FastaFileIterator (SnpEff 5.1 API)

java.lang.Object
- org.snpeff.fileIterator.FileIterator<java.lang.String>
- - org.snpeff.fileIterator.FastaFileIterator

All Implemented Interfaces:

java.lang.Iterable<java.lang.String>, java.util.Iterator<java.lang.String>
```
public class FastaFileIterator
extends FileIterator<java.lang.String>
```
Opens a fasta file and iterates over all fasta sequences in the file

Author:

pcingola

Field Summary

Fields
Modifier and Type Field Description

static char[] TRANSCRIPT_ID_SEPARATORS

static java.lang.String TRANSCRIPT_ID_SEPARATORS_REGEX
- Fields inherited from class org.snpeff.fileIterator.FileIterator
  autoClose, countNewLineChars, debug, fileName, fileSize, line, lineNum, next, nextLine, reader, verbose

Constructor Summary

Constructors
Constructor Description

FastaFileIterator(java.lang.String fastaFileName)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`java.util.List<java.lang.String>`	`fastaHeader2Ids()`	Try to parse IDs from a fasta header
`java.lang.String`	`getHeader()`	Current sequence header
`java.lang.String`	`getName()`	Sequence name (first 'word') It extracts the characters after the leading '>' and before the first space, then removes leading 'chr', 'chr:', etc.
`java.lang.String`	`getTranscriptId()`	Get transcript name from FASTA header (ENSEMBL protein files) Format example: '>ENSP00000356130 pep:known chromosome:GRCh37:1:205111633:205180694:-1 gene:ENSG00000133059 transcript:ENST00000367162'
`protected java.lang.String`	`readNext()`	Read a sequence from the file

Methods 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

- Field Detail
  - TRANSCRIPT_ID_SEPARATORS_REGEX
```
public static java.lang.String TRANSCRIPT_ID_SEPARATORS_REGEX
```
  - TRANSCRIPT_ID_SEPARATORS
```
public static char[] TRANSCRIPT_ID_SEPARATORS
```
- Constructor Detail
  - FastaFileIterator
```
public FastaFileIterator(java.lang.String fastaFileName)
```
- Method Detail
  - fastaHeader2Ids
```
public java.util.List<java.lang.String> fastaHeader2Ids()
```
    Try to parse IDs from a fasta header
  - getHeader
```
public java.lang.String getHeader()
```
    Current sequence header
  - getName
```
public java.lang.String getName()
```
    Sequence name (first 'word') It extracts the characters after the leading '>' and before the first space, then removes leading 'chr', 'chr:', etc.
  - getTranscriptId
```
public java.lang.String getTranscriptId()
```
    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
```
protected java.lang.String readNext()
```
    Read a sequence from the file
    
    Specified by:
    
    readNext in class FileIterator<java.lang.String>