Output example of generate file types R code from pbcommand

out.txt

(pbsmrtpipe_test)21326a76b5b1ca7c27f82fc74fe4ea7b $> ipython -i generate_file_types_r_code.py 
Python 2.7.10 (default, Jul 13 2015, 12:05:58) 
Type "copyright", "credits" or "license" for more information.

IPython 5.0.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: print generate()
pls -> toF("PacBio.ReadFile.PulseFile", "file", "pls", "application/octet-stream")
sa -> toF("PacBio.Index.SaWriterIndex", "file", "sa", "application/octet-stream")
gff -> toF("PacBio.FileTypes.gff", "file", "gff", "text/plain")
rsmoviemetadataxml -> toF("PacBio.FileTypes.rs_movie_metadata", "file", "rs_movie.metadata.xml", "application/xml")
gz -> toF("PacBio.FileTypes.gzip", "file", "gz", "application/x-gzip")
barcodefasta -> toF("PacBio.BarcodeFile.BarcodeFastaFile", "file", "barcode.fasta", "text/plain")
ccsbam -> toF("PacBio.ConsensusReadFile.ConsensusReadBamFile", "file", "ccs.bam", "application/octet-stream")
consensusreadsetxml -> toF("PacBio.DataSet.ConsensusReadSet", "file", "consensusreadset.xml", "application/xml")
barcodesetxml -> toF("PacBio.DataSet.BarcodeSet", "file", "barcodeset.xml", "application/xml")
subreadsetxml -> toF("PacBio.DataSet.SubreadSet", "file", "subreadset.xml", "application/xml")
referencesetxml -> toF("PacBio.DataSet.ReferenceSet", "file", "referenceset.xml", "application/xml")
json -> toF("PacBio.FileTypes.GCHUNK", "gather_chunk", "json", "application/json")
fofn -> toF("PacBio.FileTypes.rgn_fofn", "region", "fofn", "text/plain")
json -> toF("PacBio.FileTypes.JsonReport", "report", "json", "application/json")
alignmentsetxml -> toF("PacBio.DataSet.AlignmentSet", "file", "alignmentset.xml", "application/xml")
cfg -> toF("PacBio.FileTypes.cfg", "config", "cfg", "text/plain")
pbreferencefasta -> toF("PacBio.ReferenceFile.ReferenceFastaFile", "file", "pbreference.fasta", "text/plain")
adaptersfasta -> toF("PacBio.SubreadFile.AdapterFastaFile", "file", "adapters.fasta", "text/plain")
vcf -> toF("PacBio.FileTypes.vcf", "file", "vcf", "text/plain")
json -> toF("PacBio.FileTypes.SCHUNK", "scatter_chunk", "json", "application/json")
fasta -> toF("PacBio.FileTypes.Fasta", "file", "fasta", "text/plain")
gmapreferencesetxml -> toF("PacBio.DataSet.GmapReferenceSet", "file", "gmapreferenceset.xml", "application/xml")
json -> toF("PacBio.FileTypes.json", "file", "json", "application/json")
hdfsubreadsetxml -> toF("PacBio.DataSet.HdfSubreadSet", "file", "hdfsubreadset.xml", "application/xml")
ccsalignbam -> toF("PacBio.AlignmentFile.ConsensusAlignmentBamFile", "file", "ccs_align.bam", "application/octet-stream")
cmph5 -> toF("PacBio.FileTypes.alignment_cmp_h5", "alignments", "cmp.h5", "application/octet-stream")
fastq -> toF("PacBio.FileTypes.Fastq", "file", "fastq", "text/plain")
csv -> toF("PacBio.FileTypes.csv", "file", "csv", "text/csv")
xml -> toF("PacBio.FileTypes.xml", "file", "xml", "application/xml")
zip -> toF("PacBio.FileTypes.zip", "file", "zip", "application/zip")
m4 -> toF("PacBio.FileTypes.blasr_file", "blasr", "m4", "text/plain")
txt -> toF("PacBio.FileTypes.txt", "file", "txt", "text/plain")
subreadbam -> toF("PacBio.SubreadFile.SubreadBamFile", "file", "subread.bam", "application/octet-stream")
samindex -> toF("PacBio.Index.SamIndex", "file", "sam.index", "application/octet-stream")
bambai -> toF("PacBio.Index.BamIndex", "file", "bam.bai", "application/octet-stream")
pbi -> toF("PacBio.Index.PacBioIndex", "file", "pbi", "application/octet-stream")
json -> toF("PacBio.FileTypes.CHUNK", "chunk", "json", "application/json")
bw -> toF("PacBio.FileTypes.bigwig", "annotations", "bw", "application/octet-stream")
fofn -> toF("PacBio.FileTypes.movie_fofn", "movie", "fofn", "text/plain")
conditions-reseqjson -> toF("PacBio.FileTypes.COND_RESEQ", "file", "conditions-reseq.json", "application/json")
consensusalignmentsetxml -> toF("PacBio.DataSet.ConsensusAlignmentSet", "file", "consensusalignmentset.xml", "application/xml")
contigfasta -> toF("PacBio.ContigFile.ContigFastaFile", "file", "contig.fasta", "text/plain")
bed -> toF("PacBio.FileTypes.bed", "file", "bed", "text/plain")
fofn -> toF("PacBio.FileTypes.generic_fofn", "generic", "fofn", "text/plain")
baz -> toF("PacBio.ReadFile.BazFile", "file", "baz", "application/octet-stream")
trc -> toF("PacBio.ReadFile.TraceFile", "file", "trc", "application/octet-stream")
bambai -> toF("PacBio.FileTypes.bam_bai", "alignments", "bam.bai", "application/octet-stream")
stsxml -> toF("PacBio.SubreadFile.ChipStatsFile", "file", "sts.xml", "application/xml")
baxh5 -> toF("PacBio.SubreadFile.BaxFile", "file", "bax.h5", "application/octet-stream")
bam -> toF("PacBio.FileTypes.bam", "alignments", "bam", "application/octet-stream")
xml -> toF("PacBio.FileTypes.reference_info_xml", "reference.info.xml", "xml", "application/xml")
log -> toF("PacBio.FileTypes.log", "file", "log", "text/plain")
sam -> toF("PacBio.FileTypes.sam", "alignments", "sam", "application/octet-stream")
fastaindex -> toF("PacBio.Index.Indexer", "file", "fasta.index", "text/plain")
pickle -> toF("PacBio.FileTypes.pickle", "file", "pickle", "application/python-pickle")
controlfasta -> toF("PacBio.SubreadFile.ControlFastaFile", "file", "control.fasta", "text/plain")
alignmentbam -> toF("PacBio.AlignmentFile.AlignmentBamFile", "file", "alignment.bam", "application/octet-stream")
contigsetxml -> toF("PacBio.DataSet.ContigSet", "file", "contigset.xml", "application/xml")
h5 -> toF("PacBio.FileTypes.h5", "file", "h5", "application/octet-stream")
fastacontigindex -> toF("PacBio.Index.FastaContigIndex", "file", "fasta.contig.index", "text/plain")
xml -> toF("PacBio.FileTypes.input_xml", "input", "xml", "application/xml")

return c(PLS = pls
,SA = sa
,GFF = gff
,RSMOVIEMETADATAXML = rsmoviemetadataxml
,GZ = gz
,BARCODEFASTA = barcodefasta
,CCSBAM = ccsbam
,CONSENSUSREADSETXML = consensusreadsetxml
,BARCODESETXML = barcodesetxml
,SUBREADSETXML = subreadsetxml
,REFERENCESETXML = referencesetxml
,JSON = json
,FOFN = fofn
,JSON = json
,ALIGNMENTSETXML = alignmentsetxml
,CFG = cfg
,PBREFERENCEFASTA = pbreferencefasta
,ADAPTERSFASTA = adaptersfasta
,VCF = vcf
,JSON = json
,FASTA = fasta
,GMAPREFERENCESETXML = gmapreferencesetxml
,JSON = json
,HDFSUBREADSETXML = hdfsubreadsetxml
,CCSALIGNBAM = ccsalignbam
,CMPH5 = cmph5
,FASTQ = fastq
,CSV = csv
,XML = xml
,ZIP = zip
,M4 = m4
,TXT = txt
,SUBREADBAM = subreadbam
,SAMINDEX = samindex
,BAMBAI = bambai
,PBI = pbi
,JSON = json
,BW = bw
,FOFN = fofn
,CONDITIONS-RESEQJSON = conditions-reseqjson
,CONSENSUSALIGNMENTSETXML = consensusalignmentsetxml
,CONTIGFASTA = contigfasta
,BED = bed
,FOFN = fofn
,BAZ = baz
,TRC = trc
,BAMBAI = bambai
,STSXML = stsxml
,BAXH5 = baxh5
,BAM = bam
,XML = xml
,LOG = log
,SAM = sam
,FASTAINDEX = fastaindex
,PICKLE = pickle
,CONTROLFASTA = controlfasta
,ALIGNMENTBAM = alignmentbam
,CONTIGSETXML = contigsetxml
,H5 = h5
,FASTACONTIGINDEX = fastacontigindex
,XML = xml)