Package org.biojava.bio.program.gff
Class GFFTools
java.lang.Object
org.biojava.bio.program.gff.GFFTools
- Since:
- 1.2
- Author:
- Mark Schreiber, Matthew Pocock
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic Sequence
annotateSequence
(Sequence seq, GFFEntrySet ents) Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence.static Sequence
annotateSequence
(Sequence seq, GFFEntrySet ents, boolean checkSeqName) Annotates a sequence with the features from a GFF entry set.static SequenceDB
annotateSequences
(SequenceDB seqs, GFFEntrySet ents) Annotates all sequences in a sequence DB with features from a GFF entry set.static GFFEntrySet
gffFromSeqDB
(SequenceDB seqDB) Creates a GFFEntrySet containing one entry for each feature on each sequence of a SequenceDB.static GFFEntrySet
gffFromSequence
(Sequence seq) Creates a GFFEntrySet containing one entry for each feature on a sequence.static GFFEntrySet
readGFF
(BufferedReader gffIn) Read all GFF entries from a buffered reader.static GFFEntrySet
readGFF
(BufferedReader gffIn, GFFRecordFilter recFilt) Read all GFF entries matching a filter from a buffered reader.static GFFEntrySet
Reads aGFFEntrySet
from a file with no filtering.static GFFEntrySet
readGFF
(File inFile, GFFRecordFilter recFilt) Reads a GFFEntrySet from a file with the specified filter.static GFFEntrySet
Deprecated.use: readGff(File)static GFFEntrySet
readGFF
(String fileName, GFFRecordFilter recFilt) Deprecated.use: readGff(File,GFFRecordFilter)static void
writeGFF
(File outFile, GFFEntrySet ents) Writes a GFFEntrySet to a file.static void
writeGFF
(PrintWriter pw, GFFEntrySet ents) Writes a GFFEntrySet to a PrintWriter.static void
writeGFF
(String fileName, GFFEntrySet ents) Writes a GFFEntrySet to a file.
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Field Details
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NO_SCORE
Flag to indicate that there is no score info. -
NO_FRAME
Flag to indicate that there is no frame info.
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Constructor Details
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GFFTools
public GFFTools()
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Method Details
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readGFF
public static GFFEntrySet readGFF(String fileName) throws FileNotFoundException, ParserException, BioException, IOException Deprecated.use: readGff(File)Reads aGFFEntrySet
from a file with no filtering.- Parameters:
fileName
- the file containing the GFF- Returns:
- a
GFFEntrySet
encapsulating the records read from the file - Throws:
FileNotFoundException
- if file is not foundParserException
- if format is wrongBioException
- if format is wrongIOException
- if file reading error occurs
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readGFF
public static GFFEntrySet readGFF(String fileName, GFFRecordFilter recFilt) throws FileNotFoundException, ParserException, BioException, IOException Deprecated.use: readGff(File,GFFRecordFilter)Reads a GFFEntrySet from a file with the specified filter.- Parameters:
fileName
- the file containing the GFFrecFilt
- the filter to use- Returns:
- a
GFFEntrySet
encapsulating the records read from the file - Throws:
FileNotFoundException
- if file is not foundParserException
- if format is wrongBioException
- if format is wrongIOException
- if file reading error occurs
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readGFF
public static GFFEntrySet readGFF(File inFile) throws FileNotFoundException, ParserException, BioException, IOException Reads aGFFEntrySet
from a file with no filtering.- Parameters:
inFile
- the File containing the GFF- Returns:
- a
GFFEntrySet
encapsulating the records read from the file - Throws:
FileNotFoundException
- if file is not foundParserException
- if format is wrongBioException
- if format is wrongIOException
- if file reading error occurs
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readGFF
public static GFFEntrySet readGFF(File inFile, GFFRecordFilter recFilt) throws FileNotFoundException, ParserException, BioException, IOException Reads a GFFEntrySet from a file with the specified filter.- Parameters:
inFile
- the File containing the GFFrecFilt
- the filter to use- Returns:
- a
GFFEntrySet
encapsulating the records read from the file - Throws:
FileNotFoundException
- if file is not foundParserException
- if format is wrongBioException
- if format is wrongIOException
- if file reading error occurs
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readGFF
public static GFFEntrySet readGFF(BufferedReader gffIn) throws ParserException, BioException, IOException Read all GFF entries from a buffered reader. This will read up untill the end of the reader.- Parameters:
gffIn
- the BufferedReader to read text from- Returns:
- a GFFEntrySet containing all of the GFF that could be read
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readGFF
public static GFFEntrySet readGFF(BufferedReader gffIn, GFFRecordFilter recFilt) throws ParserException, BioException, IOException Read all GFF entries matching a filter from a buffered reader. This will read up untill the end of the reader.- Parameters:
gffIn
- the BufferedReader to read text from- Returns:
- a GFFEntrySet containing all of the GFF that could be read
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writeGFF
Writes a GFFEntrySet to a file.- Parameters:
fileName
- the file to write toents
- the entries to write- Throws:
IOException
- if file writing fails
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writeGFF
Writes a GFFEntrySet to a file.- Parameters:
outFile
- the file to write toents
- the entry set to write- Throws:
IOException
- if writing to the file fails
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writeGFF
Writes a GFFEntrySet to a PrintWriter.- Parameters:
pw
- the PrintWriter to write toents
- the entries to write- Throws:
IOException
- if file writing fails
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annotateSequence
Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence.- Parameters:
seq
- theSequence
to annotate.ents
- the the GFF features to annotate it with.- Returns:
- a reference to a newly annotated sequence.
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annotateSequence
Annotates a sequence with the features from a GFF entry set.- Parameters:
seq
- theSequence
to annotate.ents
- the the GFF features to annotate it with.checkSeqName
- boolean flat, if true only annotate sequence with features that have matching sequence names, otherwise annotate all features- Returns:
- a reference to a newly annotated sequence.
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annotateSequences
public static SequenceDB annotateSequences(SequenceDB seqs, GFFEntrySet ents) throws IllegalIDException, BioException Annotates all sequences in a sequence DB with features from a GFF entry set.- Parameters:
seqs
- the SequenceDB to annotateents
- the GFFEntrySet to annote with- Returns:
- a SequenceDB with all the annotations on
- Throws:
IllegalIDException
BioException
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gffFromSequence
Creates a GFFEntrySet containing one entry for each feature on a sequence.- Parameters:
seq
- the Sequence to create features for- Returns:
- a new GFFEntrySet with gff records for each featre on the sequence
- Throws:
BioException
- if something went wrong GFF-ifying the sequences features
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gffFromSeqDB
Creates a GFFEntrySet containing one entry for each feature on each sequence of a SequenceDB.Note: This converts all features in the whole database to in-memorey GFFRecord instances. This will take up considerable memory for large databases.
- Parameters:
seqDB
- the SequenceDB to create features for- Returns:
- a new GFFEntrySet with gff records for each feature on the database
- Throws:
BioException
- if something went wrong GFF-ifying the sequences features
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