (default) python2.7 GFF3toolkit/bin/gff3-merge.py -g1 GFF3toolkit/example_file/new_models.gff3 -g2 GFF3toolkit/example_file/reference.gff3 -f GFF3toolkit/example_file/reference.fa -og merged.gff -r merged_report.txt

  • If your GFF3 files have proper replace tags at column 9 (Format: replace=[Transcript ID]), you can merge the two GFF3 files without auto-assignment of replace tags. python2.7 GFF3toolkit/bin/gff3-merge.py -g1 GFF3toolkit/example_file/new_models.gff3 -g2 GFF3toolkit/example_file/reference.gff3 -f GFF3toolkit/example_file/reference.fa -og merged.gff -r merged_report.txt -noAuto

Optional arguments

  1. -h, --help
    • show this help message and exit
  2. -og OUTPUT_GFF, --output_gff OUTPUT_GFF
    • The merged GFF3 file (default: merged.gff)
  3. -r REPORT_FILE, --report_file REPORT_FILE
    • Log file for the integration (default: merge_report.txt)
  4. -noAuto, --auto_assignment
    • Turn off the auto-assignment of replace tags, if you have had the replace tags in your update gff (default: Automatically assign replace tags and then merge the gff files)
  5. -v, --version
    • show program's version number and exit

More information