pbcommand Models

Pacbio Registered FileTypes

class pbcommand.models.FileTypes[source]

Bases: object

Registry of all PacBio Files types

This needs to be cleaned up and solidified. The old pre-SA3 file types need to be deleted.

ALIGNMENT_CMP_H5 = <FileType id=PacBio.FileTypes.alignment_cmp_h5 name=alignments >
static ALL()[source]

Returns a Dict of id->FileType

:rtype dict[str, FileType]

static ALL_DATASET_TYPES()[source]
BAM = <FileType id=PacBio.FileTypes.bam name=alignments >
BAMBAI = <FileType id=PacBio.FileTypes.bam_bai name=alignments >
BAM_ALN = <FileType id=PacBio.AlignmentFile.AlignmentBamFile name=file >
BAM_CCS = <FileType id=PacBio.ConsensusReadFile.ConsensusReadBamFile name=file >
BAM_CCS_ALN = <FileType id=PacBio.AlignmentFile.ConsensusAlignmentBamFile name=file >
BAM_SUB = <FileType id=PacBio.SubreadFile.SubreadBamFile name=file >
BAM_TRANSCRIPT = <FileType id=PacBio.TranscriptFile.TranscriptBamFile name=file >
BAM_TRANSCRIPT_ALN = <FileType id=PacBio.AlignmentFile.TranscriptAlignmentBamFile name=file >
BAX = <FileType id=PacBio.SubreadFile.BaxFile name=file >
BAZ = <FileType id=PacBio.ReadFile.BazFile name=file >
BED = <FileType id=PacBio.FileTypes.bed name=file >
BIGWIG = <FileType id=PacBio.FileTypes.bigwig name=annotations >
BLASR_M4 = <FileType id=PacBio.FileTypes.blasr_file name=blasr >
CFG = <FileType id=PacBio.FileTypes.cfg name=config >
CHUNK = <FileType id=PacBio.FileTypes.CHUNK name=chunk >
COND_RESEQ = <FileType id=PacBio.FileTypes.COND_RESEQ name=file >
CONTIG_FA = <FileType id=PacBio.ContigFile.ContigFastaFile name=file >
CSV = <FileType id=PacBio.FileTypes.csv name=file >
DATASTORE = <FileType id=PacBio.FileTypes.Datastore name=file >
DS_ALIGN = <DataSetFileType id=PacBio.DataSet.AlignmentSet name=file >
DS_ALIGN_CCS = <DataSetFileType id=PacBio.DataSet.ConsensusAlignmentSet name=file >
DS_ALIGN_TRANSCRIPT = <DataSetFileType id=PacBio.DataSet.TranscriptAlignmentSet name=file >
DS_BARCODE = <DataSetFileType id=PacBio.DataSet.BarcodeSet name=file >
DS_CCS = <DataSetFileType id=PacBio.DataSet.ConsensusReadSet name=file >
DS_CONTIG = <DataSetFileType id=PacBio.DataSet.ContigSet name=file >
DS_GMAP_REF = <DataSetFileType id=PacBio.DataSet.GmapReferenceSet name=file >
DS_REF = <DataSetFileType id=PacBio.DataSet.ReferenceSet name=file >
DS_SUBREADS = <DataSetFileType id=PacBio.DataSet.SubreadSet name=file >
DS_SUBREADS_H5 = <DataSetFileType id=PacBio.DataSet.HdfSubreadSet name=file >
DS_TRANSCRIPT = <DataSetFileType id=PacBio.DataSet.TranscriptSet name=file >
FASTA = <FileType id=PacBio.FileTypes.Fasta name=file >
FASTA_ADAPTER = <FileType id=PacBio.SubreadFile.AdapterFastaFile name=file >
FASTA_BC = <FileType id=PacBio.BarcodeFile.BarcodeFastaFile name=file >
FASTA_CONTROL = <FileType id=PacBio.SubreadFile.ControlFastaFile name=file >
FASTA_REF = <FileType id=PacBio.ReferenceFile.ReferenceFastaFile name=file >
FASTQ = <FileType id=PacBio.FileTypes.Fastq name=file >
FOFN = <FileType id=PacBio.FileTypes.generic_fofn name=generic >
GCHUNK = <FileType id=PacBio.FileTypes.GCHUNK name=gather_chunk >
GFF = <FileType id=PacBio.FileTypes.gff name=file >
GZIP = <FileType id=PacBio.FileTypes.gzip name=file >
H5 = <FileType id=PacBio.FileTypes.h5 name=file >
HTML = <FileType id=PacBio.FileTypes.html name=file >
INPUT_XML = <FileType id=PacBio.FileTypes.input_xml name=input >
I_BAI = <FileType id=PacBio.Index.BamIndex name=file >
I_FCI = <FileType id=PacBio.Index.FastaContigIndex name=file >
I_INDEXER = <FileType id=PacBio.Index.Indexer name=file >
I_NGMLR_ENC = <FileType id=PacBio.Index.NgmlrRefEncoded name=file >
I_NGMLR_TAB = <FileType id=PacBio.Index.NgmlrRefTable name=file >
I_PBI = <FileType id=PacBio.Index.PacBioIndex name=file >
I_SAM = <FileType id=PacBio.Index.SamIndex name=file >
I_SAW = <FileType id=PacBio.Index.SaWriterIndex name=file >
JSON = <FileType id=PacBio.FileTypes.json name=file >
LOG = <FileType id=PacBio.FileTypes.log name=file >
MOVIE_FOFN = <FileType id=PacBio.FileTypes.movie_fofn name=movie >
PICKLE = <FileType id=PacBio.FileTypes.pickle name=file >
PLS = <FileType id=PacBio.ReadFile.PulseFile name=file >
REF_ENTRY_XML = <FileType id=PacBio.FileTypes.reference_info_xml name=reference.info.xml >
REPORT = <FileType id=PacBio.FileTypes.JsonReport name=report >
RGN_FOFN = <FileType id=PacBio.FileTypes.rgn_fofn name=region >
RS_MOVIE_XML = <FileType id=PacBio.FileTypes.rs_movie_metadata name=file >
SAM = <FileType id=PacBio.FileTypes.sam name=alignments >
SCHUNK = <FileType id=PacBio.FileTypes.SCHUNK name=scatter_chunk >
STS_H5 = <FileType id=PacBio.SubreadFile.ChipStatsH5File name=file >
STS_XML = <FileType id=PacBio.SubreadFile.ChipStatsFile name=file >
SVG = <FileType id=PacBio.FileTypes.svg name=file >
TGZ = <FileType id=PacBio.FileTypes.tgz name=file >
TRC = <FileType id=PacBio.ReadFile.TraceFile name=file >
TXT = <FileType id=PacBio.FileTypes.txt name=file >
VCF = <FileType id=PacBio.FileTypes.vcf name=file >
XML = <FileType id=PacBio.FileTypes.xml name=file >
ZIP = <FileType id=PacBio.FileTypes.zip name=file >
static is_valid_id(file_type_id)[source]