Description Usage Arguments Fields and Methods Compression Filenames On different FASTA files Author(s) See Also
Package: aroma.seq
Class FastaReferenceFile
Object
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FullNameInterface
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GenericDataFile
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SequenceContigsInterface
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FastaReferenceFile
Directly known subclasses:
public abstract static class FastaReferenceFile
extends SequenceContigsInterface
A FastaReferenceFile object represents a FASTA reference file.
1 |
... |
Arguments passed to |
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
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