FastaReferenceFile: The FastaReferenceFile class
In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

Description Usage Arguments Fields and Methods Compression Filenames On different FASTA files Author(s) See Also

Package: aroma.seq
Class FastaReferenceFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--SequenceContigsInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FastaReferenceFile

Directly known subclasses:

public abstract static class FastaReferenceFile
extends SequenceContigsInterface

A FastaReferenceFile object represents a FASTA reference file.

1	FastaReferenceFile(...)

...

Arguments passed to GenericDataFile.

Methods:

	`buildBowtie2IndexSet`	-
	`buildBwaIndexSet`	-
	`buildDictionary`	-
	`buildIndex`	-
	`byOrganism`	-
	`getIndexFile`	-
	`getOrganism`	-
	`getSeqChecksums`	-
	`getSeqLengths`	-
	`hasIndex`	-
	`isCompatibleWith`	-

Methods inherited from SequenceContigsInterface:
cleanSeqNames, getSeqGenericSummary, getSeqLengths, getSeqNames, getSeqOrdering, getTotalSeqLength, hasDuplicatedSeqs, hasSeqLengths, isCompatibleWithBySeqLengths, isCompatibleWithBySeqNames, isCompatibleWithBySeqs, nbrOfSeqs

Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, directoryItem, directoryItems, directoryStructure, directoryStructure<-, getDataSetName, getOrganismName, getSampleName, loadCacheFile, loadCacheFileItem, memoizedCall2, saveCacheFile, saveCacheFileItem, getParentName

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, findRspReportTemplate, asThis

Currently, the package only supports non-compressed FASTA files.

Currently, FASTA files with commas in their filenames should be avoided because they are not supported by Bowtie2.

Some FASTA files represent nucleotides as upper-case letters A, C, G, T (and N), whereas others as lower-case letters a, c, g, t (and n). The format of the sequence names differ between FASTA file (even for the same genome/organism), e.g. 'chr1' versus '1'.

Henrik Bengtsson

[1] http://www.wikipedia.org/wiki/FASTA_format

HenrikBengtsson/aroma.seq documentation built on Feb. 15, 2021, 2:21 a.m.