Package ubic.gemma.core.analysis.service

Interface ArrayDesignAnnotationService

All Known Implementing Classes:

ArrayDesignAnnotationServiceImpl

public interface ArrayDesignAnnotationService

Methods to generate annotations for array designs, based on information already in the database. This can be used to generate annotation files used for ermineJ, for example. The file format:

• The file is tab-delimited text. Comma-delimited files or Excel spreadsheets (for example) are not supported.
• There is a one-line header included in the file for readability.
• The first column contains the probe identifier
• The second column contains a gene symbol(s). Clusters are delimited by '|' and genes within clusters are delimited by ','
• The third column contains the gene names (or description). Clusters are delimited by '|' and names within clusters are delimited by '$'
• The fourth column contains a delimited list of GO identifiers. These include the "GO:" prefix. Thus they read "GO:00494494" and not "494494". Delimited by '|'.

Note that for backwards compatibility, GO terms are not segregated by gene cluster.

Author:

paul

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static enum	ArrayDesignAnnotationService.OutputType

Field Summary

Fields

Modifier and Type	Field	Description
static final String	ANNOTATION_FILE_SUFFIX
static final String	BIO_PROCESS_FILE_SUFFIX
static final String	NO_PARENTS_FILE_SUFFIX
static final String	STANDARD_FILE_SUFFIX	String included in file names for standard (default) annotation files.

Method Summary

Modifier and Type	Method	Description
void	create(ArrayDesign inputAd, Boolean useGO, boolean deleteOtherFiles)	Create (or update) all the annotation files for the given platform.
void	deleteExistingFiles(ArrayDesign arrayDesign)
int	generateAnnotationFile(Writer writer, Collection<Gene> genes, Boolean useGO)	Generate an annotation for a list of genes, instead of probes.
Path	getAnnotDataDir()	Obtain the directory where platform annotations are located.
Map<CompositeSequence,String[]>	readAnnotationFile(ArrayDesign arrayDesign)	This tries to read one of the annotation files (noparents, bioprocess or regular) to get the gene information - GO annotations are not part of the result.

Field Details

ANNOTATION_FILE_SUFFIX

static final String ANNOTATION_FILE_SUFFIX

See Also:

• Constant Field Values

BIO_PROCESS_FILE_SUFFIX

static final String BIO_PROCESS_FILE_SUFFIX

See Also:

• Constant Field Values

NO_PARENTS_FILE_SUFFIX

static final String NO_PARENTS_FILE_SUFFIX

See Also:

• Constant Field Values

STANDARD_FILE_SUFFIX

static final String STANDARD_FILE_SUFFIX

String included in file names for standard (default) annotation files. These include GO terms and all parents.

See Also:

• Constant Field Values

Method Details

getAnnotDataDir

Path getAnnotDataDir()

Obtain the directory where platform annotations are located.

deleteExistingFiles

void deleteExistingFiles(ArrayDesign arrayDesign)

readAnnotationFile

Map<CompositeSequence,String[]> readAnnotationFile(ArrayDesign arrayDesign)
                                            throws IOException

This tries to read one of the annotation files (noparents, bioprocess or regular) to get the gene information - GO annotations are not part of the result.

Parameters:

arrayDesign - array design

Returns:

Map of composite sequence ids to an array of delimited strings: [probe name,genes symbol, gene Name, gemma gene id, ncbi id] for a given probe id. format of string is geneSymbol then geneNames same as found in annotation file.

Throws:

IOException

create

void create(ArrayDesign inputAd,
 Boolean useGO,
 boolean deleteOtherFiles)
     throws IOException

Create (or update) all the annotation files for the given platform. Side effect: any expression experiment data files that use this platform will be deleted. Format details: There is a one-line header. The columns are:

1. Probe name
2. Gene symbol. Genes located at different genome locations are delimited by "|"; multiple genes at the same location are delimited by ",". Both can happen simultaneously.
3. Gene name, delimited as for the symbol except '$' is used instead of ','.
4. GO terms, delimited by '|'; multiple genes are not handled specially (for compatibility with ermineJ) -- unless useGO is false
5. Gemma's gene ids, delimited by '|'
6. NCBI gene ids, delimited by '|'
7. Ensembl gene ids, delimited by '|'

Parameters:

inputAd - platform to process

useGO - if true, GO terms will be included

deleteOtherFiles - if true, other files conaining the annotations for this platform will be deleted, such as DEA results and data flat files.

Throws:

IOException

generateAnnotationFile

int generateAnnotationFile(Writer writer,
 Collection<Gene> genes,
 Boolean useGO)

Generate an annotation for a list of genes, instead of probes. The second column will contain the NCBI id, if available. Will generate the 'short' version.

Parameters:

writer - the writer

genes - genes

useGO - if true, GO terms will be included

Returns:

code