Welcome to pygtftk documentation page

The Python GTF toolkit (pygtftk) package is intented to ease handling of GTF/GFF2.0 files (Gene Transfer Format). It currently does not support GFF3 file format. The pygtftk package is compatible with Python >=3.5,<3.7 and relies on libgtftk, a library of functions written in C.

The package comes with a set of UNIX commands that can be accessed through the gtftk main Unix program. The gtftk program exposes several subcommands than can be piped, for instance, to filter, convert, extract or delete data from GTF files. The gtftk set of Unix commands, can be easily extended using a basic plugin architecture. All these aspects are covered in the help section.

While the gtftk Unix program comes with hundreds of unitary and functional tests, it is still upon active development thus feel free to post any problem or required enhancement through the github interface.

Table of content

• Warning about supported GTF file formats
  • Naming conventions
• Installing pygtftk/gtftk
• Help on gtftk Unix commands
  • Main parser arguments of gtftk
  • Command-wide arguments
• Commands from section ‘information’
  • apropos
  • retrieve
  • get_example
  • add_exon_nb
  • count
  • count_key_values
  • get_attr_list
  • get_attr_value_list
  • get_feature_list
  • nb_exons
  • nb_transcripts
  • seqid_list
  • tss_dist
  • feature_size
• Commands from section ‘Editing’
  • add_prefix
  • del_attr
  • join_attr
  • join_multi_file
  • merge_attr
  • discretize_key
• Commands from section ‘selection’
  • select_by_key
  • select_by_regexp
  • select_by_intron_size
  • select_by_max_exon_nb
  • select_by_loc
  • select_by_nb_exon
  • select_by_numeric_value
  • random_list
  • random_tx
  • rm_dup_tss
  • select_by_go
  • select_by_tx_size
  • select_most_5p_tx
  • short_long
• Commands from section ‘conversion’
  • convert
  • tabulate
  • bed_to_gtf
  • convert_ensembl
• Commands from section ‘annotation’
  • closest_genes
  • overlapping
  • divergent
  • convergent
  • exon_sizes
  • intron_sizes
• Commands from section ‘ologram’
  • ologram
  • ologram (multiple overlaps)
  • ologram_merge_stats
  • ologram_modl_treeify
  • ologram_merge_runs
  • Notes
  • OLOGRAM file structure
• Commands from section ‘coordinates’
  • midpoints
  • get_5p_3p_coords
  • intergenic
  • intronic
  • splicing_site
  • shift
• Commands from section ‘sequence’
  • get_tx_seq
  • get_feat_seq
• Commands from section ‘coverage’
  • coverage
  • mk_matrix
  • profile
• Commands from section ‘miscellaneous’
  • control_list
  • col_from_tab
• Help on Python package (pygtftk)
  • The GTF class
  • The FASTA class
  • The TAB class
  • The Line module
  • The pygtftk.stats.intersect.overlap_stats_shuffling module
  • The pygtftk.stats.intersect.overlap_stats_compute module
  • The pygtftk.stats.negbin_fit module
  • The pygtftk.stats.beta module
  • The pygtftk.stats.intersect.modl.tree module
  • The pygtftk.stats.intersect.modl.dict_learning module
  • The pygtftk.stats.intersect.modl.subroutines module
  • The gtftk.utils module
• The pygtftk.bwig.bw_coverage module
• Writing your own commands