o Uݢg@sJdZddlmZddlmZddlZGdddeZGdddejZdS) zEInterface for the pyfasta.Fasta API that uses pyfaidx under the hood.) annotations) NamedTupleNc@s:eZdZUdZded<ded<ded<ded<ded<d S) BedCoordzCoordinates in BED format.strchromintstartendnamestrandN)__name__ __module__ __qualname____doc____annotations__rr]/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/python/common/pyfasta.pyr s  rcs.eZdZdZd d fdd Zdd d ZZS) FastaIndexedaA wrapper around pyfaidx.Fasta that implements a `pyfasta.Fasta` interface. This helps upgrade old code that was dependent on `pyfasta.Fasta`. Any new code should directly use pyfaidx. .. deprecated::4.0 Do not use for new code. Use `pyfaidx` instead. FreturnNonecstj|d|ddS)zCreate a pyfaidx.Fasta object from a fasta file. Note that the header after the first. " " is ignored. And we use 0-based half-open intervals for indexing. F)filenameZone_based_attributes build_indexN)super__init__)selfZ fasta_namer __class__rrr szFastaIndexed.__init__ bed_coordrpyfaidx.SequencecCs<|jdvs Jd|j|j|j|jd|j|jdkdS)z{Get sequence from chrom, [start, end) and reverse complement if strand. (either `+` or `-` or `.`) is `-` )-+.zInvalid strand = r)r rr rc)r Zget_seqrrr )rrrrrget_sequence_region'sz FastaIndexed.get_sequence_region)F)rr)rrrr)r r rrrr$ __classcell__rrrrrsr) r __future__rtypingrpyfaidxrZFastarrrrrs