analysis¶
This section is auto-generated from the help text for the tripaille command
analysis.
add_analysis command¶
Usage:
tripaille analysis add_analysis [OPTIONS] NAME PROGRAM PROGRAMVERSION
Help
Create an analysis
Output
Analysis information
Options:
--algorithm TEXT analysis algorithm
--sourceversion TEXT analysis sourceversion
--sourceuri TEXT analysis sourceuri
--description TEXT analysis description
--date_executed TEXT analysis date_executed (yyyy-mm-dd)
-h, --help Show this message and exit.
delete_orphans command¶
Usage:
tripaille analysis delete_orphans [OPTIONS]
Help
Delete orphans Drupal analysis nodes
Output
status
Options:
--job_name TEXT Name of the job
--no_wait Return immediately without waiting for job completion
-h, --help Show this message and exit.
get_analyses command¶
Usage:
tripaille analysis get_analyses [OPTIONS]
Help
Get analyses
Output
Analysis information
Options:
--analysis_id TEXT An analysis ID
--name TEXT analysis name
--program TEXT analysis program
--programversion TEXT analysis programversion
--algorithm TEXT analysis algorithm
--sourcename TEXT analysis sourcename
--sourceversion TEXT analysis sourceversion
--sourceuri TEXT analysis sourceuri
--date_executed TEXT analysis date_executed (yyyy-mm-dd)
-h, --help Show this message and exit.
get_analyses_tripal command¶
Usage:
tripaille analysis get_analyses_tripal [OPTIONS]
Help
Get analysis entities
Output
Analysis entity/node information
Options:
--analysis_id INTEGER An analysis entity/node ID
-h, --help Show this message and exit.
load_blast command¶
Usage:
tripaille analysis load_blast [OPTIONS] NAME PROGRAM PROGRAMVERSION
Help
Create a Blast analysis
Output
Loading information
Options:
--blast_ext TEXT If looking for files in a directory, extension of the
blast result files
--blastdb TEXT Name of the database blasted against (must be in the
Chado db table)
--blastdb_id TEXT ID of the database blasted against (must be in the
Chado db table)
--blast_parameters TEXT Blast parameters used to produce these results
--query_re TEXT The regular expression that can uniquely identify the
query name. This parameters is required if the
feature name is not the first word in the blast query
name.
--query_type TEXT The feature type (e.g. 'gene', 'mRNA', 'contig') of
the query. It must be a valid Sequence Ontology term.
--query_uniquename Use this if the --query-re regular expression matches
unique names instead of names in the database.
--is_concat If the blast result file is simply a list of
concatenated blast results.
--search_keywords Extract keywords for Tripal search
--no_parsed TEXT Maximum number of hits to parse per feature.
Default=all [default: all]
--no_wait Do not wait for job to complete
--algorithm TEXT analysis algorithm
--sourceversion TEXT analysis sourceversion
--sourceuri TEXT analysis sourceuri
--description TEXT analysis description
--date_executed TEXT analysis date_executed (yyyy-mm-dd)
-h, --help Show this message and exit.
load_fasta command¶
Usage:
tripaille analysis load_fasta [OPTIONS] FASTA
Help
Load fasta sequences
Output
Loading information
Options:
--organism TEXT Organism common name or abbreviation
--organism_id INTEGER Organism ID
--analysis TEXT Analysis name
--analysis_id INTEGER Analysis ID
--sequence_type TEXT Sequence type [default: contig]
--re_name TEXT Regular expression for the name
--re_uniquename TEXT Regular expression for the unique name
--db_ext_id TEXT External DB ID
--re_accession TEXT Regular expression for the accession from external DB
--rel_type TEXT Relation type (part_of or derives_from)
--rel_subject_re TEXT Relation subject regular expression (used to extract
id of related entity)
--rel_subject_type TEXT Relation subject type (must match already loaded
data, e.g. mRNA)
--method TEXT Insertion method (insert, update or insup,
default=insup (Insert and Update)) [default: insup]
--match_type TEXT Match type for already loaded features (name or
uniquename; default=uniquename; used for "Update
only" or "Insert and update" methods)' [default:
uniquename]
--job_name TEXT Name of the job
--no_wait Do not wait for job to complete
-h, --help Show this message and exit.
load_gff3 command¶
Usage:
tripaille analysis load_gff3 [OPTIONS] GFF
Help
Load GFF3 file
Output
Loading information
Options:
--organism TEXT Organism common name or abbreviation
--organism_id INTEGER Organism ID
--analysis TEXT Analysis name
--analysis_id INTEGER Analysis ID
--import_mode TEXT Import mode (add_only=existing features won't be
touched, update=existing features will be
updated and obsolete attributes kept)')
[default: update]
--target_organism TEXT In case of Target attribute in the GFF3, choose
the organism abbreviation or common name to
which target sequences belong. Select this only
if target sequences belong to a different
organism than the one specified with --organism-
id. And only choose an organism here if all of
the target sequences belong to the same species.
If the targets in the GFF file belong to
multiple different species then the organism
must be specified using the
'target_organism=genus:species' attribute in the
GFF file.')
--target_organism_id INTEGER In case of Target attribute in the GFF3, choose
the organism ID to which target sequences
belong. Select this only if target sequences
belong to a different organism than the one
specified with --organism-id. And only choose an
organism here if all of the target sequences
belong to the same species. If the targets in
the GFF file belong to multiple different
species then the organism must be specified
using the 'target_organism=genus:species'
attribute in the GFF file.')
--target_type TEXT In case of Target attribute in the GFF3, if the
unique name for a target sequence is not unique
(e.g. a protein and an mRNA have the same name)
then you must specify the type for all targets
in the GFF file. If the targets are of different
types then the type must be specified using the
'target_type=type' attribute in the GFF file.
This must be a valid Sequence Ontology (SO)
term.')
--target_create In case of Target attribute in the GFF3, if the
target feature cannot be found, create one using
the organism and type specified above, or using
the 'target_organism' and 'target_type' fields
specified in the GFF file. Values specified in
the GFF file take precedence over those
specified above.')
--start_line INTEGER The line in the GFF file where importing should
start
--landmark_type TEXT A Sequence Ontology type for the landmark
sequences in the GFF fie (e.g. 'chromosome').
--alt_id_attr TEXT When ID attribute is absent, specify which other
attribute can uniquely identify the feature.
--create_organism Create organisms when encountering organism
attribute (these lines will be skip otherwise)
--re_mrna TEXT Regular expression for the mRNA name
--re_protein TEXT Replacement string for the protein name
--job_name TEXT Name of the job
--no_wait Do not wait for job to complete
-h, --help Show this message and exit.
load_go command¶
Usage:
tripaille analysis load_go [OPTIONS] NAME PROGRAM PROGRAMVERSION
Help
Create a GO analysis
Output
Loading information
Options:
--organism TEXT Organism common name or abbreviation
--organism_id INTEGER Organism ID
--gaf_ext TEXT If looking for files in a directory, extension of the
GAF files
--query_type TEXT The feature type (e.g. 'gene', 'mRNA', 'contig') of the
query. It must be a valid Sequence Ontology term.
--query_matching TEXT Method to match identifiers to features in the
database. ('name', 'uniquename' or 'dbxref') [default:
uniquename]
--method TEXT Import method ('add' or 'remove') [default: add]
--name_column INTEGER Column containing the feature identifiers (2, 3, 10 or
11; default=2). [default: 2]
--re_name TEXT Regular expression to extract the feature name from GAF
file.
--no_wait Do not wait for job to complete
--algorithm TEXT analysis algorithm
--sourceversion TEXT analysis sourceversion
--sourceuri TEXT analysis sourceuri
--description TEXT analysis description
--date_executed TEXT analysis date_executed (yyyy-mm-dd)
-h, --help Show this message and exit.
load_interpro command¶
Usage:
tripaille analysis load_interpro [OPTIONS] NAME PROGRAM PROGRAMVERSION
Help
Create an Interpro analysis
Output
Loading information
Options:
--interpro_parameters TEXT InterProScan parameters used to produce these
results
--query_re TEXT The regular expression that can uniquely identify
the query name. This parameters is required if the
feature name is not the first word in the blast
query name.
--query_type TEXT The feature type (e.g. 'gene', 'mRNA', 'contig')
of the query. It must be a valid Sequence Ontology
term.
--query_uniquename Use this if the query_re regular expression
matches unique names instead of names in the
database.
--parse_go Load GO annotation to the database
--no_wait Do not wait for job to complete
--algorithm TEXT analysis algorithm
--sourceversion TEXT analysis sourceversion
--sourceuri TEXT analysis sourceuri
--description TEXT analysis description
--date_executed TEXT analysis date_executed (yyyy-mm-dd)
-h, --help Show this message and exit.
sync command¶
Usage:
tripaille analysis sync [OPTIONS]
Help
Synchronize an analysis
Output
status
Options:
--analysis TEXT Analysis name
--analysis_id TEXT ID of the analysis to sync
--job_name TEXT Name of the job
--no_wait Return immediately without waiting for job completion
-h, --help Show this message and exit.