a VA(f@s\ddlmZmZmZmZmZddlmZGdddeZ Gddde Z Gddde Z d S) )CallableListTupleIterableUnion)_pysam_dispatchc@s eZdZdZddZddZdS) SamtoolsErrorzJexception raised in case of an error incurred in the samtools library.cCs ||_dSN)value)selfr r *lib/python3.9/site-packages/pysam/utils.py__init__szSamtoolsError.__init__cCs t|jSr )reprr r r r r __str__szSamtoolsError.__str__N)__name__ __module__ __qualname____doc__rrr r r r r src @seZdZdZdZdZdZeeee ee e ee efge ee efffdddZ ee ee efdddZd d Zd d ZdS) PysamDispatcheraThe dispatcher emulates the samtools/bctools command line. Captures stdout and stderr. Raises a :class:`pysam.SamtoolsError` exception in case samtools exits with an error code other than 0. Some command line options are associated with parsers. For example, the samtools command "pileup -c" creates a tab-separated table on standard output. In order to associate parsers with options, an optional list of parsers can be supplied. The list will be processed in order checking for the presence of each option. If no parser is given or no appropriate parser is found, the stdout output of samtools/bcftools commands will be returned. N) collectiondispatchparserscCs||_||_||_g|_dSr )rrrstderr)r rrrr r r r/szPysamDispatcher.__init__)argsreturnc Ost|j|j||dd|ddd\}}}|ddrL|}|rL|}|rftd|j|||f||_|d s|r|jr|jD]*\}}|D]}||vrqq||Sq|S) a execute a samtools command. Keyword arguments: catch_stdout -- redirect stdout from the samtools command and return as variable (default True) save_stdout -- redirect stdout to a filename. raw -- ignore any parsers associated with this samtools command. split_lines -- return stdout (if catch_stdout is True and stderr as a list of strings. catch_stdoutT save_stdoutN)rrZ split_linesFz/%s returned with error %i: stdout=%s, stderr=%sraw)rrrget splitlinesrrr) r rkwargsretvalrstdoutZoptionsparserZoptionr r r __call__:s:    zPysamDispatcher.__call__cCs|jSr )rrr r r get_messageshszPysamDispatcher.get_messagescCs*t|j|jddd\}}}|r"|S|SdS)z6return the samtools usage information for this commandT)Zis_usagerN)rrr)r r#rr$r r r usageks zPysamDispatcher.usage)rrrrrrrstrrrrrrrr&r'r(r r r r rs0 .rc@seZdZdZdS) unquoted_strzTag a value as an unquoted string. Meta-information in the VCF header takes the form of key=value pairs. By default, pysam will enclose the value in quotation marks. Tagging that value with unquoted_str will prevent this quoting.N)rrrrr r r r r*ysr*N)typingrrrrrZpysam.libcutilsr Exceptionrobjectrr)r*r r r r s  b