static public List<MolecularSequence> parse( final File f ) throws IOException { return parse( new FileInputStream( f ) ); }
System.out.println( "STARTING..." ); final List<MolecularSequence> orig = FastaParser .parse( new FileInputStream( "C:\\Users\\zma\\Desktop\\RRMa_domains_ext_20.fasta" ) ); final Msa msa = FastaParser.parseMsa( new FileInputStream( "C:\\Users\\zma\\Desktop\\test3_sorted.fasta" ) ); final Set<MolecularSequence> all_found_seqs = new HashSet<MolecularSequence>();
static public Msa parseMsa( final InputStream is ) throws IOException { return BasicMsa.createInstance( parse( is ) ); }
private static void execute( final File outdir, final File infile ) { final File outfile = new File( outdir.getAbsolutePath().toString() + "/" + infile.getName() ); if ( outfile.exists() ) { System.out.println( outfile + " already exists" ); } else { try { final List<MolecularSequence> seqs = FastaParser.parse( new FileInputStream( infile ) ); final Map<String, Short> names = new HashMap<String, Short>(); int duplicates = 0; for( final MolecularSequence seq : seqs ) { if ( procSeq( infile.toString(), names, seq ) ) { ++duplicates; } } if ( duplicates > 0 ) { SequenceWriter.writeSeqs( seqs, outfile, SEQ_FORMAT.FASTA, 60 ); } } catch ( final IOException e ) { ForesterUtil.fatalError( PRG_NAME, e.getMessage() ); } } }
seqs = FastaParser.parse( new FileInputStream( infile ) );
try { if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) { seqs = FastaParser.parse( new FileInputStream( file ) ); for( final MolecularSequence seq : seqs ) { System.out.println( SequenceWriter.toFasta( seq, 60 ) );
final List<MolecularSequence> too_short = new ArrayList<MolecularSequence>(); final List<MolecularSequence> orig = FastaParser .parse( new FileInputStream( "C:\\Users\\zma\\Desktop\\RRMa_domains_ext_20_2.fasta" ) ); final int initial_number = orig.size(); final List<String> new_seqs = new ArrayList<String>();
private static Map<String, String> readFastaFileIntoMap( final File mapping_infile, final boolean verbose ) { List<MolecularSequence> seqs = null; try { seqs = FastaParser.parse( new FileInputStream( mapping_infile ) );
for( int i = 1; i < cla.getNumberOfNames(); i++ ) { final String fasta_name = cla.getName( i ); final List<MolecularSequence> seqs = FastaParser.parse( new File( fasta_name ) ); for( int s = 0; s < seqs.size(); s++ ) { final MolecularSequence seq = seqs.get( s );
try { if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) { seqs = FastaParser.parse( new FileInputStream( file ) );