python-chado and chakin¶

Contents:

Chado Library¶

A Python library for interacting with a Chado database.

Installation¶

$ pip install chado

# On first use you'll need to create a config file to connect to the database, just run:

$ chakin init
Welcome to Chado's Chakin! (茶巾)
PGHOST: xxxx
PGDATABASE: xxxx
PGUSER: xxxx
PGPASS:
PGPORT: 5432
PGSCHEMA: public

This will create a chakin config file in ~/.chakin.yml

Examples¶

from chado import ChadoInstance
ci = ChadoInstance(dbhost="localhost", dbname="chado", dbuser="chado", dbpass="chado", dbschema="public", dbport=5432)

# Create human species
org = ci.organism.add_organism(genus="Homo", species="sapiens", common="Human", abbr="H.sapiens")

# Then display the list of organisms
orgs = ci.organism.get_organisms()

for org in orgs:
    print('{} {}'.format(org.genus, org.species))

# Create an analysis
an = ci.analysis.add_analysis(name="My cool analysis",
                                   program="Something",
                                   programversion="1.0",
                                   algorithm="Google",
                                   sourcename="src",
                                   sourceversion="2.1beta",
                                   sourceuri="http://example.org/",
                                   date_executed="2018-02-03")

# And load some data
ci.feature.load_fasta(fasta="./test-data/genome.fa", analysis_id=an['analysis_id'], organism_id=orgs[0]['organism_id'])
ci.feature.load_gff(gff="./test-data/annot.gff", analysis_id=an['analysis_id'], organism_id=orgs[0]['organism_id'])

Or with the Chakin client:

$ my_org=`chakin organism add_organism --species sapiens Homo Human H.sapiens  | jq -r '.organism_id'`

$ chakin organism get_organisms
[
    {
        "organism_id": 1133,
        "genus": "Homo",
        "species": "sapiens",
        "abbreviation": "H.sapiens",
        "common_name": "Human",
        "comment": null
    }
]

# Then load some data
$ my_analysis=`chakin analysis add_analysis \
    "My cool analysis" \
    "Something" \
    "v1.0" \
    "src" | jq -r '.analysis_id'`


$ chakin feature load_fasta \
    --analysis_id $my_analysis \
    --sequence_type contig \
    ./test-data/genome.fa $my_org

History¶

2.3.9
- URL decode GFF ids when loading blast/interpro/others
2.3.8
- Fix connection closed error when loading big interproscan files
2.3.7
- Fix loading of expression data when first column header is not empty
2.3.6
- Fix loading of GO terms from GFF
2.3.5
- Fix has_table() calls with recent sqlalchemy versions
2.3.4
- Now requires biopython >=1.78
- Fixes biopython sequence usage in recent biopython
2.3.3
- Now requires python >= 3.6
- Better error reporting for blast loader
2.3.2
- Fix interproscan loader only loading the first result of XML v5
- Fix interproscan loader failing to load IPR by name
2.3.1
- Fix data loading in Tripal database
2.3.0
- Fix non working –re_parent option in fasta loader
- allow connection using a preformatted url (needed by galaxy tools using pgutil)
- added loading of Blast and InterProScan data
- moved chakin feature load_go to chakin load go
- fix sequence computing when landmark sequence is available in the db
- add more options to match features in expression matrix loader (query_type, match_on_name, re_name, skip_missing)
2.2.6
- fix requirement name for psycopg2 (name change for version >=2.8)
2.2.5
- Added support for units in expression loaders
- Fix error in load_gff when no source is specified
2.2.4
- Fix broken –skip_missing option for load_go
2.2.3
- Throw a warning instead of an exception when a GFF target feature does not exist
2.2.2
- Bug fixes and improvements to the expression module
2.2.1
- Minor release to fix broken package at pypi, no code change
2.2.0
- Added feature.load_go() to load GO annotation (blast2go results)
- Added feature.get_feature_analyses() to fetch the analyses associated with a feature
- Added feature.get_feature_cvterms() to fetch the cvterms associated with a feature
- Added support for biomaterial/expression data (as used by tripal_analysis_expression)
- New –protein_id_attr option for feature.load_gff()
2.1.5
- bugfix: fix features deletion when deleting an analysis
2.1.4
- bugfix: fix sporadic errors with AnalysisFeature class declaration
2.1.3
- bugfix: make –species a mandatory arg for organism creation
- bugfix: fix features deletion when deleting an analysis or an organism
- update chado docker image
2.1.2
- skip whole database schema reflection for simple tasks (analysis and organism management)
- fix polypeptide creation for genes beginning at position 0
- fix various small bugs in phylogeny and featureprop loading
- fix bug in cvterm creation
- fix crashes in gbk/gff exporters
2.1.1
- newick: remove prefix from node labels too
- newick: fix errors with named internal nodes
2.1
- auto reflect db schema
- add phylogeny module
- load features from fasta
- load features from gff3
- load featureprops from tabular file
- make chakin util commands work when db is offline
- add unit tests
2.0
- “Chakin” CLI utility
- Complete package restructure
- Nearly all functions renamed

License¶

Available under the MIT License

Commands¶

Chakin is a set of wrappers for accessing Chado. Each utility is implemented as a subcommand of chakin. This section of the documentation describes these commands.

analysis¶

This section is auto-generated from the help text for the chakin command analysis.

`add_analysis` command¶

Usage:

chakin 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_analyses` command¶

Usage:

chakin analysis delete_analyses [OPTIONS]

Help

Delete analysis

Output

None

Options:

--analysis_id INTEGER  analysis_id filter
--name TEXT            analysis name filter
--program TEXT         analysis program filter
--programversion TEXT  analysis programversion filter
--algorithm TEXT       analysis algorithm filter
--sourcename TEXT      analysis sourcename filter
--sourceversion TEXT   analysis sourceversion filter
--sourceuri TEXT       analysis sourceuri filter
--description TEXT     analysis description
-h, --help             Show this message and exit.

`get_analyses` command¶

Usage:

chakin analysis get_analyses [OPTIONS]

Help

Get all or some analyses

Output

Analysis information

Options:

--analysis_id INTEGER  analysis_id filter
--name TEXT            analysis name filter
--program TEXT         analysis program filter
--programversion TEXT  analysis programversion filter
--algorithm TEXT       analysis algorithm filter
--sourcename TEXT      analysis sourcename filter
--sourceversion TEXT   analysis sourceversion filter
--sourceuri TEXT       analysis sourceuri filter
--description TEXT     analysis description
-h, --help             Show this message and exit.

export¶

This section is auto-generated from the help text for the chakin command export.

`export_fasta` command¶

Usage:

chakin export export_fasta [OPTIONS] ORGANISM_ID

Help

Export reference sequences as fasta.

Output

None

Options:

--file      If true, write to files in CWD
-h, --help  Show this message and exit.

`export_gbk` command¶

Usage:

chakin export export_gbk [OPTIONS] ORGANISM_ID

Help

Export organism features as genbank

Output

None

Options:

-h, --help  Show this message and exit.

`export_gff3` command¶

Usage:

chakin export export_gff3 [OPTIONS] ORGANISM_ID

Help

Export organism features as GFF3

Output

None

Options:

-h, --help  Show this message and exit.

expression¶

This section is auto-generated from the help text for the chakin command expression.

`add_biomaterial` command¶

Usage:

chakin expression add_biomaterial [OPTIONS] BIOMATERIAL_NAME ORGANISM_ID

Help

Add a new biomaterial to the database

Output

Biomaterial details

Options:

--description TEXT           Description of the biomaterial
--biomaterial_provider TEXT  Biomaterial provider name
--biosample_accession TEXT   Biosample accession number
--sra_accession TEXT         SRA accession number
--bioproject_accession TEXT  Bioproject accession number
--attributes TEXT            Custom attributes (In JSON dict form)
-h, --help                   Show this message and exit.

`add_expression` command¶

Usage:

chakin expression add_expression [OPTIONS] ORGANISM_ID ANALYSIS_ID

Help

Add an expression matrix file to the database

Output

Number of expression data loaded

Options:

--separator TEXT   Separating character in the matrix file (ex : ','). Default
                   character is tab.  [default:        ]
--unit TEXT        The units associated with the loaded values (ie, FPKM,
                   RPKM, raw counts)
--query_type TEXT  The feature type (e.g. 'gene', 'mRNA', 'polypeptide',
                   'contig') of the query. It must be a valid Sequence
                   Ontology term.  [default: mRNA]
--match_on_name    Match features using their name instead of their uniquename
--re_name TEXT     Regular expression to extract the feature name from the
                   input file (first capturing group will be used).
--skip_missing     Skip lines with unknown features or GO id instead of
                   aborting everything.
-h, --help         Show this message and exit.

`delete_all_biomaterials` command¶

Usage:

chakin expression delete_all_biomaterials [OPTIONS]

Help

Delete all biomaterials

Output

None

Options:

--confirm   Confirm that you really do want to delete ALL of the biomaterials.
-h, --help  Show this message and exit.

`delete_biomaterial` command¶

Usage:

chakin expression delete_biomaterial [OPTIONS]

Help

Output

I have no idea

Options:

--names TEXT        JSON list of biomaterial names to delete.  [default: []]
--ids TEXT          JSON list of biomaterial ids to delete.  [default: []]
--organism_id TEXT  Delete all biomaterial associated with this organism id.
--analysis_id TEXT  Delete all biomaterial associated with this analysis id.
-h, --help          Show this message and exit.

`delete_biomaterials` command¶

Usage:

chakin expression delete_biomaterials [OPTIONS]

Help

Will delete biomaterials based on selector. Only one selector will be used.

Output

Number of deleted biomaterials

Options:

--names TEXT           JSON list of biomaterial names to delete.
--ids TEXT             JSON list of biomaterial ids to delete.
--organism_id INTEGER  Delete all biomaterial associated with this organism
                       id.
--analysis_id INTEGER  Delete all biomaterial associated with this analysis
                       id.
-h, --help             Show this message and exit.

`get_biomaterials` command¶

Usage:

chakin expression get_biomaterials [OPTIONS]

Help

List biomaterials in the database

Output

List of biomaterials

Options:

--provider_id INTEGER     Limit query to the selected provider
--biomaterial_id INTEGER  Limit query to the selected biomaterial id
--organism_id INTEGER     Limit query to the selected organism
--biomaterial_name TEXT   Limit query to the selected biomaterial name
--analysis_id INTEGER     Limit query to the selected analysis_id
-h, --help                Show this message and exit.

feature¶

This section is auto-generated from the help text for the chakin command feature.

`delete_features` command¶

Usage:

chakin feature delete_features [OPTIONS]

Help

Get all or some features

Output

Features information

Options:

--organism_id INTEGER  organism_id filter
--analysis_id INTEGER  analysis_id filter
--name TEXT            name filter
--uniquename TEXT      uniquename filter
-h, --help             Show this message and exit.

`get_feature_analyses` command¶

Usage:

chakin feature get_feature_analyses [OPTIONS] FEATURE_ID

Help

Get analyses associated with a feature

Output

Feature analyses

Options:

-h, --help  Show this message and exit.

`get_feature_cvterms` command¶

Usage:

chakin feature get_feature_cvterms [OPTIONS] FEATURE_ID

Help

Get cvterms associated with a feature

Output

Feature cvterms

Options:

-h, --help  Show this message and exit.

`get_features` command¶

Usage:

chakin feature get_features [OPTIONS]

Help

Get all or some features

Output

Features information

Options:

--organism_id INTEGER  organism_id filter
--analysis_id INTEGER  analysis_id filter
--name TEXT            name filter
--uniquename TEXT      uniquename filter
-h, --help             Show this message and exit.

`load_fasta` command¶

Usage:

chakin feature load_fasta [OPTIONS] FASTA ORGANISM_ID

Help

Load features from a fasta file

Output

Number of inserted sequences

Options:

--sequence_type TEXT    Sequence type  [default: contig]
--analysis_id INTEGER   Analysis ID
--re_name TEXT          Regular expression to extract the feature name from
                        the fasta sequence id (first capturing group will be
                        used).
--re_uniquename TEXT    Regular expression to extract the feature name from
                        the fasta sequence id (first capturing group will be
                        used).
--match_on_name         Match existing features using their name instead of
                        their uniquename
--update                Update existing feature with new sequence instead of
                        throwing an error
--db INTEGER            External database to cross reference to.
--re_db_accession TEXT  Regular expression to extract an external database
                        accession from the fasta sequence id (first capturing
                        group will be used).
--rel_type TEXT         Relation type to parent feature ('part_of' or
                        'derives_from').
--re_parent TEXT        Regular expression to extract parent uniquename from
                        the fasta sequence id (first capturing group will be
                        used).
--parent_type TEXT      Sequence type of the parent feature
-h, --help              Show this message and exit.

`load_featureprops` command¶

Usage:

chakin feature load_featureprops [OPTIONS] TAB_FILE ANALYSIS_ID

Help

Load feature properties from a tabular file (Column1: feature name or uniquename, Column2: property value)

Output

Number of inserted featureprop

Options:

--feature_type TEXT  Type of the target features in sequence ontology (will
                     speed up loading if specified)
--match_on_name      Match features using their name instead of their
                     uniquename
-h, --help           Show this message and exit.

`load_gff` command¶

Usage:

chakin feature load_gff [OPTIONS] GFF ANALYSIS_ID ORGANISM_ID

Help

Load features from a gff file

Output

None

Options:

--landmark_type TEXT       Type of the landmarks (will speed up loading if
                           provided, e.g. contig, should be a term of the
                           Sequence ontology)
--re_protein TEXT          Replacement string for the protein name using
                           capturing groups defined by --re_protein_capture
--re_protein_capture TEXT  Regular expression to capture groups in mRNA name
                           to use in --re_protein (e.g. "^(.*?)-R([A-Z]+)$",
                           default="^(.*?)$")  [default: ^(.*?)$]
--fasta TEXT               Path to a Fasta containing sequences for some
                           features. When creating a feature, if its sequence
                           is in this fasta file it will be loaded. Otherwise
                           for mRNA and polypeptides it will be computed from
                           the genome sequence (if available), otherwise it
                           will be left empty.
--no_seq_compute           Disable the computation of mRNA and polypeptides
                           sequences based on genome sequence and positions.
--quiet                    Hide progress information
--add_only                 Use this flag if you're not updating existing
                           features, but just adding new features to the
                           selected analysis and organism. It will speedup
                           loading, and reduce memory usage, but might produce
                           errors in case of already existing feature.
--protein_id_attr TEXT     Attribute containing the protein uniquename. It is
                           searched at the mRNA level, and if not found at CDS
                           level.
-h, --help                 Show this message and exit.

`load_go` command¶

Usage:

chakin feature load_go [OPTIONS] INPUT ORGANISM_ID ANALYSIS_ID

Help

Load GO annotation from a tabular file

Output

Number of inserted GO terms

Options:

--query_type TEXT      The feature type (e.g. 'gene', 'mRNA', 'polypeptide',
                       'contig') of the query. It must be a valid Sequence
                       Ontology term.  [default: polypeptide]
--match_on_name        Match features using their name instead of their
                       uniquename
--name_column INTEGER  Column containing the feature identifiers (2, 3, 10 or
                       11; default=2).  [default: 2]
--go_column INTEGER    Column containing the GO id (default=5).  [default: 5]
--re_name TEXT         Regular expression to extract the feature name from the
                       input file (first capturing group will be used).
--skip_missing         Skip lines with unknown features or GO id instead of
                       aborting everything.
-h, --help             Show this message and exit.

load¶

This section is auto-generated from the help text for the chakin command load.

`blast` command¶

Usage:

chakin load blast [OPTIONS] ANALYSIS_ID ORGANISM_ID INPUT

Help

Load a blast analysis, in the same way as does the tripal_analysis_blast module

Output

Number of processed hits

Options:

--blastdb TEXT        Name of the database blasted against (must be in the
                      Chado db table)
--blastdb_id INTEGER  ID of the database blasted against (must be in the Chado
                      db table)
--re_name TEXT        Regular expression to extract the feature name from the
                      input file (first capturing group will be used).
--query_type TEXT     The feature type (e.g. 'gene', 'mRNA', 'polypeptide',
                      'contig') of the query. It must be a valid Sequence
                      Ontology term.  [default: polypeptide]
--match_on_name       Match features using their name instead of their
                      uniquename
--skip_missing        Skip lines with unknown features or GO id instead of
                      aborting everything.
-h, --help            Show this message and exit.

`go` command¶

Usage:

chakin load go [OPTIONS] INPUT ORGANISM_ID ANALYSIS_ID

Help

Load GO annotation from a tabular file, in the same way as does the tripal_analysis_go module

Output

Number of inserted GO terms

Options:

--query_type TEXT      The feature type (e.g. 'gene', 'mRNA', 'polypeptide',
                       'contig') of the query. It must be a valid Sequence
                       Ontology term.  [default: polypeptide]
--match_on_name        Match features using their name instead of their
                       uniquename
--name_column INTEGER  Column containing the feature identifiers (2, 3, 10 or
                       11; default=2).  [default: 2]
--go_column INTEGER    Column containing the GO id (default=5).  [default: 5]
--re_name TEXT         Regular expression to extract the feature name from the
                       input file (first capturing group will be used).
--skip_missing         Skip lines with unknown features or GO id instead of
                       aborting everything.
-h, --help             Show this message and exit.

`interpro` command¶

Usage:

chakin load interpro [OPTIONS] ANALYSIS_ID ORGANISM_ID INPUT

Help

Load an InterProScan analysis, in the same way as does the tripal_analysis_intepro module

Output

Number of processed hits

Options:

--parse_go         Load GO annotation to the database
--re_name TEXT     Regular expression to extract the feature name from the
                   input file (first capturing group will be used).
--query_type TEXT  The feature type (e.g. 'gene', 'mRNA', 'polypeptide',
                   'contig') of the query. It must be a valid Sequence
                   Ontology term.  [default: polypeptide]
--match_on_name    Match features using their name instead of their uniquename
--skip_missing     Skip lines with unknown features or GO id instead of
                   aborting everything.
-h, --help         Show this message and exit.

organism¶

This section is auto-generated from the help text for the chakin command organism.

`add_organism` command¶

Usage:

chakin organism add_organism [OPTIONS] GENUS SPECIES COMMON ABBR

Help

Add a new organism to the Chado database

Output

Organism information

Options:

--comment TEXT  A comment / description
-h, --help      Show this message and exit.

`delete_all_organisms` command¶

Usage:

chakin organism delete_all_organisms [OPTIONS]

Help

Delete all organisms

Output

None

Options:

--confirm   Confirm that you really do want to delete ALL of the organisms.
-h, --help  Show this message and exit.

`delete_organisms` command¶

Usage:

chakin organism delete_organisms [OPTIONS]

Help

Delete all organisms

Output

None

Options:

--organism_id INTEGER  organism_id filter
--genus TEXT           genus filter
--species TEXT         species filter
--common TEXT          common filter
--abbr TEXT            abbr filter
--comment TEXT         comment filter
-h, --help             Show this message and exit.

`get_organisms` command¶

Usage:

chakin organism get_organisms [OPTIONS]

Help

Get all or some organisms

Output

Organisms information

Options:

--organism_id INTEGER  organism_id filter
--genus TEXT           genus filter
--species TEXT         species filter
--common TEXT          common filter
--abbr TEXT            abbr filter
--comment TEXT         comment filter
-h, --help             Show this message and exit.

phylogeny¶

This section is auto-generated from the help text for the chakin command phylogeny.

`add_cvterms` command¶

Usage:

chakin phylogeny add_cvterms [OPTIONS]

Help

Make sure required cvterms are loaded

Output

created cvterms

Options:

-h, --help  Show this message and exit.

`gene_families` command¶

Usage:

chakin phylogeny gene_families [OPTIONS]

Help

Adds an entry in the featureprop table in a chado database for each family a gene belongs to (for use in https://github.com/legumeinfo/lis_context_viewer/).

Output

None

Options:

--family_name TEXT  Restrict to families beginning with given prefix
--nuke              Removes all previous gene families data
-h, --help          Show this message and exit.

`gene_order` command¶

Usage:

chakin phylogeny gene_order [OPTIONS]

Help

Orders all the genes in the database by their order on their respective chromosomes in the gene_order table (for use in https://github.com/legumeinfo/lis_context_viewer/).

Output

None

Options:

--nuke      Removes all previous gene ordering data
-h, --help  Show this message and exit.

`load_tree` command¶

Usage:

chakin phylogeny load_tree [OPTIONS] NEWICK ANALYSIS_ID

Help

Load a phylogenetic tree (Newick format) into Chado db

Output

Number of inserted trees

Options:

--name TEXT            The name given to the phylotree entry in the database
                       (default=<filename>)
--xref_db TEXT         The name of the db to link dbxrefs for the trees
                       (default: "null")  [default: null]
--xref_accession TEXT  The accession to use for dbxrefs for the trees (assumed
                       same as name unless otherwise specified)
--match_on_name        Match polypeptide features using their name instead of
                       their uniquename
--prefix TEXT          Comma-separated list of prefix to be removed from
                       identifiers (e.g species prefixes when loading
                       OrthoFinder output)
-h, --help             Show this message and exit.

util¶

This section is auto-generated from the help text for the chakin command util.

`dbshell` command¶

Usage:

chakin util dbshell [OPTIONS]

Help

Open a psql session to the database

Output

None

Options:

-h, --help  Show this message and exit.

`launch_docker_image` command¶

Usage:

chakin util launch_docker_image [OPTIONS]

Help

Launch a chado docker image.

Output

None

Options:

--background  Launch the image in the background
--no_yeast    Disable loading of example yeast data
-h, --help    Show this message and exit.

chado package¶

Subpackages¶

chado.analysis package¶

Module contents¶

Contains possible interactions with the Chado Analysis Module

class chado.analysis.AnalysisClient(engine, metadata, session, ci)¶

Bases: chado.client.Client

Access to the chado analysis table

add_analysis(name, program, programversion, sourcename, algorithm=None, sourceversion=None, sourceuri=None, description=None, date_executed=None)¶

Create an analysis

Parameters:	name (str) – analysis name program (str) – analysis program programversion (str) – analysis programversion algorithm (str) – analysis algorithm sourcename (str) – analysis sourcename sourceversion (str) – analysis sourceversion sourceuri (str) – analysis sourceuri description (str) – analysis description date_executed (str) – analysis date_executed (yyyy-mm-dd)
Return type:	dict
Returns:	Analysis information

delete_analyses(analysis_id=None, name=None, program=None, programversion=None, algorithm=None, sourcename=None, sourceversion=None, sourceuri=None, description=None)¶

Delete analysis

Parameters:	analysis_id (int) – analysis_id filter name (str) – analysis name filter program (str) – analysis program filter programversion (str) – analysis programversion filter algorithm (str) – analysis algorithm filter sourcename (str) – analysis sourcename filter sourceversion (str) – analysis sourceversion filter sourceuri (str) – analysis sourceuri filter description (str) – analysis description
Return type:	None
Returns:	None

get_analyses(analysis_id=None, name=None, program=None, programversion=None, algorithm=None, sourcename=None, sourceversion=None, sourceuri=None, description=None)¶

Get all or some analyses

Parameters:	analysis_id (int) – analysis_id filter name (str) – analysis name filter program (str) – analysis program filter programversion (str) – analysis programversion filter algorithm (str) – analysis algorithm filter sourcename (str) – analysis sourcename filter sourceversion (str) – analysis sourceversion filter sourceuri (str) – analysis sourceuri filter description (str) – analysis description
Return type:	list of dict
Returns:	Analysis information

chado.export package¶

Module contents¶

Export data from chado

class chado.export.ExportClient(engine, metadata, session, ci)¶

Bases: chado.client.Client

Export data from the chado database

export_fasta(organism_id, file=False)¶

Export reference sequences as fasta.

Parameters:	organism_id (int) – Organism ID file (bool) – If true, write to files in CWD
Return type:	None
Returns:	None

export_gbk(organism_id)¶

Export organism features as genbank

Parameters:	organism_id (int) – Organism ID
Return type:	None
Returns:	None

export_gff3(organism_id)¶

Export organism features as GFF3

Parameters:	organism_id (int) – Organism ID
Return type:	None
Returns:	None

chado.expression package¶

Module contents¶

Contains possible interactions with the Chado base for expressions and biomaterials

class chado.expression.ExpressionClient(engine, metadata, session, ci)¶

Bases: chado.client.Client

Interact with expressions

add_biomaterial(biomaterial_name, organism_id, description='', biomaterial_provider='', biosample_accession='', sra_accession='', bioproject_accession='', attributes={})¶

Add a new biomaterial to the database

Parameters:	biomaterial_name (str) – Biomaterial name organism_id (int) – The id of the associated organism description (str) – Description of the biomaterial biomaterial_provider (str) – Biomaterial provider name biosample_accession (str) – Biosample accession number sra_accession (str) – SRA accession number bioproject_accession (str) – Bioproject accession number attributes (str) – Custom attributes (In JSON dict form)
Return type:	dict
Returns:	Biomaterial details

add_expression(organism_id, analysis_id, file_path, separator='\t', unit=None, query_type='mRNA', match_on_name=False, re_name=None, skip_missing=False)¶

Add an expression matrix file to the database

Parameters:	organism_id (int) – The id of the associated organism analysis_id (int) – The id of the associated analysis file_path (str) – File path separator (str) – Separating character in the matrix file (ex : ‘,’). Default character is tab. unit (str) – The units associated with the loaded values (ie, FPKM, RPKM, raw counts) query_type (str) – The feature type (e.g. ‘gene’, ‘mRNA’, ‘polypeptide’, ‘contig’) of the query. It must be a valid Sequence Ontology term. match_on_name (bool) – Match features using their name instead of their uniquename re_name (str) – Regular expression to extract the feature name from the input file (first capturing group will be used). skip_missing (bool) – Skip lines with unknown features or GO id instead of aborting everything.
Return type:	str
Returns:	Number of expression data loaded

delete_all_biomaterials(confirm=False)¶

Delete all biomaterials

Parameters:	confirm (bool) – Confirm that you really do want to delete ALL of the biomaterials.
Return type:	None
Returns:	None

delete_biomaterials(names=None, ids=None, organism_id='', analysis_id='')¶

Will delete biomaterials based on selector. Only one selector will be used.

Parameters:	names (str) – JSON list of biomaterial names to delete. ids (str) – JSON list of biomaterial ids to delete. organism_id (int) – Delete all biomaterial associated with this organism id. analysis_id (int) – Delete all biomaterial associated with this analysis id.
Return type:	str
Returns:	Number of deleted biomaterials

get_biomaterials(provider_id='', biomaterial_id='', organism_id='', biomaterial_name='', analysis_id='')¶

List biomaterials in the database

Parameters:	organism_id (int) – Limit query to the selected organism biomaterial_id (int) – Limit query to the selected biomaterial id provider_id (int) – Limit query to the selected provider biomaterial_name (str) – Limit query to the selected biomaterial name analysis_id (int) – Limit query to the selected analysis_id
Return type:	list
Returns:	List of biomaterials

chado.feature package¶

Module contents¶

Contains possible interactions with the Chado Features

class chado.feature.FeatureClient(engine, metadata, session, ci)¶

Bases: chado.client.Client

Access to the chado features

delete_features(organism_id=None, analysis_id=None, name=None, uniquename=None)¶

Get all or some features

Parameters:	organism_id (int) – organism_id filter analysis_id (int) – analysis_id filter name (str) – name filter uniquename (str) – uniquename filter
Return type:	list of dict
Returns:	Features information

get_feature_analyses(feature_id)¶

Get analyses associated with a feature

Parameters:	feature_id (int) – Id of the feature
Return type:	list
Returns:	Feature analyses

get_feature_cvterms(feature_id)¶

Get cvterms associated with a feature

Parameters:	feature_id (int) – Id of the feature
Return type:	list
Returns:	Feature cvterms

get_features(organism_id=None, analysis_id=None, name=None, uniquename=None)¶

Get all or some features

Parameters:	organism_id (int) – organism_id filter analysis_id (int) – analysis_id filter name (str) – name filter uniquename (str) – uniquename filter
Return type:	list of dict
Returns:	Features information

load_fasta(fasta, organism_id, sequence_type='contig', analysis_id=None, re_name=None, re_uniquename=None, match_on_name=False, update=False, db=None, re_db_accession=None, rel_type=None, re_parent=None, parent_type=None)¶

Load features from a fasta file

Parameters:	fasta (str) – Path to the Fasta file to load organism_id (int) – Organism ID sequence_type (str) – Sequence type analysis_id (int) – Analysis ID re_name (str) – Regular expression to extract the feature name from the fasta sequence id (first capturing group will be used). re_uniquename (str) – Regular expression to extract the feature name from the fasta sequence id (first capturing group will be used). match_on_name (bool) – Match existing features using their name instead of their uniquename update (bool) – Update existing feature with new sequence instead of throwing an error db (int) – External database to cross reference to. re_db_accession (str) – Regular expression to extract an external database accession from the fasta sequence id (first capturing group will be used). rel_type (str) – Relation type to parent feature (‘part_of’ or ‘derives_from’). re_parent (str) – Regular expression to extract parent uniquename from the fasta sequence id (first capturing group will be used). parent_type (str) – Sequence type of the parent feature
Return type:	dict
Returns:	Number of inserted sequences

load_featureprops(tab_file, analysis_id, organism_id, prop_type, feature_type=None, match_on_name=False)¶

Load feature properties from a tabular file (Column1: feature name or uniquename, Column2: property value)

Parameters:	tab_file (str) – Path to the tabular file to load analysis_id (int) – Analysis ID organism_id (int) – Organism ID prop_type (str) – Type of the feature property (cvterm will be created if it doesn’t exist) feature_type (str) – Type of the target features in sequence ontology (will speed up loading if specified) match_on_name (bool) – Match features using their name instead of their uniquename
Return type:	dict
Returns:	Number of inserted featureprop

load_gff(gff, analysis_id, organism_id, landmark_type=None, re_protein=None, re_protein_capture='^(.*?)$', fasta=None, no_seq_compute=False, quiet=False, add_only=False, protein_id_attr=None)¶

Load features from a gff file

Parameters:	gff (str) – Path to the Fasta file to load analysis_id (int) – Analysis ID organism_id (int) – Organism ID landmark_type (str) – Type of the landmarks (will speed up loading if provided, e.g. contig, should be a term of the Sequence ontology) re_protein (str) – Replacement string for the protein name using capturing groups defined by –re_protein_capture re_protein_capture (str) – Regular expression to capture groups in mRNA name to use in –re_protein (e.g. “^(.?)-R([A-Z]+)$”, default=”^(.?)$”) protein_id_attr (str) – Attribute containing the protein uniquename. It is searched at the mRNA level, and if not found at CDS level. fasta (str) – Path to a Fasta containing sequences for some features. When creating a feature, if its sequence is in this fasta file it will be loaded. Otherwise for mRNA and polypeptides it will be computed from the genome sequence (if available), otherwise it will be left empty. no_seq_compute (bool) – Disable the computation of mRNA and polypeptides sequences based on genome sequence and positions. quiet (bool) – Hide progress information add_only (bool) – Use this flag if you’re not updating existing features, but just adding new features to the selected analysis and organism. It will speedup loading, and reduce memory usage, but might produce errors in case of already existing feature.
Return type:	None
Returns:	None

load_go(input, organism_id, analysis_id, query_type='polypeptide', match_on_name=False, name_column=2, go_column=5, re_name=None, skip_missing=False)¶

Load GO annotation from a tabular file

Parameters:	input (str) – Path to the input tabular file to load organism_id (int) – Organism ID analysis_id (int) – Analysis ID query_type (str) – The feature type (e.g. ‘gene’, ‘mRNA’, ‘polypeptide’, ‘contig’) of the query. It must be a valid Sequence Ontology term. match_on_name (bool) – Match features using their name instead of their uniquename name_column (int) – Column containing the feature identifiers (2, 3, 10 or 11; default=2). go_column (int) – Column containing the GO id (default=5). re_name (str) – Regular expression to extract the feature name from the input file (first capturing group will be used). skip_missing (bool) – Skip lines with unknown features or GO id instead of aborting everything.
Return type:	dict
Returns:	Number of inserted GO terms

chado.load package¶

Module contents¶

Contains loader methods

class chado.load.LoadClient(engine, metadata, session, ci)¶

Bases: chado.client.Client

blast(analysis_id, organism_id, input, blastdb=None, blastdb_id=None, re_name=None, query_type='polypeptide', match_on_name=False, skip_missing=False)¶

Load a blast analysis, in the same way as does the tripal_analysis_blast module

Parameters:	analysis_id (int) – Analysis ID organism_id (int) – Organism ID input (str) – Path to the Blast XML file to load blastdb (str) – Name of the database blasted against (must be in the Chado db table) blastdb_id (int) – ID of the database blasted against (must be in the Chado db table) query_type (str) – The feature type (e.g. ‘gene’, ‘mRNA’, ‘polypeptide’, ‘contig’) of the query. It must be a valid Sequence Ontology term. match_on_name (bool) – Match features using their name instead of their uniquename re_name (str) – Regular expression to extract the feature name from the input file (first capturing group will be used). skip_missing (bool) – Skip lines with unknown features or GO id instead of aborting everything.
Return type:	dict
Returns:	Number of processed hits

go(input, organism_id, analysis_id, query_type='polypeptide', match_on_name=False, name_column=2, go_column=5, re_name=None, skip_missing=False)¶

Load GO annotation from a tabular file, in the same way as does the tripal_analysis_go module

Parameters:	input (str) – Path to the input tabular file to load organism_id (int) – Organism ID analysis_id (int) – Analysis ID query_type (str) – The feature type (e.g. ‘gene’, ‘mRNA’, ‘polypeptide’, ‘contig’) of the query. It must be a valid Sequence Ontology term. match_on_name (bool) – Match features using their name instead of their uniquename name_column (int) – Column containing the feature identifiers (2, 3, 10 or 11; default=2). go_column (int) – Column containing the GO id (default=5). re_name (str) – Regular expression to extract the feature name from the input file (first capturing group will be used). skip_missing (bool) – Skip lines with unknown features or GO id instead of aborting everything.
Return type:	dict
Returns:	Number of inserted GO terms

interpro(analysis_id, organism_id, input, parse_go=False, re_name=None, query_type='polypeptide', match_on_name=False, skip_missing=False)¶

Load an InterProScan analysis, in the same way as does the tripal_analysis_intepro module

Parameters:	analysis_id (int) – Analysis ID organism_id (int) – Organism ID input (str) – Path to the InterProScan file to load parse_go (bool) – Load GO annotation to the database query_type (str) – The feature type (e.g. ‘gene’, ‘mRNA’, ‘polypeptide’, ‘contig’) of the query. It must be a valid Sequence Ontology term. match_on_name (bool) – Match features using their name instead of their uniquename re_name (str) – Regular expression to extract the feature name from the input file (first capturing group will be used). skip_missing (bool) – Skip lines with unknown features or GO id instead of aborting everything.
Return type:	dict
Returns:	Number of processed hits

chado.organism package¶

Module contents¶

Contains possible interactions with the Chado Organisms Module

class chado.organism.OrganismClient(engine, metadata, session, ci)¶

Bases: chado.client.Client

Access to the chado organism table

add_organism(genus, species, common, abbr, comment=None)¶

Add a new organism to the Chado database

Parameters:	genus (str) – The genus of the organism species (str) – The species of the organism common (str) – The common name of the organism abbr (str) – The abbreviation of the organism comment (str) – A comment / description
Return type:	dict
Returns:	Organism information

delete_all_organisms(confirm=False)¶

Delete all organisms

Parameters:	confirm (bool) – Confirm that you really do want to delete ALL of the organisms.
Return type:	None
Returns:	None

delete_organisms(organism_id=None, genus=None, species=None, common=None, abbr=None, comment=None)¶

Delete all organisms

Parameters:	organism_id (int) – organism_id filter genus (str) – genus filter species (str) – species filter common (str) – common filter abbr (str) – abbr filter comment (str) – comment filter
Return type:	None
Returns:	None

get_organisms(organism_id=None, genus=None, species=None, common=None, abbr=None, comment=None)¶

Get all or some organisms

Parameters:	organism_id (int) – organism_id filter genus (str) – genus filter species (str) – species filter common (str) – common filter abbr (str) – abbr filter comment (str) – comment filter
Return type:	list of dict
Returns:	Organisms information

chado.phylogeny package¶

Module contents¶

Contains possible interactions with the Chado Phylogeny Module http://gmod.org/wiki/Chado_Phylogeny_Module As implemented in https://github.com/legumeinfo/tripal_phylotree and https://github.com/legumeinfo/lis_context_viewer/

class chado.phylogeny.PhylogenyClient(engine, metadata, session, ci)¶

Bases: chado.client.Client

Access to the chado phylogeny content

add_cvterms()¶

Make sure required cvterms are loaded

Return type:	list of dict
Returns:	created cvterms

gene_families(family_name='', nuke=False)¶

Adds an entry in the featureprop table in a chado database for each family a gene belongs to (for use in https://github.com/legumeinfo/lis_context_viewer/).

Parameters:	family_name (str) – Restrict to families beginning with given prefix nuke (bool) – Removes all previous gene families data
Return type:	None
Returns:	None

gene_order(nuke=False)¶

Orders all the genes in the database by their order on their respective chromosomes in the gene_order table (for use in https://github.com/legumeinfo/lis_context_viewer/).

Parameters:	nuke (bool) – Removes all previous gene ordering data
Return type:	None
Returns:	None

load_tree(newick, analysis_id, name=None, xref_db='null', xref_accession=None, match_on_name=False, prefix='')¶

Load a phylogenetic tree (Newick format) into Chado db

Parameters:	newick (str) – Newick file to load (or directory containing multiple newick files to load) analysis_id (int) – Analysis ID name (str) – The name given to the phylotree entry in the database (default=<filename>) xref_db (str) – The name of the db to link dbxrefs for the trees (default: “null”) xref_accession (str) – The accession to use for dbxrefs for the trees (assumed same as name unless otherwise specified) match_on_name (bool) – Match polypeptide features using their name instead of their uniquename prefix (str) – Comma-separated list of prefix to be removed from identifiers (e.g species prefixes when loading OrthoFinder output)
Return type:	dict
Returns:	Number of inserted trees

chado.util package¶

Module contents¶

class chado.util.UtilClient(engine, metadata, session, ci)¶

Bases: chado.client.Client

Some chado utilities

dbshell()¶

Open a psql session to the database

Return type:	None
Returns:	None

launch_docker_image(background=False, no_yeast=False)¶

Launch a chado docker image.

Parameters:	background (bool) – Launch the image in the background no_yeast (bool) – Disable loading of example yeast data
Return type:	None
Returns:	None

Submodules¶

chado.client module¶

Base chado client

class chado.client.Client(engine, metadata, session, ci)¶

Bases: object

Base client class implementing methods to make queries to the server

chado.exceptions module¶

exception chado.exceptions.RecordNotFoundError¶

Bases: Exception

Raised when a db select failed.

chado.util module¶

class chado.util.UtilClient(engine, metadata, session, ci)¶

Bases: chado.client.Client

Some chado utilities

dbshell()¶

Open a psql session to the database

Return type:	None
Returns:	None

launch_docker_image(background=False, no_yeast=False)¶

Launch a chado docker image.

Parameters:	background (bool) – Launch the image in the background no_yeast (bool) – Disable loading of example yeast data
Return type:	None
Returns:	None

Module contents¶

class chado.ChadoInstance(dbhost='localhost', dbname='chado', dbuser='chado', dbpass='chado', dbschema='public', dbport=5432, dburl=None, offline=False, no_reflect=False, reflect_tripal_tables=False, pool_connections=True, **kwargs)¶

Bases: object

create_cvterm(term, cv_name, db_name, term_definition='', cv_definition='', db_definition='', accession='')¶

get_cvterm_id(name, cv, allow_synonyms=False)¶: get_cvterm_id allows lookup of CV terms by their name. This method caches the result in order to not hit the DB for every query. Maybe should investigate pre-loading popular terms? (E.g. gene, mRNA, etc)

get_cvterm_name(cv_id)¶: get_cvterm_name allows lookup of CV terms by their ID. This method caches the result in order to not hit the DB for every query. Maybe should investigate pre-loading popular terms? (E.g. gene, mRNA, etc)

get_pub_id(name)¶: Allows lookup of publication by their uniquename. This method caches the result in order to not hit the DB for every query.

class chado.ChadoModel¶: Bases: object

python-chado and chakin¶

Chado Library¶

Installation¶

Examples¶

History¶

License¶

Commands¶

analysis¶

add_analysis command¶

delete_analyses command¶

get_analyses command¶

export¶

export_fasta command¶

export_gbk command¶

export_gff3 command¶

expression¶

add_biomaterial command¶

add_expression command¶

delete_all_biomaterials command¶

delete_biomaterial command¶

delete_biomaterials command¶

get_biomaterials command¶

feature¶

delete_features command¶

get_feature_analyses command¶

get_feature_cvterms command¶

get_features command¶

load_fasta command¶

load_featureprops command¶

load_gff command¶

load_go command¶

load¶

blast command¶

go command¶

interpro command¶

organism¶

add_organism command¶

delete_all_organisms command¶

delete_organisms command¶

get_organisms command¶

phylogeny¶

add_cvterms command¶

gene_families command¶

gene_order command¶

load_tree command¶

util¶

dbshell command¶

launch_docker_image command¶

chado package¶

Subpackages¶

chado.analysis package¶

Module contents¶

chado.export package¶

Module contents¶

chado.expression package¶

Module contents¶

chado.feature package¶

Module contents¶

chado.load package¶

Module contents¶

chado.organism package¶

Module contents¶

chado.phylogeny package¶

Module contents¶

chado.util package¶

Module contents¶

Submodules¶

chado.client module¶

chado.exceptions module¶

chado.util module¶

Module contents¶

Indices and tables¶

`add_analysis` command¶

`delete_analyses` command¶

`get_analyses` command¶

`export_fasta` command¶

`export_gbk` command¶

`export_gff3` command¶

`add_biomaterial` command¶

`add_expression` command¶

`delete_all_biomaterials` command¶

`delete_biomaterial` command¶

`delete_biomaterials` command¶

`get_biomaterials` command¶

`delete_features` command¶

`get_feature_analyses` command¶

`get_feature_cvterms` command¶

`get_features` command¶

`load_fasta` command¶

`load_featureprops` command¶

`load_gff` command¶

`load_go` command¶

`blast` command¶

`go` command¶

`interpro` command¶

`add_organism` command¶

`delete_all_organisms` command¶

`delete_organisms` command¶

`get_organisms` command¶

`add_cvterms` command¶

`gene_families` command¶

`gene_order` command¶

`load_tree` command¶

`dbshell` command¶

`launch_docker_image` command¶