Class FastaFileIterator

java.lang.Object
org.snpeff.fileIterator.FileIterator<String>
org.snpeff.fileIterator.FastaFileIterator
All Implemented Interfaces:
Iterable<String>, Iterator<String>
public class FastaFileIterator extends FileIterator<String>
Opens a fasta file and iterates over all fasta sequences in the file
Author:
pcingola

  • Field Details

    • TRANSCRIPT_ID_SEPARATORS_REGEX

      public static String TRANSCRIPT_ID_SEPARATORS_REGEX

    • TRANSCRIPT_ID_SEPARATORS

      public static char[] TRANSCRIPT_ID_SEPARATORS

  • Constructor Details

    • FastaFileIterator

      public FastaFileIterator(String fastaFileName)

  • Method Details

    • fastaHeader2Ids

      public List<String> fastaHeader2Ids()
      Try to parse IDs from a fasta header

    • getHeader

      public String getHeader()
      Current sequence header

    • getName

      public String getName()
      Sequence name (first 'word') It extracts the characters after the leading '>' and before the first space, then removes leading 'chr', 'chr:', etc.

    • getIdFromFastaHeader

      public String 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

      protected String readNext()
      Read a sequence from the file
      Specified by:
      readNext in class FileIterator<String>