-
*
- bio_seq_id *
- sequence from which this segment is derived
*
- contains an accession number *
- start *
- start position of segment (inclusive) *
- end *
- end position of segment (inclusive)
*
- In the case that start defines a 'between' position, end is unused *
- complement *
- true if segment should be complemented before any further manipulations *
-
*
- op *
- operator defining what to do with the nodes
*
-
*
- join *
- The indicated elements should be joined (placed end-to-end) * to form one contiguous sequence *
- order *
- The elements can be found in the specified order * (5' to 3' direction), but nothing is implied about the * reasonableness about joining them *
- childIds *
- identifiers of the child nodes
*
- Ids is an array of IDs relative to the current node * e.g if the current node is at position x in the LocationNodes sequence * and there is a childId with value j * then the position of this child in the LocationNodes sequence will be x+j *
* this is a stripped down version of the featuremeta IDL. Types which
* are typedefs of the same base-type in featuremeta are not
* distinguished here.
* @see featuremeta
*/
typedef long QualifierTypeCode;
// values 1-100 are reserved for EBI QualifierTypeCodes
const long string_qtc = 1;
const long boolean_qtc = 2;
const long integer_qtc = 3;
const long real_qtc = 4;
const long TranslationException_qtc = 17;
const long CodonTranslation_qtc = 18;
const long Anticodon_qtc = 19;
const long SpliceConsensus_qtc = 20;
const long RepeatUnit_qtc = 21;
const long DbXref_qtc = 22;
union QualifierValue_u switch (QualifierTypeCode) {
// EBI typecodes
case boolean_qtc : boolean applicable;
case string_qtc : string text;
case integer_qtc : long integer;
case real_qtc : float real;
case TranslationException_qtc : type::TranslationException translation_exception;
case CodonTranslation_qtc : type::CodonTranslation codon_translation;
case Anticodon_qtc : type::AntiCodon anti_codon;
case SpliceConsensus_qtc : type::SpliceConsensus splice_consensus;
case RepeatUnit_qtc : type::RepeatUnit repeat_unit;
case DbXref_qtc : type::DbXref db_xref;
// add your own extension types below
#ifdef ANALYSIS
// analysis qualifier extension
// see analysis.idl
case ANALYSIS::Analysis_qtc : ANALYSIS::Scores score;
#endif
};
typedef sequence
*
* This method can be used instead of the getAnySeq()
* method in seqdb::BioSeq
* @see seqdb::BioSeq
*/
string getSeq();
/**
* Checksum on sequence to allow validation.
*
*/
unsigned long getCheckSum();
/**
* topology of the nucleotide sequence
* @see meta::nsdb
*/
string getTopology();
/**
* molecule type of the nucleotide sequence
* @see meta::nsdb
*/
string getMoleculeType();
/**
* retrieve sequence of NucFeatureList associated with
* the nucleotide sequence.
* A sequence has ownership of all these
* features. It is possible on the other hand that
* features, owned by another sequence, reference
* the current sequence. Currently there is no way to find out.
* @raises type::NoResult if no features are owned by the sequence
*/
NucFeatureList getNucFeatures()
raises (type::NoResult);
/**
* A location of a NucFeature can span multiple sequences.
* If only the location of a feature relevant to the current
* sequence is required, this method will calculate that.
* @parm nuc_feature Feature from which location needs to be
* intersected with the current sequence.
* @raises type::InvalidRelation if the nuc_feature
* is not associated to the current sequence
*/
Location getLocalLocation(in NucFeature nuc_feature)
raises (type::InvalidRelation);
/**
* organism(s) from which the NucSeq was obtained.
* If the sequence is chimeric, multiple organisms will be returned.
* For each organism, there should be a source feature associated
* with the current sequence. This source feature has a location
* defining which part of the sequence was derived from the specified
* organism.
* This method provides a shortcut to:
* invoke getNucFeaturesByKey("source"), invoke getQualifiers() on each
* source feature and loop through qualifiers to find DbXref.
* @raises type::NoResult if no source features are associated with
* the sequence (should never happen).
*/
type::DbXrefList getOrganisms()
raises (type::NoResult);
/**
* retreive all features of a specific kind (FeatureKey)
* @parm key Type of features to be retrieved
* @raises type::NoResult if the sequence has no associated features
* of the requested type.
* @raises type::InvalidArgumentValue if the key is not a
*
* valid feature key
* @see NucFeature
*/
NucFeatureList getNucFeaturesByKey(in string key)
raises (type::NoResult, type::InvalidArgumentValue);
/**
* Create nucleotide sequence of the segment specified
* The first base in the sequence is numbered 1
*
* @parm start first base of sub-sequence (inclusive)
* @parm end last base of sub-sequence (inclusive)
* @raises type::IndexOutOfRange if start < 1
* or end > length
*/
string getSubSeq(in unsigned long start, in unsigned long end)
raises (type::IndexOutOfRange);
/**
* Create nucleotide sequence of the location derived from the specified feature
* and contained in the current NucSeq.
* @raises type::InvalidRelation if the nuc_feature
* is not associated to the current sequence
* @raises InexactLocation if an exact sequence cannot be
* determined due to the feature's location being inexact
*/
string getSubSeqByFeature(in NucFeature feature)
raises (type::InvalidRelation, InexactLocation);
/**
* @raises type::InvalidRelation if reference does not exist
* @raises type::InvalidRelation if reference is not
* associated to the current sequence
* @raises type::NoResult if there is no location associated with this reference
*/
Location getReferenceLocation(in string reference_id)
raises (type::InvalidRelation, type::NoResult);
};
/**
* EMBL Nucleotide sequence interface. An EMBL sequence contains all information
* to generate a flat-file entry out of it.
* It defines no new behaviour but inherits from
* several interfaces and acts as a container of the combined functionality.
*/
interface EmblSeq : NucSeq, seqdb::SeqInfo , EntryInfo {
};
/**
* Entry point for Nucleotide Sequence Database.
* Query methods on the database are defined here.
* Currently this is minimal, but should be extended later on.
*/
interface Embl {
exception Superceded { type::stringList bio_seq_ids; };
/**
* retrieve Nucleotide sequence, given it's accession number. If a client only supports
* NucSeq, and not EmblSeq, than it can widen the EmblSeq to a NucSeq (implicit).
* @raises type::NoResult if the accession number does not exist.
* @raises Superceded if the sequence referenced by the accession
* number does not exist any more, because it was merged, or split.
*/
EmblSeq getEmblSeq(in string bio_seq_id)
raises (type::NoResult, Superceded);
};
};
#endif // embl_ebi_nsdb_idl
Artemis-16.0.17/corba/nsdb_write.idl 0000664 0000000 0000000 00000022361 13015260127 0017213 0 ustar 00root root 0000000 0000000 #ifndef EMBL_EBI_NSDB_WRITE_IDL
#define EMBL_EBI_NSDB_WRITE_IDL
#include "nsdb.idl"
module nsdb {
exception OutOfDate { };
exception ReadOnlyException { };
exception LocationParse {
string reason;
};
exception QualifierParse {
string reason;
};
exception InvalidQualifier { };
interface EmblSeqWriter;
interface NucFeatureWriter;
typedef sequence
*/
struct Person {
string surname;
string firstname;
string midinitial;
};
typedef sequence
*
*
*
* ÜÀ ëèÖ8n°Œn‰ÓØè8*À‰vcÁþ ×¼ÄÕ%ÐÁ í—lPJÁ ËH„ÁˆXtK °,ŽA u²Sžô´'>ßñ‚h¸ÃD@×>Õ!d"ò
=ÙŒ Ã[ðì–J9ÁR—v#؆(0 f(Âh¨Hß1Î+¨R,ðÖ:Û鎙ÖzØÃ;pñŽSpAŸD
— ž0Òk8€éhÅjáÓ…
Õ«”P‡+&` ¬Ž³
K¨ƒØÑ-üV ß±Ôn%¨EVÇ)Np"îïÞ±Žˆ¾ÂØ'M[
Œw#í8ĪP†
v¦í ¬[Á%/,T…Ø@·fÀ w€£ÝþhAPØpô[yp‚ôÜQ BLAST is used to generate the ACT comparison file (for more details see the ACT manual) one of the
sequences needs to be made the database sequence and indexed with formatdb:
The other sequence is the query and you can then search for matches between these:
or
Use the '-m 8' option to provide the tabular output that ACT uses.
An alternative to this is to use WebACT or Double ACT to generate the comparison file.
f)À €4Z# À4NE A%5Ú+(@°æeZfE¨ƒ d€% §E4gM@wÀ(Œâ'9% V[RìÃ,ªçz²g{ºçzÊ"{Æ'|~ {rB‰!B%
À \˜-°)ÜASÚ˜xþFÅ(ØÚJèK€!È‘1ÔÑ[½ÂyêFè YÑ5\C6ÜʆB„@ ‡R†ÞÊ6dÃ5PÃ44ƒ1l‚ðB1¦#8جUÄ2H^Ðyæè(›‰ƒ- HXÎ:àfvæHÌcHP5°Ž
ÅŽvD6Ø•’Î’‚TZOyÚÑù9¨#qi—z©—BÒWÁ ÐÀWñBŒý€f¡F…"x K¸©‚™"ÈÑ2¬€,}€™½#°¢l Ã0‚"]Ã6€¹ÐË¡"j¢*ꢒ 8lCŠ"Ã#ÀFbD_æFA¡6Œ„,D‚lÒãx²†• –>BS4Ã5 jªªêª²jþ«ºê«Âê)ÔJ0X@,ÐÊU„šn$ )â^0Lƒù $C,TBŸÆ†7 Ây–žPÈÁô …8€C® "ÞÌ¥ãmЃ38ƒx…„48à Îæ€Ö•¹^Ä4< e»¸ë»Â뺼B0Ñ+½*N½R°‚!èê•Þ˜å&|5Äà ÀÄ5 C,l²Â† In this tutorial we present how to install and configure
Artemis and
ACT to use with a
Chado database. The first two sections relate to installing Postgres
and Chado, this is included for completeness only and you should refer
to the Chado session for more details on this.
Added the line to data/postgresql.conf:
Create the database:
Now compile Chado and install the standard components (schema and ontologies):
In this section we detail how to load 3 Plasmodium sequences into Chado for viewing in Artemis and ACT. Alternatively you can use your own sequences of interest.
The GenBank files are available from Entrez with the links below. Make sure you download it with the sequence by clicking on the option 'Show sequence' and 'Update View'. Then go to the Download menu and select GenBank(Full):
These are usually downloaded to the Desktop directory (depending on the browser). They are saved as something like sequences.gbwithparts. Re-name them as NC_004314.gbk, NC_011907.gbk and NC_011909.gbk. Pfalciparum and Pknowlesi will need to be added to your organism table in Chado.
Using the perl script 'bp_genbank2gff3.pl' to convert the GenBank files to GFF3 format:
You need to modify the gff files so that the correct SO term is used:
Then load the GFF3 files that have been created:
You can download Artemis and ACT from their home pages at the Sanger Institute. For the most up-to-date developments download the software from the CVS server:
Now compile the software:
Or download the development version from the Development section on the Artemis home page. Note that on the Artemis web site there is also a stable release available.
Try running the 'art' script in the download:
This opens the login window:
The Artemis Database Manager and File Manager will open once your login has been authenticated. The top part of this relates to the Chado database and the bottom comprises the file management:
Select the sequence NC_004314 and double click on it to open it up in Artemis.
There are 3 main components to the Artemis window. The two top Feature Displays show the sequence at different levels of granularity and below these is a feature list:
These three components are connected, so that if you select a feature in one then that feature becomes selected in the others. Double clicking on the feature centers the feature in both feature displays. The scroll bars on the right hand side of the feature displays allow you to zoom in and out.
The alternative way to open your sequence is to provide the entry (e.g. Pfalciparum:NC_004314) you want to open as a command line argument:
For any of the gene features in Artemis you can select them and press the short cut key 'E' (Edit->Selected Features in Editor). This opens up the Gene Builder. Within this the Gene Model can be edited and annotation added.
It is also possible to launch the Artemis Gene Builder in a standalone mode for a particular gene:
or in read-only mode you can open a gene in GeneDB (at the Sanger Institute):
Note using the JVM option 'show_log' will open the log window.
Edit 'etc/options' (to change settings globally) or create a file ~/.artemis_options in your home directory (for your own settings). There are various flags that can be used to configure Artemis and ACT with Chado.
chado_servers This allows you to provide a list of available servers for the user to select:
product_cv In the Pathogen Genomics Group the product qualifiers are stored as an ontology (as a cv in feature_cvterm). This can be changed so that they are stored as featureprop's by setting the product_cv option:
This will mean that the product will be shown in the "Core" section of the Artemis Gene Builder rather than the "Controlled Vocabulary" section.
synonym_cvname If synonym types are loaded into a CV, Artemis checks this ontology.
set_obsolete_on_delete This will set the default behaviour of Artemis when features are deleted. If set to:
the features will be made obsolete. The user is still prompted with the option to permanently delete the feature. If this line is not in the option file the default is to permanently delete features.
Selecting an alternative gene model Artemis supports 2 types of gene model representations:
A) Pathogen Genomics Gene Model - implicit CDS + explicit UTRs
B) implicit CDS + UTRs
The Artemis default is model A. To use model B then set:
sequence_update_features This lists the features that Artemis will maintain the feature.residue column for. This is generally useful for polypeptide and transcript features.
The database manager provides the list of organisms that have features with residues (currently Artemis searches for these on features of type: '*chromosome*', '*sequence*', 'supercontig', 'ultra_scaffold', 'golden_path_region', 'contig'). The database manager is cached between sessions (this is on by default and can be switched off with -Ddatabase_manager_cache_off). There is an option under the File menu to clear this cache.
These use evidence codes which are stored as a feature_cvtermprop's with a type_id which corresponds to a cvterm.name = 'evidence'. There is a useful SQL script (etc/chado_extra.sql) in the Artemis distribution for creating this term in Chado. Run this on the chado_pathogen instance of the database:
(This will also create other terms that are used to store literature (PMID's) qualifiers.)
GO terms can now be selected in the Controlled Vocabulary (CV) section of the Gene Builder and added to features. Additional custom CV's can also be used. For Artemis to recognise it and display it the name of the CV needs to be prefixed by 'CC_'. These then appear in a drop down list when adding CV terms to a feature. Try adding a new CV:
and create a CvTerm in this CV:
Now re-launch Artemis and open the Gene Builder at any feature and go to the 'Controlled Vocabulary' section and click the 'ADD' button. This CV (CC_test) will appear in the drop down menu:
Click on CC_test and hit the 'Next' button. This opens a keyword selection box. If you leave this blank all the terms are retrieved and displayed. If you keep clicking 'Next' this term is then added to the 'Controlled Vocabulary' section.
This tool can be accessed from the Gene Builder - look for the TAT button. It allows you to transfer annotation between sequences. In database mode Artemis provides an editable list of genes constructed from ortholog/parlog links. These links can be added in the Gene Builder in the Match section (for example you can try creating the ortholog link between PF10_0165 in Pfalciparum and PKH_060110 in Pknowlesi).
Note that you can easily access the logging information Artemis produces. In the Artemis launch window under the 'Options' menu select the 'Show Log Window', this provides the logs. This is controlled by etc/log4j.properties. The logs can be useful for debugging and for monitoring activity if appended to a central file. See the log4j documentation for more information.
ACT can read sequences in from the database as well. However, it currently does not read the BLAST comparisons from Chado but reads this data from files. These comparisons are displayed as the matches between the sequences. To distinguish forward and reverse matches the forward matches are red and reverse matches are blue.
For convenience the comparison files have been pre-generated for this exercise and can be downloaded from:
Note that both Artemis and ACT automatically open gzipped files. For details on generating these files go to ACT Comparison Files.
To run ACT use the 'act' script:
From the 'File' menu select the option 'Open Database and SSH File Manager' and login. Drag and drop the Plasmodium entries from the Database Manager into the ACT selection window. Also, drag and drop the comparison files into this window, so it looks something like this (note the featureId numbers may well be different as these are the Chado feature_id):
Click on Apply to read these entries and open up ACT. You can use the right hand scroll bar to zoom in and out. If you zoom out you can indentify the regions that match between these sequences.
ACT can display multiple pairwise comparison. So the two P.knowlesi sequences can be compared to the P.falciparum sequence. From the ACT launch window go to the File menu and select 'Open Database and SSH File Manager'. Drag in the sequences and comparison files (clicking on 'more files' to add the additional sequence and comparison).
Zooming out you will see that Pfalciparum chromosome 10 matches to regions in Pknowlesi chromosome 7 and 9.
Artemis can write out EMBL and GFF files for an entry opened from the database. You can optionally flatten the gene model (i.e. gene, transcript, exon) to just a CDS feature. Also an option is given to ignore any obsolete features. For EMBL it uses mappings for conversion of the keys and qualifiers. These mappings are stored in the 'etc/key_mapping' and 'etc/qualifier_mapping' files.
A utility script (etc/write_db_entry) is also provided as a means of writing out multiple sequences from the database. The script takes the following options:
Try running:
There is an Artemis mailing list: artemis-user.
Artemis home page
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#ñ·þ3V“
*
*/
struct Qualifier {
string name;
QualifierValueList values;
};
typedef sequence
*
*/
struct Date {
unsigned short day;
unsigned short month;
unsigned short year;
};
typedef sequence
*
*
*/
struct Revision {
Date date;
string type;
};
typedef sequence
*
*/
struct DbXref {
string db;
string primary_id;
unsigned long version;
string label;
};
typedef sequence
*
*/
struct AminoAcid {
char code;
string name;
string abbreviation;
};
typedef sequence
*
*/
struct AntiCodon {
long start;
long end;
AminoAcid amino_acid;
};
typedef sequence
*
*/
struct TranslationException {
string primary_acc;
long start;
long end;
AminoAcid amino_acid;
};
typedef sequenceGenerating ACT Comparison File
formatdb -i NC_004314.fasta -p 'F'
blastall -p tblastx -d NC_004314.fasta -i NC_011907.fasta -o NC_004314_v_NC_011907_tblastx -m 8
blastall -p blastn -d NC_004314.fasta -i NC_011907.fasta -o NC_004314_v_NC_011907_blastn -m 8 -e 0.1
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Contents
Overview
Download and Install Postgres
./configure --prefix=/home/gmod/gmod_test/pgsl --with-pgport=5432 --with-includes=/Developer
make
make install
cd /home/gmod/gmod_test/pgsl
bin/initdb -D data/
listen_addresses = 'localhost'
postmaster -D data &
createuser --createdb username
createlang plpgsql template1
createdb --port=5432 chado_pathogen
Download and Install Chado
export GMOD_ROOT=/usr/local/gmod CHADO_DB_NAME=chado_pathogen CHADO_DB_USERNAME=username CHADO_DB_PORT=5432
perl Makefile.PL
make
sudo make install
make load_schema
make prepdb
make ontologies
Examples of Loading Sequences into the Database
psql chado_pathogen
INSERT INTO organism
( abbreviation, genus, species, common_name )
VALUES
( 'Pfalciparum', 'Plasmodium', 'falciparum', 'Pfalciparum'),
( 'Pknowlesi', 'Plasmodium', 'knowlesi', 'Pknowlesi');
bp_genbank2gff3.pl -noCDS *.gbk
perl -pi~ -e s'|processed_transcript|mature_transcript|' *.gff
gmod_bulk_load_gff3.pl -organism Pfalciparum -dbname chado_pathogen \
-dbuser gmod -dbport 5432 -dbpass dd -recreate_cache < NC_004314.gbk.gff
gmod_bulk_load_gff3.pl -organism Pknowlesi -dbname chado_pathogen \
-dbuser gmod -dbport 5432 -dbpass dd -recreate_cache < NC_011907.gbk.gff
gmod_bulk_load_gff3.pl -organism Pknowlesi -dbname chado_pathogen \
-dbuser gmod -dbport 5432 -dbpass dd -recreate_cache < NC_011909.gbk.gff
Download Artemis and ACT
cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/pathsoft co artemis
cd artemis
make
Running Artemis
./art -Dchado="localhost:5432/chado_pathogen?gmod" -Dibatis
./art -Dchado="localhost:5432/chado_pathogen?gmod" -Dibatis \
Pfalciparum:NC_004314
etc/gene_builder -Dchado="localhost:5432/chado_pathogen?gmod" -Dibatis -Dshow_log PF10_0003
etc/gene_builder -Dchado="db.genedb.org:5432/snapshot?genedb_ro" -Dibatis -Dshow_log -Dread_only PFA0010c
Configuration Options
chado_servers = \
Plasmodium localhost:5432/chado_pathogen?username \
GeneDB db.genedb.org:5432/snapshot?genedb_ro
product_cv=no
set_obsolete_on_delete=yes
gene
|
|- part_of mRNA
|
|---- part_of exon
|
|---- derives_from polypeptide
|
|---- part_of five_prime_UTR
|
|---- part_of three_prime_UTR
gene
|
|- part_of mRNA
|
|---- part_of exon
|
|---- derives_from polypeptide
chado_infer_CDS_UTR=yes
Artemis Database Manager
Adding Controlled Vocabulary Qualifiers in the Artemis Gene Builder
psql -d chado_pathogen -f etc/chado_extra.sql
psql chado_pathogen
INSERT INTO cv ( name, definition ) VALUES ( 'CC_test', 'test' );
INSERT INTO dbxref
( db_id, accession )
VALUES
( (SELECT db_id FROM db WHERE name = 'CCGEN'), 'test1' );
INSERT INTO cvterm
( cv_id, name, dbxref_id )
VALUES
( (SELECT cv_id FROM cv WHERE name ='CC_test'), 'test1',
(SELECT dbxref_id FROM dbxref WHERE accession='test1') );
Transfer Annotation Tool (TAT)
Logging Information
Running ACT
wget ftp://ftp.sanger.ac.uk/pub/pathogens/workshops/GMOD2009/NC_004314_v_NC_011907_tblastx.gz
wget ftp://ftp.sanger.ac.uk/pub/pathogens/workshops/GMOD2009/NC_004314_v_NC_011909_tblastx.gz
./act -Dchado="localhost:5432/chado_pathogen?gmod" -Dibatis
Writing Out Sequence Files
-h show help
-f [y|n] flatten the gene model, default is y
-i [y|n] ignore obsolete features, default is y
-s space separated list of sequences to read and write out
-o [EMBL|GFF] output format, default is EMBL
-a [y|n] for EMBL submission format change to n, default is y
etc/writedb_entry -Dchado="localhost:5432/chado_pathogen?gmod" NC_004314
Mailing List
References
ACT home page
Artemis Connecting to Chado Databases
User Practical Guide