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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,242 @@ | ||
| #!/usr/bin/env perl | ||
| use v5.24; | ||
| use warnings; | ||
| use experimental 'signatures'; | ||
| no warnings 'experimental::signatures'; | ||
| use File::Basename; | ||
|
|
||
| use AGAT::AppEaser qw< run d >; | ||
| use AGAT::AGAT; | ||
|
|
||
| # set env variable to save location of this script | ||
| my $agat_bin; | ||
| if( -l __FILE__){ | ||
| $agat_bin = dirname(readlink(__FILE__)); | ||
| } else{ | ||
| $agat_bin = dirname(__FILE__); | ||
| } | ||
| $ENV{'AGAT_BIN'}=$agat_bin; | ||
|
|
||
| my $APPNAME = 'agat'; | ||
| my $header = get_agat_header(); | ||
| my $application = { | ||
| factory => {prefixes => {'#' => 'AGAT::AGAT#'}}, | ||
| configuration => { | ||
|
|
||
| # the name of the application, set it above in $APPNAME | ||
| name => $APPNAME, | ||
|
|
||
| # figure out names of environment variables automatically | ||
| # 'auto-environment' => 1, | ||
|
|
||
| # sub-commands without children are leaves (no sub help/commands) | ||
| 'auto-leaves' => 0, | ||
|
|
||
| # help goes to standard error by default, override to stdout | ||
| # 'help-on-stderr' => 0, | ||
|
|
||
| # Where to get the specifications for commands | ||
| # specfetch => '+SpecFromHash', # default | ||
| # specfetch => '+SpecFromHashOrModule', # possible alternative | ||
| }, | ||
| commands => { | ||
| MAIN => { | ||
| help => $header, | ||
| description => | ||
| 'AGAT has the power to check, fix, pad missing information (features/ | ||
| attributes) of any kind of GTF and GFF to create complete, sorted and | ||
| standardised gff3 format. Over the years it has been enriched by many many | ||
| tools to perform just about any tasks that is possible related to GTF/GFF | ||
| format files (sanitizing, conversions, merging, modifying, filtering, FASTA | ||
| sequence extraction, adding information, etc). Comparing to other methods | ||
| AGAT is robust to even the most despicable GTF/GFF files.', | ||
| children => [qw< levels config >], | ||
|
|
||
| # allow for configuration files | ||
| sources => '+SourcesWithFiles', | ||
| # 'config-files' => ["/etc/$APPNAME.json"], | ||
| options => [ | ||
| { | ||
| getopt => 'help|h!', | ||
| shortbool => 1, #shortbool added by JDainat to avoid --no-help | ||
| help => 'Display the help', | ||
| }, | ||
| { | ||
| getopt => 'version|v!', | ||
| shortbool => 1, | ||
| help => 'Display the AGAT version', | ||
| }, | ||
| { | ||
| getopt => 'tools|t!', | ||
| shortbool => 1, | ||
| help => 'Display the AGAT tools available', | ||
| }, | ||
| ], | ||
| commit => '#handle_main', | ||
| }, | ||
|
|
||
| # ================================== LEVELS ==================================== | ||
| levels => { | ||
| help => 'Handle feature types and relationships', | ||
| description => | ||
| 'If you want to see, add or modified the feature relationships you will have to | ||
| use this option. It will copy past in you working directory the feature_levels.yaml file | ||
| used to define the relationships between feature types and their level organisation. | ||
| Typical level organisation: Level1 => gene; Level2 => mRNA; level3 => exon,cds, | ||
| utrs. If you get warning from the Omniscient parser that a feature relationship | ||
| is not defined, you can provide information about it within the exposed feature_levels.yaml | ||
| file. Indeed, if the feature_levels.yaml file exists in your working directory, it will be | ||
| used by default.', | ||
| options => [ | ||
| { | ||
| getopt => 'help|h!', | ||
| shortbool => 1, | ||
| help => 'Display the help', | ||
| }, | ||
| { | ||
| getopt => 'expose|e!', | ||
| shortbool => 1, | ||
| help => 'Expose the feature_levels.yaml file.', | ||
| }, | ||
| ], | ||
| commit => '#handle_levels', | ||
| }, | ||
| # ================================== CONFIG ==================================== | ||
| config => { | ||
| help => 'Handle agat configuration used by _sp_ scripts', | ||
| description => | ||
| 'The _sp_ scripts use the AGAT parser that can be tuned in many way. The | ||
| default parameters are stored within a YAML file. You can see this configuration | ||
| file using the expose command that will copy it in you working directory. You | ||
| are then free to modify it at your convenience. Wen a config YAML file is | ||
| available within the working directory, AGAT will use it in priority. (For | ||
| convenience and automation, the parameters can be modified on the fly when using | ||
| the expose command. In such case you will get a modified copy of the config file.) | ||
| The _sq_ scripts can be tuned only by few options of the config file: | ||
| force_gff_input_version, gtf_output_version, gff_output_version and output_format. | ||
| ', | ||
| options => [ | ||
| { | ||
| getopt => 'help|h!', | ||
| help => 'Display the help', | ||
| shortbool => 1, | ||
| }, | ||
| { | ||
| getopt => 'expose|e!', | ||
| help => 'Expose the config file (A config.yaml will be set in your working directory). If any AGAT use the config.yaml from the current directory over the default one.', | ||
| shortbool => 1, | ||
| }, | ||
| { | ||
| getopt => 'verbose=i', | ||
| help => 'Verbosity during the GFF/GTF parsing. 0 is quiet. 1,2,3 or 4 to increase verbosity.[Default 1]', | ||
| }, | ||
| { | ||
| getopt => 'progress_bar!', | ||
| help => 'To activate / deactivate the progress bar. [Default activated]', | ||
| }, | ||
| { | ||
| getopt => 'log!', | ||
| help => 'To create a log file while parsing the input file to keep track of modification made by AGAT. [Default activated]', | ||
| }, | ||
| { | ||
| getopt => 'debug!', | ||
| help => 'Extra verbosity for debugging. [Default deactivated]', | ||
| }, | ||
| { | ||
| getopt => 'tabix!', | ||
| help => 'To sort the output in tabix format. [Default deactivated]', | ||
| }, | ||
| { | ||
| getopt => 'merge_loci!', | ||
| help => 'To merge loci that overlap at CDS level in a single locus. [Default deactivated]', | ||
| }, | ||
| { | ||
| getopt => 'throw_fasta!', | ||
| help => 'To throw the fasta embedded in the input file. [Default deactivated]', | ||
| }, | ||
| { | ||
| getopt => 'force_gff_input_version=f', | ||
| help => 'To force AGAT to use a specific version of the bioperl parser. Choice: 0, 1, 2, 2.5 or 3. 0 means let AGAT choose automatically. [Default 0]', | ||
| }, | ||
| { | ||
| getopt => 'output_format=s', | ||
| help => 'Set the output format. Choice GFF or GTF. [Default GFF]', | ||
| }, | ||
| { | ||
| getopt => 'gff_output_version=f', | ||
| help => 'Set the GFF output version. Choice 1, 2, 2.5, 3. [Default 3]', | ||
| }, | ||
| { | ||
| getopt => 'gtf_output_version=s', | ||
| help => 'Set the GTF output vesion. Choice 1, 2, 2.1, 2.2, 2.5, 3 or relax. [Default relax]', | ||
| }, | ||
| { | ||
| getopt => 'create_l3_for_l2_orphan!', | ||
| help => 'To create l3 feature for l2 feature without any. [Default activated]', | ||
| }, | ||
| { | ||
| getopt => 'locus_tag=s', | ||
| help => 'Coma separated list of attribute tag to use to define locus. Will be used if no Parent/id GFF relationship exist or gene_id/transcript_id GTF tag. [Default locus_tag, gene_id ]', | ||
| }, | ||
| { | ||
| getopt => 'prefix_new_id=s', | ||
| help => 'Prefix to be used for ID of newly created feature. [Default nbis]', | ||
| }, | ||
| { | ||
| getopt => 'check_sequential!', | ||
| help => 'Expert only - To take care of feature without any proper relationship.[Default activated]', | ||
| }, | ||
| { | ||
| getopt => 'check_l2_linked_to_l3!', | ||
| help => 'Expert only - To check that all l3 feature has a parental l2 feature. And create one if any missing. [Default activated]', | ||
| }, | ||
| { | ||
| getopt => 'check_l1_linked_to_l2!', | ||
| help => 'Expert only - To check that all l2 feature has a prental l1 feature. And create one if any missing. [Default activated]', | ||
| }, | ||
| { | ||
| getopt => 'remove_orphan_l1!', | ||
| help => 'Expert only - To remove level1 feature whithout children features (except top and standalone features that do not have children by definition). [Default activated]', | ||
| }, | ||
| { | ||
| getopt => 'check_all_level3_locations!', | ||
| help => 'To check location of level3 features: merge overlapping and adjacent exons and adjacent CDS. [Default activated]', | ||
| }, | ||
| { | ||
| getopt => 'check_cds!', | ||
| help => 'To check when stop codons are definied that they are part of the CDS. If not AGAT extends the CDS to include it. [Default activated]', | ||
| }, | ||
| { | ||
| getopt => 'check_exons!', | ||
| help => 'To check that exons include all other l3 feature types that are included within exon (see feature_levels.yaml file e.g: cds:"exon"). [Default activated]', | ||
| }, | ||
| { | ||
| getopt => 'check_utrs!', | ||
| help => 'To create UTRs if missing based on CDS and exon features. [Default activated]', | ||
| }, | ||
| { | ||
| getopt => 'check_all_level2_locations!', | ||
| help => 'To check that l2 feature locations do not span belong their exon locations. [Default activated]', | ||
| }, | ||
| { | ||
| getopt => 'check_all_level1_locations!', | ||
| help => 'To check that l1 feature locations do not span belong their l2 locations. [Default activated]', | ||
| }, | ||
| { | ||
| getopt => 'check_identical_isoforms!', | ||
| help => 'To remove identical isoforms (same exon,cds,locations). [Default activated]', | ||
| }, | ||
| ], | ||
| commit => '#handle_config', | ||
| }, | ||
| } | ||
| }; | ||
| run($application, [@ARGV]); | ||
| exit; | ||
|
|
||
|
|
||
| # implementation of sub-command bar | ||
| sub cat ($general, $config, $args) { | ||
| say defined($config->{galook}) ? $config->{galook} : '*undef*'; | ||
| return; | ||
| } |
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