ó ¤>dc@sèdZddlZddlZddlZddlmZddlmZm Z ddl m Z ddl m Z mZddlmZmZddlmZmZd efd „ƒYZd e fd „ƒYZd efd„ƒYZdS(s8 Basic API for reading/writing single-read fast5 files. iÿÿÿÿN(tCURRENT_FAST5_VERSION(tVBZtraise_missing_vbz_error_read(t Fast5Read(t Fast5InfotReadInfo(tsupported_modestmode_docstring(t_sanitize_data_for_readingt_sanitize_data_for_writingtFast5FileTypeErrorcBseZRS((t__name__t __module__(((sA/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/fast5_file.pyR st Fast5FilecBsÔeZdZdd„Zd„Zd„Zd„Zed„ƒZd„Z ed„ƒZ ed „ƒZ e d „Z ddde d „Zded „Zd „Zed„ƒZed„ƒZd„Zd„ZRS(s; This object encapsulates a read fast5 file. It can be used instead of directly using the h5py API in order to help maintain consistency in fast5 file format, and simplify common tasks. The object will contain a field called **status** that is a Fast5Status object with details about the file. trcCsYd|_|tkr0tdj|tƒƒ‚n||_d|_||_|j ƒdS(s“ Constructor. Opens the specified file. :param fname: Filename to open. :param mode: File open mode (r, r+, w, w-, x, a). sUniqueGlobalKey/s&Unsupported file handle mode : '{}' {}N( t global_keyRtIOErrortformatRtfilenametNonethandletmodet_initialise_file(tselftfnameR((sA/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/fast5_file.pyt__init__s     ccs|j|jƒƒVdS(N(tget_readt get_read_id(R((sA/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/fast5_file.pyt get_reads,scCs |jƒgS(N(R(R((sA/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/fast5_file.pyt get_read_ids0scCs7||jƒkr3tdj||jƒƒƒ‚n|S(Ns4read_id given: {} does not match read_id in file: {}(RtKeyErrorR(Rtread_id((sA/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/fast5_file.pyR3s cCs|jjdjS(Ni(tstatust read_infoR(R((sA/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/fast5_file.pyR9scCstdƒ|jS(NsP'read.get_read_id()' will be deprecated. Use the property 'read.read_id' instead(tDeprecationWarningR(R((sA/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/fast5_file.pyR=s cCs|jƒ}dj|ƒS(NsRaw/Reads/Read_{}(t_get_only_read_numberR(Rt read_number((sA/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/fast5_file.pytraw_dataset_group_nameAs cCsd|j|jd kS(Nt context_tagsiÿÿÿÿ(RR(R((sA/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/fast5_file.pythas_context_tagsFscCs(|jƒ|j|jd||ƒdS(s  Add channel info data to the channel_id group. :param data: A dictionary of key/value pairs. Keys must be strings. Values can be strings or numeric values. :param clear: If set, any existing channel info data will be removed. t channel_idN(tassert_writeablet_add_attributesR(Rtdatatclear((sA/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/fast5_file.pytadd_channel_infoJs cCsY|jƒ|j|jkr@dj||jƒ}t|ƒ‚n|j|j|||ƒS(s† Pull raw data from the file. :param read_number: The read number you want raw data from. Pass None if there is only one read, and will grab that read's raw data. :param start: The first sample to pull. Default is to pull from the beginning. :param end: One past the last sample to pull. Default is to pull until the end. :param scale: If set, the returned data will be scaled floating point values, in pA. Otherwise raw DAQ values are returned as 16 bit integers. :returns: Raw data as either 32 bit floats, or 16 bit integers. s,Fast5 file has no raw data for read {} in {}(t assert_opentraw_dataset_nameRRRRt _load_raw(RR$tstarttendtscaletmsg((sA/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/fast5_file.pyt get_raw_dataTs  cCs |jƒ|j|jkrCd}t|j|j|jƒƒ‚n|j}||jkrn|jj|ƒny-|j|jdd|ddt |ƒWnt k rº}t |ƒnX|j j |jƒ}t|j j|_|dk r |j||dtƒndS(s Add raw data for a read. :param read_number: The number of the read the raw data is for. :param data: The raw data DAQ values (16 bit integers). The read must already exist in the file. It must not already have raw data. s1Fast5 file already has raw data for read {} in {}tSignalR+tdtypeti2R,N(R)R/RRRRR%t create_grouptcreate_datasettvarst ValueErrorRR tread_number_mapR#tTrueR!t has_raw_dataRR*(RR+tattrst compressionR4t group_nametet read_index((sA/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/fast5_file.pyt add_raw_datahs ! - c CsÁ|jƒt||||d|d|ƒ}|jjj|ƒt|jjƒd}||jj|<||jj|<|j} i|d6|d6|d6|d6|d6|d6} |j | | ƒd S( sm Add a new read to the file. :param read_number: The read number to assign to the read. :param read_id: The unique read-id for the read. :param start_time: The start time (in samples) of the read. :param duration: The duration (in samples) of the read. :param mux: The mux set at the time of the read. :param median_before: The median level of the data before the read. Note that most tools assume a file contains only one read. Putting multiple reads into a file severely limits the ability to operate on those reads with standard tools. tmuxt median_beforeiR$Rt start_timetdurationt start_muxN( R)RR R!tappendtlenR=t read_id_mapR%t _add_group( RR$RRHRIRFRGR!tnRBR@((sA/tmp/pip-install-m8tpmx/ont-fast5-api/ont_fast5_api/fast5_file.pytadd_read…s !   c Cs“t|ƒ}|js-tdj|ƒƒ‚ntj|dƒN}x›|jD]}dj|jƒ}||kr}||}n|j|ƒ}|j|j d<|j |j d<|j |j d<|j |j d<|j |j ds   ÿ