DUf ddlZddlmZmZmZddlZgdZejdZ gdZ ejdd de Dzej Z d eeeefd efd Zd ed efd Zd ed efdZd ed eeeeffdZd ed eeeeffdZ dddd eeefdeeeejfded eeeeffdZdS)N)OptionalTupleUnion) parse_regionparse_region_stringis_complete_ucsc_stringto_ucsc_stringz ([0-9,.]+)))HYPHEN-)COORDz[0-9,]+(\.[0-9]*)?(?:[a-z]+)?)OTHERz.+z\s*z|\s*c#.K|]\}}d|d|dVdS)z(?P<>)N).0nametokens T/var/www/html/software/conda/lib/python3.11/site-packages/bioframe/core/stringops.py rs:VVkdE1$11111VVVVVVgrangereturncdj|S)z Convert a grange to a UCSC string. Parameters ---------- grange : tuple or other iterable chrom, start, end Returns ------- str UCSC-style genomic range string, '{chrom}:{start}-{end}' z{}:{}-{})format)rs rr r s : f %%rscbt|tsdSt|\}}}|dSdS)z Returns True if a string can be parsed into a completely informative (chrom, start, end) format. Parameters ---------- s : str Returns ------- bool True if able to be parsed and ``end`` is known. FNT) isinstancestrr)r_ends rrr,s= a  u#A&&IAq# {u 4rct|dd\}}}t|st |St |}|}|dvr|dz}n'|dvr|dz}n|dvr|dz}ntd |d t |S) N,)KKBi)MMBi@B)GGBiʚ;zUnknown unit '') NUMERIC_REGEXsplitreplacelenintfloatupperstrip ValueError)rr valueunits r_parse_humanized_intr7Cs"((3););<._tokenizeksT ))!,, * *E?D D))) ) ) ) ) * *rcft|d\}}|dkrtd|d|t|}t|d\}}|dkrtd|d|t|d\}}|d}n+|dkrt|}ntd|d|||fS)N)NNr z&Expected COORD; got unexpected token: z: r z'Expected HYPHEN; got unexpected token: )nextr4r7) token_streamrrstartr!s r _parse_rangez)parse_region_string.._parse_rangeps<66 e 7??UdUUeUUVV V$U++<66 e 8  VtVVuVVWW W<66 e <CC W__&u--CCUdUUeUUVV Vczr:rzChromosome name cannot be emptyN)r-r3r/r4)rr@rEpartschromrDr!s rrrXs&*** ( GGCLLE !HNN  E u::<:;;; 5zzA~~tT""iia1122JE3 % rct|dkrtd|dd\}}}t|}|t|n|}|t|n|}|||fS)a Coerce a genomic range record into a triple. Parameters ---------- grange : str or tuple * A triple (chrom, start, end), where ``start`` or ``end`` may be ``None``. * A quadruple or higher-order tuple, e.g. (chrom, start, end, name). ``name`` and other fields will be ignored. Returns ------- tuple A well-formed genomic range triple (str, int, int). z-Length of a range record should be at least 3N)r/r4rr0)rrJrDr!s r_parse_region_recordrMsu" 6{{QHIIIrr E5# JJE+CJJJEo#c(((3C % rT) check_bounds chromsizesrNcjt|trt|\}}}nt|\}}}d}|. ||}n #t$rt d|wxYw||}|d}|||krt d|r$|dks|||krt d|d|d|||fS)a Coerce a genomic range string or sequence type into a triple. Parameters ---------- grange : str or tuple * A UCSC-style genomic range string, e.g. "chr5:10,100,000-30,000,000". * A triple (chrom, start, end), where ``start`` or ``end`` may be ``None``. * A quadruple or higher-order tuple, e.g. (chrom, start, end, name). ``name`` and other fields will be ignored. chromsizes : dict or Series, optional Lookup table of sequence lengths for bounds checking and for filling in a missing end coordinate. check_bounds : bool, optional [default: True] If True, check that the genomic range is within the bounds of the sequence. Returns ------- tuple A well-formed genomic range triple (str, int, int). Notes ----- Genomic ranges are interpreted as half-open intervals (0-based starts, 1-based ends) along the length coordinate of a sequence. Sequence names may contain any character except for whitespace and colon. The start coordinate should be 0 or greater and the end coordinate should be less than or equal to the length of the sequence, if the latter is known. These are enforced when ``check_bounds`` is ``True``. If the start coordinate is missing, it is assumed to be 0. If the end coordinate is missing and chromsizes are provided, it is replaced with the length of the sequence. The end coordinate **must** be greater than or equal to the start. The start and end coordinates may be suffixed with k(b), M(b), or G(b) multipliers, case-insentive. e.g. "chr1:1K-2M" is equivalent to "chr1:1000-2000000". NzUnknown sequence label: rzEnd cannot be less than startzGenomic range out of bounds: [z, r)rrrrMKeyErrorr4)rrOrNrJrDr!clens rrrsh&#9/77ucc088uc D Ae$DD A A A???@@ @ A ;C } C%KK8999Kt'7C$JJI%II3IIIJJJ % s A A(r:)retypingrrrpandaspd__all__compiler,RANGE_TOKEN_SPECjoin IGNORECASEr;rr0r boolrr7rtuplerMdictSeriesrrrrr`s ))))))))))    <((  bj W\\VVEUVVV V VVM &5c3/&C&&&&"st.CC*7375c3#77777t5c3+?848M MMM #u* MtRY/0M M  3S= MMMMMMr