outrigger.commandline module¶

class outrigger.commandline.CommandLine(input_options=None)[source]¶

Bases: object

Methods

`do_usage_and_die`(str)	Cleanly exit if incorrect parameters are given
`index`()
`psi`()
`validate`()

do_usage_and_die(str)[source]¶

Cleanly exit if incorrect parameters are given

If a critical error is encountered, where it is suspected that the program is not being called with consistent parameters or data, this method will write out an error string (str), then terminate execution of the program.

index()[source]¶

psi()[source]¶

validate()[source]¶

class outrigger.commandline.Index(**kwargs)[source]¶

Bases: outrigger.commandline.Subcommand

Attributes

`folders`
`gtf_folder`
`index_folder`
`junction_reads_filename`
`junctions_folder`
`output_folder`
`splice_abbrevs`

gffutils_db
gtf_filename
sj_out_tab

Methods

`csv`()	Create a csv file of compiled splice junctions
`execute`()
`filter_junctions_on_reads`(spliced_reads)
`get_event_attributes`(db, event_df, splice_type)
`junction_metadata`(spliced_reads, csv)	Get just the junction info from the concatenated read files
`make_events_by_traversing_graph`(event_maker, db)	Search the splice graph for alternative exons
`make_exon_junction_adjacencies`(metadata, db)	Get annotated exon_cols next to junctions in data
`make_graph`(junction_exon_triples, db)	Create graph database of exon-junction adjacencies
`make_junction_reads_file`()
`maybe_make_db`()	Get GFFutils database from file or create from a gtf
`maybe_make_folder`(folder)
`maybe_overwrite`(filename)	Ensures that filename is not overwritten unless user-specified
`write_new_gtf`(db)

execute()[source]¶

get_event_attributes(db, event_df, splice_type)[source]¶

make_events_by_traversing_graph(event_maker, db)[source]¶: Search the splice graph for alternative exons

make_exon_junction_adjacencies(metadata, db)[source]¶: Get annotated exon_cols next to junctions in data

static make_graph(junction_exon_triples, db)[source]¶: Create graph database of exon-junction adjacencies

max_de_novo_exon_length = 100¶

splice_abbrevs¶

write_new_gtf(db)[source]¶

class outrigger.commandline.Psi(**kwargs)[source]¶

Bases: outrigger.commandline.SubcommandAfterIndex

Attributes

`folders`
`gtf_folder`
`index_folder`
`input_index`	Where to read the index from
`junction_reads_filename`
`junctions_folder`
`output_folder`
`psi_folder`
`splice_type_folders`

gffutils_db
gtf_filename
junction_id_col
reads_col
sample_id_col
sj_out_tab

Methods

`csv`()	Create a csv file of compiled splice junctions
`execute`()	Calculate percent spliced in (psi) of splicing events
`filter_junctions_on_reads`(spliced_reads)
`junction_metadata`(spliced_reads, csv)	Get just the junction info from the concatenated read files
`make_junction_reads_file`()
`maybe_get_validated_events`(splice_abbrev)
`maybe_make_db`()	Get GFFutils database from file or create from a gtf
`maybe_make_folder`(folder)
`maybe_overwrite`(filename)	Ensures that filename is not overwritten unless user-specified
`maybe_read_junction_reads`()
`validate_junction_reads_data`(junction_reads)

execute()[source]¶: Calculate percent spliced in (psi) of splicing events

folders¶

junction_id_col = None¶

maybe_get_validated_events(splice_abbrev)[source]¶

maybe_read_junction_reads()[source]¶

psi_folder¶

reads_col = None¶

required_cols = {'--reads-col': None, '--sample-id-col': None, '--junction-id-col': None}¶

sample_id_col = None¶

splice_type_folders¶

validate_junction_reads_data(junction_reads)[source]¶

class outrigger.commandline.Subcommand(**kwargs)[source]¶

Bases: object

Attributes

`folders`
`gtf_folder`
`index_folder`
`junction_reads_filename`
`junctions_folder`
`output_folder`

gffutils_db
gtf_filename
sj_out_tab

Methods

`csv`()	Create a csv file of compiled splice junctions
`filter_junctions_on_reads`(spliced_reads)
`junction_metadata`(spliced_reads, csv)	Get just the junction info from the concatenated read files
`make_junction_reads_file`()
`maybe_make_db`()	Get GFFutils database from file or create from a gtf
`maybe_make_folder`(folder)
`maybe_overwrite`(filename)	Ensures that filename is not overwritten unless user-specified

csv()[source]¶: Create a csv file of compiled splice junctions

debug = False¶

filter_junctions_on_reads(spliced_reads)[source]¶

folders¶

force = False¶

gffutils_db = None¶

gtf_filename = None¶

gtf_folder¶

ignore_multimapping = False¶

index_folder¶

static junction_metadata(spliced_reads, csv)[source]¶: Get just the junction info from the concatenated read files

junction_reads_filename¶

junctions_folder¶

make_junction_reads_file()[source]¶

maybe_make_db()[source]¶: Get GFFutils database from file or create from a gtf

maybe_make_folder(folder)[source]¶

maybe_overwrite(filename)[source]¶

Ensures that filename is not overwritten unless user-specified

If the file doesn’t exist, return “True”, as in “yes, please overwrite” even though there wasn’t really a file there, but the action is still to create the file in the next step
If the file exists and the user specified nothing, exit the program and complain that either –force or –resume must be specified
If the file exists and the user specified –force, then return True
If the file exists and the user specified –resume, then return False so that the file is not overwritten

Parameters:

filename : str

Path to a file that you may want to overwrite

Returns:

if_overwrite : bool

If True, then the next step in the program has the go-ahead to “overwrite” or create the file. If False, the file exists and the user doesn’t want to overwrite it

min_reads = 10¶

output_folder¶

reads_col = 'reads'¶

resume = False¶

sj_out_tab = None¶

class outrigger.commandline.SubcommandAfterIndex(**kwargs)[source]¶

Bases: outrigger.commandline.Subcommand

Can use different index folder than outrigger_output/index

Attributes

`folders`
`gtf_folder`
`index_folder`
`input_index`	Where to read the index from
`junction_reads_filename`
`junctions_folder`
`output_folder`

gffutils_db
gtf_filename
sj_out_tab

Methods

`csv`()	Create a csv file of compiled splice junctions
`filter_junctions_on_reads`(spliced_reads)
`junction_metadata`(spliced_reads, csv)	Get just the junction info from the concatenated read files
`make_junction_reads_file`()
`maybe_make_db`()	Get GFFutils database from file or create from a gtf
`maybe_make_folder`(folder)
`maybe_overwrite`(filename)	Ensures that filename is not overwritten unless user-specified

folders¶

input_index¶: Where to read the index from

exception outrigger.commandline.Usage(msg)[source]¶

Bases: Exception

Used to signal a Usage error, evoking a usage statement and eventual exit when raised

class outrigger.commandline.Validate(**kwargs)[source]¶

Bases: outrigger.commandline.SubcommandAfterIndex

Attributes

`folders`
`gtf_folder`
`index_folder`
`input_index`	Where to read the index from
`junction_reads_filename`
`junctions_folder`
`output_folder`

gffutils_db
gtf_filename
sj_out_tab

Methods

`csv`()	Create a csv file of compiled splice junctions
`execute`()
`exon_pair_splice_sites`(exonA, exonB, ...)
`filter_junctions_on_reads`(spliced_reads)
`individual_exon_splice_sites`(exon, ...)
`junction_metadata`(spliced_reads, csv)	Get just the junction info from the concatenated read files
`make_junction_reads_file`()
`maybe_make_db`()	Get GFFutils database from file or create from a gtf
`maybe_make_folder`(folder)
`maybe_overwrite`(filename)	Ensures that filename is not overwritten unless user-specified

execute()[source]¶

exon_pair_splice_sites(exonA, exonB, splice_abbrev)[source]¶

individual_exon_splice_sites(exon, splice_abbrev, direction)[source]¶

outrigger.commandline.main()[source]¶