minorg.console module

minorg.console.positive_callback(val)

Callback that checks if float or integer value is greater than zero.

Raises

typer.BadParameter – If value is not positive

minorg.console.non_negative_callback(val)

Callback that checks if float or integer value is greater than or equal to zero.

Raises

typer.BadParameter – If value is negative

minorg.console.zero_to_one_callback(val)

Callback that checks if float or integer value is between 0 and 1 (inclusive).

Raises

typer.BadParameter – If value is less than zero or greater than 1

minorg.console.seq(directory: pathlib.Path = <typer.models.OptionInfo object>, prefix: str = <typer.models.OptionInfo object>, thread: int = <typer.models.OptionInfo object>, gene: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, cluster: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, indv: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, target: pathlib.Path = <typer.models.OptionInfo object>, query: typing.Optional[typing.List[pathlib.Path]] = <typer.models.OptionInfo object>, domain: str = <typer.models.OptionInfo object>, feature: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, minid: float = <typer.models.OptionInfo object>, minlen: int = <typer.models.OptionInfo object>, mincdslen: int = <typer.models.OptionInfo object>, check_recip: bool = <typer.models.OptionInfo object>, relax_recip: bool = <typer.models.OptionInfo object>, merge_within: int = <typer.models.OptionInfo object>, check_id_before_merge: bool = <typer.models.OptionInfo object>, cluster_set: str = <typer.models.OptionInfo object>, genome_set: str = <typer.models.OptionInfo object>, reference_set: str = <typer.models.OptionInfo object>, reference: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, assembly: pathlib.Path = <typer.models.OptionInfo object>, annotation: pathlib.Path = <typer.models.OptionInfo object>, db: str = <typer.models.OptionInfo object>, attr_mod: str = <typer.models.OptionInfo object>, ext_gene: typing.Optional[typing.List[pathlib.Path]] = <typer.models.OptionInfo object>, ext_cds: typing.Optional[typing.List[pathlib.Path]] = <typer.models.OptionInfo object>, sep: str = <typer.models.OptionInfo object>, genetic_code: str = <typer.models.OptionInfo object>, remote_rps: bool = <typer.models.OptionInfo object>, genomes: bool = <typer.models.OptionInfo object>, references: bool = <typer.models.OptionInfo object>, clusters: bool = <typer.models.OptionInfo object>, members: str = <typer.models.OptionInfo object>, blastn: str = <typer.models.OptionInfo object>, rpsblast: str = <typer.models.OptionInfo object>, mafft: str = <typer.models.OptionInfo object>, bedtools: str = <typer.models.OptionInfo object>)

Subcommand seq.

Generate target sequences. If query/queries is/are non-reference genomes, conducts homologue discovery and outputs homologues. Else if querying reference genome, reference genes will be output.

minorg.console.generate_grna(thread: int = <typer.models.OptionInfo object>, out_map: pathlib.Path = <typer.models.OptionInfo object>, out_fasta: pathlib.Path = <typer.models.OptionInfo object>, out_pass: pathlib.Path = <typer.models.OptionInfo object>, directory: pathlib.Path = <typer.models.OptionInfo object>, prefix: str = <typer.models.OptionInfo object>, pam: str = <typer.models.OptionInfo object>, length: int = <typer.models.OptionInfo object>, target: pathlib.Path = <typer.models.OptionInfo object>, gene: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, cluster: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, domain: str = <typer.models.OptionInfo object>, reference: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, assembly: pathlib.Path = <typer.models.OptionInfo object>, annotation: pathlib.Path = <typer.models.OptionInfo object>, db: str = <typer.models.OptionInfo object>, attr_mod: str = <typer.models.OptionInfo object>, ext_gene: typing.Optional[typing.List[pathlib.Path]] = <typer.models.OptionInfo object>, ext_cds: typing.Optional[typing.List[pathlib.Path]] = <typer.models.OptionInfo object>, sep: str = <typer.models.OptionInfo object>, genetic_code: str = <typer.models.OptionInfo object>, remote_rps: bool = <typer.models.OptionInfo object>, gc_min: float = <typer.models.OptionInfo object>, gc_max: float = <typer.models.OptionInfo object>, feature: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, references: bool = <typer.models.OptionInfo object>, clusters: bool = <typer.models.OptionInfo object>, members: str = <typer.models.OptionInfo object>, cluster_set: str = <typer.models.OptionInfo object>, reference_set: str = <typer.models.OptionInfo object>, rpsblast: str = <typer.models.OptionInfo object>, mafft: str = <typer.models.OptionInfo object>)

Subcommand grna.

Generate gRNA from either user-provided FASTA file or reference genes

minorg.console.filter_grna(check_all: bool = <typer.models.OptionInfo object>, gc_check: bool = <typer.models.OptionInfo object>, feature_check: bool = <typer.models.OptionInfo object>, background_check: bool = <typer.models.OptionInfo object>, reset_checks: bool = <typer.models.OptionInfo object>, directory: pathlib.Path = <typer.models.OptionInfo object>, prefix: str = <typer.models.OptionInfo object>, thread: int = <typer.models.OptionInfo object>, map: pathlib.Path = <typer.models.OptionInfo object>, rename: pathlib.Path = <typer.models.OptionInfo object>, target: pathlib.Path = <typer.models.OptionInfo object>, reference: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, assembly: pathlib.Path = <typer.models.OptionInfo object>, annotation: pathlib.Path = <typer.models.OptionInfo object>, ext_gene: typing.Optional[typing.List[pathlib.Path]] = <typer.models.OptionInfo object>, ext_cds: typing.Optional[typing.List[pathlib.Path]] = <typer.models.OptionInfo object>, background: typing.Optional[typing.List[pathlib.Path]] = <typer.models.OptionInfo object>, mask: typing.Optional[typing.List[pathlib.Path]] = <typer.models.OptionInfo object>, attr_mod: str = <typer.models.OptionInfo object>, sep: str = <typer.models.OptionInfo object>, remote_rps: bool = <typer.models.OptionInfo object>, db: str = <typer.models.OptionInfo object>, genetic_code: str = <typer.models.OptionInfo object>, gc_min: float = <typer.models.OptionInfo object>, gc_max: float = <typer.models.OptionInfo object>, gene: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, cluster: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, feature: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, max_insertion: int = <typer.models.OptionInfo object>, min_within_n: int = <typer.models.OptionInfo object>, min_within_fraction: float = <typer.models.OptionInfo object>, out_map: pathlib.Path = <typer.models.OptionInfo object>, out_fasta: pathlib.Path = <typer.models.OptionInfo object>, out_pass: pathlib.Path = <typer.models.OptionInfo object>, in_place: bool = <typer.models.OptionInfo object>, screen_reference: bool = <typer.models.OptionInfo object>, unmask_ref: bool = <typer.models.OptionInfo object>, ot_indv: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, mask_gene: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, unmask_gene: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, mask_cluster: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, unmask_cluster: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, domain: str = <typer.models.OptionInfo object>, pam: str = <typer.models.OptionInfo object>, ot_pattern: str = <typer.models.OptionInfo object>, ot_unaligned_as_mismatch: bool = <typer.models.OptionInfo object>, ot_unaligned_as_gap: bool = <typer.models.OptionInfo object>, ot_pamless: bool = <typer.models.OptionInfo object>, ot_mismatch: int = <typer.models.OptionInfo object>, ot_gap: int = <typer.models.OptionInfo object>, genomes: bool = <typer.models.OptionInfo object>, references: bool = <typer.models.OptionInfo object>, clusters: bool = <typer.models.OptionInfo object>, members: str = <typer.models.OptionInfo object>, cluster_set: str = <typer.models.OptionInfo object>, genome_set: str = <typer.models.OptionInfo object>, reference_set: str = <typer.models.OptionInfo object>, mafft: str = <typer.models.OptionInfo object>, blastn: str = <typer.models.OptionInfo object>, rpsblast: str = <typer.models.OptionInfo object>)

Subcommand filter.

Filter gRNA by checks (background, feature, and GC)

minorg.console.minimumset(map: pathlib.Path = <typer.models.OptionInfo object>, rename: pathlib.Path = <typer.models.OptionInfo object>, exclude: pathlib.Path = <typer.models.OptionInfo object>, target: pathlib.Path = <typer.models.OptionInfo object>, out_map: pathlib.Path = <typer.models.OptionInfo object>, out_fasta: pathlib.Path = <typer.models.OptionInfo object>, directory: pathlib.Path = <typer.models.OptionInfo object>, prefix: str = <typer.models.OptionInfo object>, sets: int = <typer.models.OptionInfo object>, auto: bool = <typer.models.OptionInfo object>, prioritise_nr: bool = <typer.models.OptionInfo object>, accept_invalid: bool = <typer.models.OptionInfo object>)

Subcommand minimumset.

Generate minimum set(s) of gRNA required to cover all targets from mapping file and FASTA file of gRNA. Requires mapping file (generated by minorg’s ‘full’ subcommand) and a FASTA file of gRNA sequences. gRNA sequences not present in the mapping file will be ignored.

minorg.console.full(directory: pathlib.Path = <typer.models.OptionInfo object>, prefix: str = <typer.models.OptionInfo object>, thread: int = <typer.models.OptionInfo object>, gene: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, cluster: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, indv: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, target: pathlib.Path = <typer.models.OptionInfo object>, query: typing.Optional[typing.List[pathlib.Path]] = <typer.models.OptionInfo object>, domain: str = <typer.models.OptionInfo object>, minid: float = <typer.models.OptionInfo object>, minlen: int = <typer.models.OptionInfo object>, mincdslen: int = <typer.models.OptionInfo object>, check_recip: bool = <typer.models.OptionInfo object>, relax_recip: bool = <typer.models.OptionInfo object>, merge_within: int = <typer.models.OptionInfo object>, check_id_before_merge: bool = <typer.models.OptionInfo object>, reference: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, assembly: pathlib.Path = <typer.models.OptionInfo object>, annotation: pathlib.Path = <typer.models.OptionInfo object>, db: str = <typer.models.OptionInfo object>, attr_mod: str = <typer.models.OptionInfo object>, ext_gene: typing.Optional[typing.List[pathlib.Path]] = <typer.models.OptionInfo object>, ext_cds: typing.Optional[typing.List[pathlib.Path]] = <typer.models.OptionInfo object>, sep: str = <typer.models.OptionInfo object>, genetic_code: str = <typer.models.OptionInfo object>, remote_rps: bool = <typer.models.OptionInfo object>, pam: str = <typer.models.OptionInfo object>, length: int = <typer.models.OptionInfo object>, gc_min: float = <typer.models.OptionInfo object>, gc_max: float = <typer.models.OptionInfo object>, feature: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, max_insertion: int = <typer.models.OptionInfo object>, min_within_n: int = <typer.models.OptionInfo object>, min_within_fraction: float = <typer.models.OptionInfo object>, background: typing.Optional[typing.List[pathlib.Path]] = <typer.models.OptionInfo object>, mask: typing.Optional[typing.List[pathlib.Path]] = <typer.models.OptionInfo object>, screen_reference: bool = <typer.models.OptionInfo object>, unmask_ref: bool = <typer.models.OptionInfo object>, mask_gene: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, unmask_gene: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, mask_cluster: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, unmask_cluster: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, ot_pattern: str = <typer.models.OptionInfo object>, ot_unaligned_as_mismatch: bool = <typer.models.OptionInfo object>, ot_unaligned_as_gap: bool = <typer.models.OptionInfo object>, ot_pamless: bool = <typer.models.OptionInfo object>, ot_mismatch: int = <typer.models.OptionInfo object>, ot_gap: int = <typer.models.OptionInfo object>, ot_indv: typing.Optional[typing.List[str]] = <typer.models.OptionInfo object>, skip_bg_check: bool = <typer.models.OptionInfo object>, exclude: pathlib.Path = <typer.models.OptionInfo object>, accept_invalid: bool = <typer.models.OptionInfo object>, sets: int = <typer.models.OptionInfo object>, auto: bool = <typer.models.OptionInfo object>, prioritise_nr: bool = <typer.models.OptionInfo object>, output_ver: int = <typer.models.OptionInfo object>, genomes: bool = <typer.models.OptionInfo object>, references: bool = <typer.models.OptionInfo object>, clusters: bool = <typer.models.OptionInfo object>, members: str = <typer.models.OptionInfo object>, cluster_set: str = <typer.models.OptionInfo object>, genome_set: str = <typer.models.OptionInfo object>, reference_set: str = <typer.models.OptionInfo object>, blastn: str = <typer.models.OptionInfo object>, rpsblast: str = <typer.models.OptionInfo object>, mafft: str = <typer.models.OptionInfo object>, bedtools: str = <typer.models.OptionInfo object>)

Subcommand full.

Executes commands homologue, grna, filter, and minimumset in sequence to generate minimum set(s) of gRNA required to cover all targets.

minorg.console.sub_main(quiet: bool = <typer.models.OptionInfo object>, version: bool = <typer.models.OptionInfo object>)

Sub-application for redirecting to correct subcommand.

All subcommands are grouped under this application.

minorg.console.main(ctx: typer.models.Context, quiet: bool = <typer.models.OptionInfo object>, version: bool = <typer.models.OptionInfo object>, keep_on_crash: bool = <typer.models.OptionInfo object>, keep_all: bool = <typer.models.OptionInfo object>, _help: bool = <typer.models.OptionInfo object>)

Wrapper main application.

An additional application over app_sub that enables default subcommand by redirecting an execution that does not specify a subcommand to subcommand full.

Also handles some execution-level shared arguments (--version, --keep-on-crash, --keep-all).

minorg.console.app()