Package: gff3tool
GFF3toolkit - Python programs for processing GFF3 filesBackgroundTheGFF3 format(Generic Feature Format Version 3) is one of the standard formats to describe and represent genomic features. It is an incredibly flexible, 9-column format, which is easily manipulated by biologists. This flexibility, however, makes it very easy to break the format. We have developed the GFF3toolkit to help identify common problems with GFF3 files; fix 30 of these common problems; sort GFF3 files (which can aid in using down-stream processing programs and custom parsing); merge two GFF3 files into a single, non-redundant GFF3 file; and generate FASTA files from a GFF3 file for many use cases (e.g. feature types beyond mRNA).Frequently Asked Questions/FAQPrerequisitePython 3.xwheel(should have been installed for most python distributions, if you don't have, usepip install wheelto install it.)PerlInstallationStable release on PyPIpip install gff3toolLatest versionpip install git+https://github.com/NAL-i5K/GFF3toolkit.gitCurrent FunctionsDetect GFF3 format errorsCorrect GFF3 format errorsMerge two GFF3 filesSort a GFF3 fileGenerate biological sequences from a GFF3 fileUsageDetect GFF3 format errors (back)gff3_QC- Detection of GFF format errors (~50 types of errors).gff3_QC readmegff3_QC full documentationQuick start:gff3_QC -g example_file/example.gff3 -f example_file/reference.fa -o error.txt -s statistic.txtPlease refer togff3tool/lib/ERROR/ERROR.pyto see the full list of Error codes and the corresponding Error tags.Correct GFF3 format errors (back)gff3_fix- Correct GFF3 errors detected by gff3_QC.py (30 types of errors).gff3_fix readmegff3_fix full documentationQuick start:gff3_fix -qc_r error.txt -g example_file/example.gff3 -og corrected.gff3Merge two GFF3 files (back)gff3_merge- Merge two GFF3 filesgff3_merge readmegff3_merge full documentationQuick start:Merge the two file with auto-assignment of replace tags (default)gff3_merge -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -r merged_report.txtIf your gff files have assigned proper replace tags at column 9 (Format: replace=[Transcript ID]), you could merge the two gff files without auto-assignment of tags.gff3_merge -g1 example_file/new_models_w_replace.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -r merged_report.txt -noAutoSort a GFF3 file (back)gff3_sort- Sort a GFF3 file according to the order of Scaffold, coordinates on a Scaffold, and parent-child feature relationshipsgff3_sort readmeQuick start:gff3_sort -g example_file/example.gff3 -og example-sorted.gff3Generate biological sequences from a GFF3 file (back)bin/gff3_to_fasta.py - extract biological sequences (such as spliced transcripts, cds, or peptides) from specific regions of genome based on a GFF3 filegff3_to_fasta readmeQuick start:gff3_to_fasta -g example_file/example.gff3 -f example_file/reference.fa -st all -d simple -o test_sequencesExample Files (back)example_file/Example files for testingInternal Dependencies (back)gff3tool/lib/gff3/Basic data structure used for nesting the information of genome annotations in GFF3 format.gff3tool/lib/gff3_to_fasta/Extract specific sequences from genome sequences according to the GFF3 file.gff3tool/lib/ERROR/Contains the full list of Error codes and the corresponding Error taggff3tool/lib/function4gff/Functions for gff3 processinggff3tool/lib/gff3/gff3.pyThis program was contributed by Han Lin (http://gff3-py.readthedocs.org/en/latest/readme.html). Code was modified for customized usage.gff3tool/lib/inter_model/QC functions for processing multiple features between models (inter-model) in a GFF3 file.gff3tool/lib/intra_model/QC functions for processing multiple features within a model (intra-model) in a GFF3 file.gff3tool/lib/single_feature/QC functions for processing single features in a GFF3 file.