Package org.snpeff.fileIterator
Class FastaFileIterator
Opens a fasta file and iterates over all fasta sequences in the file
- Author:
- pcingola
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Field Summary
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionTry to parse IDs from a fasta headerCurrent sequence headerGet transcript name from FASTA header (ENSEMBL protein files) Format example: '>ENSP00000356130 pep:known chromosome:GRCh37:1:205111633:205180694:-1 gene:ENSG00000133059 transcript:ENST00000367162'getName()
Sequence name (first 'word') It extracts the characters after the leading '>' and before the first space, then removes leading 'chr', 'chr:', etc.protected String
readNext()
Read a sequence from the fileMethods inherited from class org.snpeff.fileIterator.FileIterator
close, countNewLineChars, getFilePointer, getLine, getLineNum, guessNewLineChars, hasNext, hasSeek, init, isDebug, iterator, load, next, readLine, ready, remove, seek, setAutoClose, setDebug, setVerbose, toString
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
Methods inherited from interface java.util.Iterator
forEachRemaining
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Field Details
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TRANSCRIPT_ID_SEPARATORS_REGEX
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TRANSCRIPT_ID_SEPARATORS
public static char[] TRANSCRIPT_ID_SEPARATORS
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Constructor Details
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FastaFileIterator
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Method Details
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fastaHeader2Ids
Try to parse IDs from a fasta header -
getHeader
Current sequence header -
getName
Sequence name (first 'word') It extracts the characters after the leading '>' and before the first space, then removes leading 'chr', 'chr:', etc. -
getIdFromFastaHeader
Get transcript name from FASTA header (ENSEMBL protein files) Format example: '>ENSP00000356130 pep:known chromosome:GRCh37:1:205111633:205180694:-1 gene:ENSG00000133059 transcript:ENST00000367162' -
readNext
Read a sequence from the file- Specified by:
readNext
in classFileIterator<String>
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