ó ¤>dc@sldZddlZddlmZddlmZddlmZddl m Z defd„ƒYZ dS( s8 Helper class for working with alignment type analyses. iÿÿÿÿN(tBaseTool(t Fast5File(tSegmentationTools(t Fast5ReadtAlignmentToolscBsSeZdZddddd„Zd„Zd„Zd„Zdd„Zd„Z RS( s= Provides helper methods specific to alignment analyses. trcCs<t|tƒr$||_t|_n9t|tƒrQt||ƒ|_t|_n tdƒ‚|dkr™|jj dƒ}|dkr™tdƒ‚q™n||_ |jj |ƒ}|dkr|dkrÕi}n|jj d|||ƒ|jj |ƒ}nd|kr8|dd kr8|jƒtdƒ‚ndS( s6 Create a new alignment tools object. :param source: Either an open Fast5File object, or a filename of a fast5 file. :param mode: The open mode (r or r+). Only if a filename is used for the source argument. :param group_name: The specific alignment analysis instance you are interested in. :param meta: Metadata for a new alignment analysis. :param config: Configuration data for a new alignment analysis. To create a new alignment analysis, provide a group name that does not already exist, and an optional dictionary with the metadata. The following fields are recommended, as a minimum: * name - The name of the basecall software used. * time_stamp - The time at which the analysis was performed. If the group name already exists, the "meta" parameter is ignored. If the specified group has a "component" attribute, and its value is not "alignment", an exception will be thrown. s(Unrecognized type for argument "source".t Alignments*No Alignment analysis group found in file.t alignmentt componenttcalibration_strands6Analysis does not appear to be an alignment component.N(RR (t isinstanceRthandletFalsetclose_handle_when_donetstrRtTruet ExceptiontNonetget_latest_analysist group_nametget_analysis_attributest add_analysistclose(tselftsourcetmodeRtmetatconfigtattrs((sO/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/analysis_tools/alignment.pyt__init__s.             cCs»|jj|jƒ}iidd6d6idd6d6idd6d6}d|krk|j|dƒ|d Get the alignment SAM and Fasta, if present. :param section: Can be 'template', 'complement', or '2d'. :return: A tuple containing the SAM and the section of the reference aligned to (both as strings). Returns None if no alignment is present for that section. s {}/Aligned_{}tSAMtFastas iN(tformatRR tget_analysis_datasetRtsplit(Rtsectiontsubgrouptsamtfastatsequence((sO/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/analysis_tools/alignment.pytget_alignment_datagscCsÎdj|ƒ}||jjdj|jƒkrJ|jj|j|ƒntj|dtƒ}|jjdj|j|ƒd|ƒtjdj||ƒdtƒ}|jjdj|j|ƒd|ƒdS( s1 Add the SAM and Fasta alignment data for a section. :param section: Can be 'template', 'complement', or '2d'. :param sam: A string containing the SAM contents. :param sequence: A string containing the section of the reference the basecall aligned to. s Aligned_{}s Analyses/{}tdtypes{}/{}R*s>{} {} R+N(R,R Rtadd_analysis_subgrouptnptarrayRtadd_analysis_dataset(RR/R1R3R0tsam_arrt fasta_arr((sO/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/analysis_tools/alignment.pytadd_alignment_dataws"%!cCsmd}|r|j|ƒ}n|jƒ|}|ddkrBdS|d}|d|d}|d}|d|d}|d} |jjƒd } |jj|jƒ} | d k rÐt| ƒjd ƒ} nd } d} | d k r7t |jd | ƒ5}|jƒ}|d k r.|d j |ƒ} nWd QXn| dkrGdS| |t | ƒ}| ||}|S(sÙ Calculate speed using alignment information. :param section: The section (template or complement) we're calculating speed for. :param alignment_results: Optional dictionary of the alignment summary, so that speed can be calculated without having to write the summary out to the fast5 file first. :return: Speed in bases per second or zero if the speed could not be calculated. The only reliable way we have of finding out how many bases have gone through the pore is by looking at how much of the reference the sequence aligned to. This takes that information and uses it to calculate speed in reference-bases-per-second. gRs match foundtref_spaniitseq_spantseq_lent sampling_ratet segmentationRs duration_{}N( R&R)R tget_channel_infot get_chainRRtdicttgetRR,tfloat(RR/talignment_resultstspeedR(R=tref_lenR>R?t total_lent sample_ratetchaintsegmentation_grouptdurationtsegR'tnormalized_duration((sO/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/analysis_tools/alignment.pytcalculate_speed‡s6        csæidd6}ˆd}|dkr1d|d<|Sd|dt num_eventsR?csi|]}ˆ||“qS(((t.0tkey(R'(sO/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/analysis_tools/alignment.pys Ís t num_alignedt num_correcttnum_insertionst num_deletionstidentitytaccuracy(tendswithtupdate(RR'R(RX((R'sO/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/analysis_tools/alignment.pyR&¾s"         N( t__name__t __module__t__doc__RRR)R4R<RQR&(((sO/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/analysis_tools/alignment.pyR s0 (   7( RjtnumpyR7t&ont_fast5_api.analysis_tools.base_toolRtont_fast5_api.fast5_fileRt)ont_fast5_api.analysis_tools.segmentationRtont_fast5_api.fast5_readRR(((sO/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/analysis_tools/alignment.pyts