pbcore.data

pbcore.data

pbcore.data.getBamAndCmpH5()

Get a “matched” (aligned) BAM and cmp.h5 file

pbcore.data.getBasH5_v20()

pbcore.data.getBasH5_v21()

pbcore.data.getBasH5_v23()

pbcore.data.getBasH5s()

pbcore.data.getBaxForBam()

Get the bax file that was mapped to produce the bam

pbcore.data.getBaxH5_v20()

pbcore.data.getBaxH5_v21()

pbcore.data.getBaxH5_v23()

pbcore.data.getBcFofn()

pbcore.data.getBcH5s()

pbcore.data.getBlasrM4()

pbcore.data.getBlasrM5()

pbcore.data.getCCSBAM()

pbcore.data.getCCSH5()

pbcore.data.getCmpH5()

pbcore.data.getCmpH5AndBas()

The returned value is a dictionary containing 2 keys: cmph5 and bash5s. The latter are the bash5s that were used to generate the cmp.h5 file.

pbcore.data.getCmpH5s()

Returns a list of dictionaries containing 2 keys: cmph5 and bash5s. The latter are the bash5s that were used to generate the cmp.h5 file.

pbcore.data.getDosFormattedFasta()

Returns the filename of an example FASTA file with DOS line endings

pbcore.data.getFasta()

Returns the filename of an example FASTA file.

pbcore.data.getFofns()

Returns a list of FOFN files

pbcore.data.getGff3()

Returns the filename of an example GFFv3 file

pbcore.data.getLambdaFasta()

Returns the filename of the FASTA of the lambda phage reference.

pbcore.data.getTinyFasta()

Returns the filename of an example FASTA file.

pbcore.data.getUnalignedBam()

Get the unaligned BAM file, corresponding to the same bax above