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| # Copyright 2011 by Wibowo Arindrarto ([email protected]) | |
| # Revisions copyright 2011-2016 by Peter Cock. | |
| # | |
| # This file is part of the Biopython distribution and governed by your | |
| # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". | |
| # Please see the LICENSE file that should have been included as part of this | |
| # package. | |
| """Bio.SeqIO parser for the ABI format. | |
| ABI is the format used by Applied Biosystem's sequencing machines to store | |
| sequencing results. | |
| For more details on the format specification, visit: | |
| http://www6.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf | |
| """ | |
| import datetime | |
| import struct | |
| import sys | |
| from os.path import basename | |
| from Bio.Seq import Seq | |
| from Bio.SeqRecord import SeqRecord | |
| from .Interfaces import SequenceIterator | |
| # dictionary for determining which tags goes into SeqRecord annotation | |
| # each key is tag_name + tag_number | |
| # if a tag entry needs to be added, just add its key and its key | |
| # for the annotations dictionary as the value | |
| # dictionary for tags that require preprocessing before use in creating | |
| # seqrecords | |
| _EXTRACT = { | |
| "TUBE1": "sample_well", | |
| "DySN1": "dye", | |
| "GTyp1": "polymer", | |
| "MODL1": "machine_model", | |
| } | |
| # Complete data structure representing 98% of the API. The general section | |
| # represents the part of the API that's common to ALL instruments, whereas the | |
| # instrument specific sections are labelled as they are in the ABIF spec | |
| # | |
| # Keys don't seem to clash from machine to machine, so when we parse, we look | |
| # for ANY key, and store that in the raw ABIF data structure attached to the | |
| # annotations, with the assumption that anyone parsing the data can look up the | |
| # spec themself | |
| # | |
| # Key definitions are retained in case end users want "nice" labels pre-made | |
| # for them for all of the available fields. | |
| _INSTRUMENT_SPECIFIC_TAGS = {} | |
| # fmt: off | |
| _INSTRUMENT_SPECIFIC_TAGS["general"] = { | |
| "APFN2": "Sequencing Analysis parameters file name", | |
| "APXV1": "Analysis Protocol XML schema version", | |
| "APrN1": "Analysis Protocol settings name", | |
| "APrV1": "Analysis Protocol settings version", | |
| "APrX1": "Analysis Protocol XML string", | |
| "CMNT1": "Sample Comment", | |
| "CTID1": "Container Identifier, a.k.a. plate barcode", | |
| "CTNM1": "Container name, usually identical to CTID, but not necessarily so", | |
| "CTTL1": "Comment Title", | |
| "CpEP1": "Capillary type electrophoresis. 1 for a capillary based machine. 0 for a slab gel based machine.", | |
| "DATA1": "Channel 1 raw data", | |
| "DATA2": "Channel 2 raw data", | |
| "DATA3": "Channel 3 raw data", | |
| "DATA4": "Channel 4 raw data", | |
| "DATA5": "Short Array holding measured volts/10 (EP voltage) during run", | |
| "DATA6": "Short Array holding measured milliAmps trace (EP current) during run", | |
| "DATA7": "Short Array holding measured milliWatts trace (Laser EP Power) during run", | |
| "DATA8": "Short Array holding measured oven Temperature (polymer temperature) trace during run", | |
| "DATA9": "Channel 9 processed data", | |
| "DATA10": "Channel 10 processed data", | |
| "DATA11": "Channel 11 processed data", | |
| "DATA12": "Channel 12 processed data", | |
| # Prism 3100/3100-Avant may provide DATA105 | |
| # 3130/3130-XL may provide DATA105 | |
| # 3530/3530-XL may provide DATA105-199, 9-12, 205-299 | |
| "DSam1": "Downsampling factor", | |
| "DySN1": "Dye set name", | |
| "Dye#1": "Number of dyes", | |
| "DyeN1": "Dye 1 name", | |
| "DyeN2": "Dye 2 name", | |
| "DyeN3": "Dye 3 name", | |
| "DyeN4": "Dye 4 name", | |
| "DyeW1": "Dye 1 wavelength", | |
| "DyeW2": "Dye 2 wavelength", | |
| "DyeW3": "Dye 3 wavelength", | |
| "DyeW4": "Dye 4 wavelength", | |
| # 'DyeN5-N': 'Dye 5-N Name', | |
| # 'DyeW5-N': 'Dye 5-N Wavelength', | |
| "EPVt1": "Electrophoresis voltage setting (volts)", | |
| "EVNT1": "Start Run event", | |
| "EVNT2": "Stop Run event", | |
| "EVNT3": "Start Collection event", | |
| "EVNT4": "Stop Collection event", | |
| "FWO_1": 'Base Order. Sequencing Analysis Filter wheel order. Fixed for 3500 at "GATC"', | |
| "GTyp1": "Gel or polymer Type", | |
| "InSc1": "Injection time (seconds)", | |
| "InVt1": "Injection voltage (volts)", | |
| "LANE1": "Lane/Capillary", | |
| "LIMS1": "Sample tracking ID", | |
| "LNTD1": "Length to detector", | |
| "LsrP1": "Laser Power setting (micro Watts)", | |
| "MCHN1": "Instrument name and serial number", | |
| "MODF1": "Data collection module file", | |
| "MODL1": "Model number", | |
| "NAVG1": "Pixels averaged per lane", | |
| "NLNE1": "Number of capillaries", | |
| "OfSc1": "List of scans that are marked off scale in Collection. (optional)", | |
| # OvrI and OrvV are listed as "1-N", and "One for each dye (unanalyzed | |
| # and/or analyzed data)" | |
| "OvrI1": "List of scan number indexes that have values greater than 32767 but did not " | |
| "saturate the camera. In Genemapper samples, this can have indexes with " | |
| "values greater than 32000. In sequencing samples, this cannot have " | |
| "indexes with values greater than 32000.", | |
| "OvrI2": "List of scan number indexes that have values greater than 32767 but did not " | |
| "saturate the camera. In Genemapper samples, this can have indexes with " | |
| "values greater than 32000. In sequencing samples, this cannot have " | |
| "indexes with values greater than 32000.", | |
| "OvrI3": "List of scan number indexes that have values greater than 32767 but did not " | |
| "saturate the camera. In Genemapper samples, this can have indexes with " | |
| "values greater than 32000. In sequencing samples, this cannot have " | |
| "indexes with values greater than 32000.", | |
| "OvrI4": "List of scan number indexes that have values greater than 32767 but did not " | |
| "saturate the camera. In Genemapper samples, this can have indexes with " | |
| "values greater than 32000. In sequencing samples, this cannot have " | |
| "indexes with values greater than 32000.", | |
| "OvrV1": "List of color data values found at the locations listed in the OvrI tag. " | |
| "There must be exactly as many numbers in this array as in the OvrI array.", | |
| "OvrV2": "List of color data values found at the locations listed in the OvrI tag. " | |
| "There must be exactly as many numbers in this array as in the OvrI array.", | |
| "OvrV3": "List of color data values found at the locations listed in the OvrI tag. " | |
| "There must be exactly as many numbers in this array as in the OvrI array.", | |
| "OvrV4": "List of color data values found at the locations listed in the OvrI tag. " | |
| "There must be exactly as many numbers in this array as in the OvrI array.", | |
| "PDMF1": "Sequencing Analysis Mobility file name chosen in collection", | |
| "RMXV1": "Run Module XML schema version", | |
| "RMdN1": "Run Module name (same as MODF)", | |
| "RMdX1": "Run Module XML string", | |
| "RPrN1": "Run Protocol name", | |
| "RPrV1": "Run Protocol version", | |
| "RUND1": "Run Started Date", | |
| "RUND2": "Run Stopped Date", | |
| "RUND3": "Data Collection Started Date", | |
| "RUND4": "Data Collection Stopped date", | |
| "RUNT1": "Run Started Time", | |
| "RUNT2": "Run Stopped Time", | |
| "RUNT3": "Data Collection Started Time", | |
| "RUNT4": "Data Collection Stopped Time", | |
| "Rate1": "Scanning Rate. Milliseconds per frame.", | |
| "RunN1": "Run Name", | |
| "SCAN1": "Number of scans", | |
| "SMED1": "Polymer lot expiration date", | |
| "SMLt1": "Polymer lot number", | |
| "SMPL1": "Sample name", | |
| "SVER1": "Data collection software version", | |
| "SVER3": "Data collection firmware version", | |
| "Satd1": "Array of longs representing the scan numbers of data points, which are flagged as saturated by data collection (optional)", | |
| "Scal1": "Rescaling divisor for color data", | |
| "Scan1": "Number of scans (legacy - use SCAN)", | |
| "TUBE1": "Well ID", | |
| "Tmpr1": "Run temperature setting", | |
| "User1": "Name of user who created the plate (optional)", | |
| } | |
| # No instrument specific tags | |
| # _INSTRUMENT_SPECIFIC_TAGS['abi_prism_3100/3100-Avant'] = { | |
| # } | |
| _INSTRUMENT_SPECIFIC_TAGS["abi_3130/3130xl"] = { | |
| "CTOw1": "Container owner", | |
| "HCFG1": "Instrument Class", | |
| "HCFG2": "Instrument Family", | |
| "HCFG3": "Official Instrument Name", | |
| "HCFG4": "Instrument Parameters", | |
| "RMdVa1": "Run Module version", | |
| } | |
| _INSTRUMENT_SPECIFIC_TAGS["abi_3530/3530xl"] = { | |
| "AAct1": "Primary Analysis Audit Active indication. True if system auditing was enabled during the last write of this file, " | |
| "false if system auditing was disabled.", | |
| "ABED1": "Anode buffer expiration date using ISO 8601 format using the patterns YYYY-MM-DDTHH:MM:SS.ss+/-HH:MM. Hundredths of a second are optional.", | |
| "ABID1": "Anode buffer tray first installed date", | |
| "ABLt1": "Anode buffer lot number", | |
| "ABRn1": "Number of runs (injections) processed with the current Anode Buffer (runs allowed - runs remaining)", | |
| "ABTp1": "Anode buffer type", | |
| "AEPt1": "Analysis Ending scan number for basecalling on initial analysis", | |
| "AEPt2": "Analysis Ending scan number for basecalling on last analysis", | |
| "APCN1": "Amplicon name", | |
| "ARTN1": "Analysis Return code. Produced only by 5 Prime basecaller 1.0b3", | |
| "ASPF1": "Flag to indicate whether adaptive processing worked or not", | |
| "ASPt1": "Analysis Starting scan number for first analysis", | |
| "ASPt2": "Analysis Starting scan number for last analysis", | |
| "AUDT2": "Audit log used across 3500 software (optional)", | |
| "AVld1": "Assay validation flag (true or false)", | |
| "AmbT1": "Record of ambient temperature readings", | |
| "AsyC1": "The assay contents (xml format)", | |
| "AsyN1": "The assay name", | |
| "AsyV1": "The assay version", | |
| "B1Pt1": "Reference scan number for mobility and spacing curves for first analysis", | |
| "B1Pt2": "Reference scan number for mobility and spacing curves for last analysis", | |
| "BCTS1": "Basecaller timestamp. Time of completion of most recent analysis", | |
| "BcRn1": "Basecalling qc code", | |
| "BcRs1": "Basecalling warnings, a concatenated comma separated string", | |
| "BcRs2": "Basecalling errors, a concatenated comma separated string", | |
| "CAED1": "Capillary array expiration", | |
| "CALt1": "Capillary array lot number", | |
| "CARn1": "Number of injections processed (including the one of which this sample was a part) through the capillary array", | |
| "CASN1": "Capillary array serial number", | |
| "CBED1": "Cathode buffer expiration date", | |
| "CBID1": "Cathode buffer tray first installed date", | |
| "CBLt1": "Cathode buffer lot number", | |
| "CBRn1": "Number of runs (injections) processed with the current Cathode Buffer (runs allowed - runs remaining)", | |
| "CBTp1": "Cathode buffer type", | |
| "CLRG1": "Start of the clear range (inclusive).", | |
| "CLRG2": "Clear range length", | |
| "CRLn1": "Contiguous read length", | |
| "CRLn2": 'One of "Pass", "Fail", or "Check"', | |
| "CTOw1": "The name entered as the Owner of a plate, in the plate editor", | |
| "CkSm1": "File checksum", | |
| "DCEv1": "A list of door-close events, separated by semicolon. Door open events are generally paired with door close events.", | |
| "DCHT1": "Reserved for backward compatibility. The detection cell heater temperature setting from the Run Module. Not used for 3500.", | |
| "DOEv1": "A list of door-open events, separated by semicolon. Door close events are generally paired with door open events.", | |
| "ESig2": "Electronic signature record used across 3500 software", | |
| "FTab1": "Feature table. Can be created by Nibbler for Clear Range.", | |
| "FVoc1": "Feature table vocabulary. Can be created by Nibbler for Clear Range.", | |
| "Feat1": "Features. Can be created by Nibbler for Clear Range.", | |
| "HCFG1": "The Instrument Class. All upper case, no spaces. Initial valid value: CE", | |
| "HCFG2": "The Instrument Family. All upper case, no spaces. Valid values: 31XX or 37XX for UDC, 35XX (for 3500)", | |
| "HCFG3": "The official instrument name. Mixed case, minus any special formatting. Initial valid values: 3130, 3130xl, 3730, 3730xl, 3500, 3500xl.", | |
| "HCFG4": "Instrument parameters. Contains key-value pairs of instrument configuration information, separated by semicolons. " | |
| "Four parameters are included initially: UnitID=<UNITD number>, CPUBoard=<board type>, " | |
| "ArraySize=<# of capillaries>, SerialNumber=<Instrument Serial#>.", | |
| "InjN1": "Injection name", | |
| "LAST1": "Parameter settings information", | |
| "NOIS1": "The estimate of rms baseline noise (S/N ratio) for each dye for a successfully analyzed sample. " | |
| "Corresponds in order to the raw data in tags DATA 1-4. KB basecaller only.", | |
| "P1AM1": "Amplitude of primary peak, which is not necessarily equal to corresponding signal strength at that position", | |
| "P1RL1": "Deviation of primary peak position from (PLoc,2), times 100, rounded to integer", | |
| "P1WD1": "Full-width Half-max of primary peak, times 100, rounded to integer. " | |
| "Corresponding signal intensity is not necessarily equal to one half of primary peak amplitude", | |
| "P2AM1": "Amplitude of secondary peak, which is not necessarily equal to corresponding signal strength at that position", | |
| "P2BA1": "Base of secondary peak", | |
| "P2RL1": "Deviation of secondary peak position from (PLoc,2), times 100, rounded to integer", | |
| "PBAS1": "Array of sequence characters edited by user", | |
| "PBAS2": "Array of sequence characters as called by Basecaller", | |
| "PCON1": "Array of quality Values (0-255) as edited by user", | |
| "PCON2": "Array of quality values (0-255) as called by Basecaller", | |
| "PDMF2": "Mobility file name chosen in most recent analysis (identical to PDMF1)", | |
| "PLOC1": "Array of peak locations edited by user", | |
| "PLOC2": "Array of peak locations as called by Basecaller", | |
| "PRJT1": "SeqScape 2.0 project template name", | |
| "PROJ4": "SeqScape 2.0 project name", | |
| "PSZE1": "Plate size. The number of sample positions in the container. Current allowed values: 96, 384.", | |
| "PTYP1": "Plate type. Current allowed values: 96-Well, 384-Well.", | |
| "PuSc1": "Median pupscore", | |
| "QV201": "QV20+ value", | |
| "QV202": 'One of "Pass", "Fail", or "Check"', | |
| "QcPa1": "QC parameters", | |
| "QcRn1": "Trimming and QC code", | |
| "QcRs1": "QC warnings, a concatenated comma separated string", | |
| "QcRs2": "QC errors, a concatenated comma separated string", | |
| "RGOw1": "The name entered as the Owner of a Results Group, in the Results Group Editor. Implemented as the user name from the results group.", | |
| "RInj1": "Reinjection number. The reinjection number that this sample belongs to. Not present if there was no reinjection.", | |
| "RNmF1": "Raman normalization factor", | |
| "RevC1": "for whether the sequence has been complemented", | |
| "RunN1": "Run name (which, for 3500, is different from injection name)", | |
| "S/N%1": "Signal strength for each dye", | |
| "SMID1": "Polymer first installed date", | |
| "SMRn1": "Number of runs (injections) processed with the current polymer (runs allowed - runs remaining)", | |
| "SPAC1": "Average peak spacing used in last analysis", | |
| "SPAC2": "Basecaller name - corresponds to name of bcp file.", | |
| "SPAC3": "Average peak spacing last calculated by the Basecaller.", | |
| "SPEC1": "Sequencing Analysis Specimen Name", | |
| "SVER2": "Basecaller version number", | |
| "SVER4": "Sample File Format Version String", | |
| "ScPa1": "The parameter string of size caller", | |
| "ScSt1": "Raw data start point. Set to 0 for 3500 data collection.", | |
| "SpeN1": "Active spectral calibration name", | |
| "TrPa1": "Trimming parameters", | |
| "TrSc1": "Trace score.", | |
| "TrSc2": 'One of "Pass", "Fail", or "Check"', | |
| "phAR1": "Trace peak aria ratio", | |
| "phCH1": 'Chemistry type ("term", "prim", "unknown"), based on DYE_1 information', | |
| "phDY1": 'Dye ("big", "d-rhod", "unknown"), based on mob file information', | |
| "phQL1": "Maximum Quality Value", | |
| "phTR1": "Set Trim region", | |
| "phTR2": "Trim probability", | |
| } | |
| _INSTRUMENT_SPECIFIC_TAGS["abi_3730/3730xl"] = { | |
| "BufT1": "Buffer tray heater temperature (degrees C)", | |
| } | |
| # fmt: on | |
| # dictionary for data unpacking format | |
| _BYTEFMT = { | |
| 1: "b", # byte | |
| 2: "s", # char | |
| 3: "H", # word | |
| 4: "h", # short | |
| 5: "i", # long | |
| 6: "2i", # rational, legacy unsupported | |
| 7: "f", # float | |
| 8: "d", # double | |
| 10: "h2B", # date | |
| 11: "4B", # time | |
| 12: "2i2b", # thumb | |
| 13: "B", # bool | |
| 14: "2h", # point, legacy unsupported | |
| 15: "4h", # rect, legacy unsupported | |
| 16: "2i", # vPoint, legacy unsupported | |
| 17: "4i", # vRect, legacy unsupported | |
| 18: "s", # pString | |
| 19: "s", # cString | |
| 20: "2i", # tag, legacy unsupported | |
| } | |
| # header data structure (excluding 4 byte ABIF marker) | |
| _HEADFMT = ">H4sI2H3I" | |
| # directory data structure | |
| _DIRFMT = ">4sI2H4I" | |
| __global_tag_listing = [] | |
| for tag in _INSTRUMENT_SPECIFIC_TAGS.values(): | |
| __global_tag_listing += tag.keys() | |
| def _get_string_tag(opt_bytes_value, default=None): | |
| """Return the string value of the given an optional raw bytes tag value. | |
| If the bytes value is None, return the given default value. | |
| """ | |
| if opt_bytes_value is None: | |
| return default | |
| try: | |
| return opt_bytes_value.decode() | |
| except UnicodeDecodeError: | |
| return opt_bytes_value.decode(encoding=sys.getdefaultencoding()) | |
| class AbiIterator(SequenceIterator): | |
| """Parser for Abi files.""" | |
| def __init__(self, source, trim=False): | |
| """Return an iterator for the Abi file format.""" | |
| self.trim = trim | |
| super().__init__(source, mode="b", fmt="ABI") | |
| def parse(self, handle): | |
| """Start parsing the file, and return a SeqRecord generator.""" | |
| # check if input file is a valid Abi file | |
| marker = handle.read(4) | |
| if not marker: | |
| # handle empty file gracefully | |
| raise ValueError("Empty file.") | |
| if marker != b"ABIF": | |
| raise OSError(f"File should start ABIF, not {marker!r}") | |
| records = self.iterate(handle) | |
| return records | |
| def iterate(self, handle): | |
| """Parse the file and generate SeqRecord objects.""" | |
| # dirty hack for handling time information | |
| times = {"RUND1": "", "RUND2": "", "RUNT1": "", "RUNT2": ""} | |
| # initialize annotations | |
| annot = dict(zip(_EXTRACT.values(), [None] * len(_EXTRACT))) | |
| # parse header and extract data from directories | |
| header = struct.unpack(_HEADFMT, handle.read(struct.calcsize(_HEADFMT))) | |
| # Set default sample ID value, which we expect to be present in most | |
| # cases in the SMPL1 tag, but may be missing. | |
| sample_id = "<unknown id>" | |
| raw = {} | |
| seq = qual = None | |
| for tag_name, tag_number, tag_data in _abi_parse_header(header, handle): | |
| key = tag_name + str(tag_number) | |
| raw[key] = tag_data | |
| # PBAS2 is base-called sequence, only available in 3530 | |
| if key == "PBAS2": | |
| seq = tag_data.decode() | |
| # PCON2 is quality values of base-called sequence | |
| elif key == "PCON2": | |
| qual = [ord(val) for val in tag_data.decode()] | |
| # SMPL1 is sample id entered before sequencing run, it must be | |
| # a string. | |
| elif key == "SMPL1": | |
| sample_id = _get_string_tag(tag_data) | |
| elif key in times: | |
| times[key] = tag_data | |
| else: | |
| if key in _EXTRACT: | |
| annot[_EXTRACT[key]] = tag_data | |
| # set time annotations | |
| annot["run_start"] = f"{times['RUND1']} {times['RUNT1']}" | |
| annot["run_finish"] = f"{times['RUND2']} {times['RUNT2']}" | |
| # raw data (for advanced end users benefit) | |
| annot["abif_raw"] = raw | |
| # fsa check | |
| is_fsa_file = all(tn not in raw for tn in ("PBAS1", "PBAS2")) | |
| if is_fsa_file: | |
| try: | |
| file_name = basename(handle.name).replace(".fsa", "") | |
| except AttributeError: | |
| file_name = "" | |
| sample_id = _get_string_tag(raw.get("LIMS1"), sample_id) | |
| description = _get_string_tag(raw.get("CTID1"), "<unknown description>") | |
| record = SeqRecord( | |
| Seq(""), | |
| id=sample_id, | |
| name=file_name, | |
| description=description, | |
| annotations=annot, | |
| ) | |
| else: | |
| # use the file name as SeqRecord.name if available | |
| try: | |
| file_name = basename(handle.name).replace(".ab1", "") | |
| except AttributeError: | |
| file_name = "" | |
| record = SeqRecord( | |
| Seq(seq), | |
| id=sample_id, | |
| name=file_name, | |
| description="", | |
| annotations=annot, | |
| ) | |
| if qual: | |
| # Expect this to be missing for FSA files. | |
| record.letter_annotations["phred_quality"] = qual | |
| elif not is_fsa_file and not qual and self.trim: | |
| raise ValueError( | |
| "The 'abi-trim' format can not be used for files without" | |
| " quality values." | |
| ) | |
| if self.trim and not is_fsa_file: | |
| record = _abi_trim(record) | |
| record.annotations["molecule_type"] = "DNA" | |
| yield record | |
| def _AbiTrimIterator(handle): | |
| """Return an iterator for the Abi file format that yields trimmed SeqRecord objects (PRIVATE).""" | |
| return AbiIterator(handle, trim=True) | |
| def _abi_parse_header(header, handle): | |
| """Return directory contents (PRIVATE).""" | |
| # header structure (after ABIF marker): | |
| # file version, tag name, tag number, | |
| # element type code, element size, number of elements | |
| # data size, data offset, handle (not file handle) | |
| head_elem_size = header[4] | |
| head_elem_num = header[5] | |
| head_offset = header[7] | |
| index = 0 | |
| while index < head_elem_num: | |
| start = head_offset + index * head_elem_size | |
| # add directory offset to tuple | |
| # to handle directories with data size <= 4 bytes | |
| handle.seek(start) | |
| dir_entry = struct.unpack(_DIRFMT, handle.read(struct.calcsize(_DIRFMT))) + ( | |
| start, | |
| ) | |
| index += 1 | |
| # only parse desired dirs | |
| key = dir_entry[0].decode() | |
| key += str(dir_entry[1]) | |
| tag_name = dir_entry[0].decode() | |
| tag_number = dir_entry[1] | |
| elem_code = dir_entry[2] | |
| elem_num = dir_entry[4] | |
| data_size = dir_entry[5] | |
| data_offset = dir_entry[6] | |
| tag_offset = dir_entry[8] | |
| # if data size <= 4 bytes, data is stored inside tag | |
| # so offset needs to be changed | |
| if data_size <= 4: | |
| data_offset = tag_offset + 20 | |
| handle.seek(data_offset) | |
| data = handle.read(data_size) | |
| yield tag_name, tag_number, _parse_tag_data(elem_code, elem_num, data) | |
| def _abi_trim(seq_record): | |
| """Trims the sequence using Richard Mott's modified trimming algorithm (PRIVATE). | |
| Arguments: | |
| - seq_record - SeqRecord object to be trimmed. | |
| Trimmed bases are determined from their segment score, which is a | |
| cumulative sum of each base's score. Base scores are calculated from | |
| their quality values. | |
| More about the trimming algorithm: | |
| http://www.phrap.org/phredphrap/phred.html | |
| http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/650/Quality_trimming.html | |
| """ | |
| start = False # flag for starting position of trimmed sequence | |
| segment = 20 # minimum sequence length | |
| trim_start = 0 # init start index | |
| cutoff = 0.05 # default cutoff value for calculating base score | |
| if len(seq_record) <= segment: | |
| return seq_record | |
| else: | |
| # calculate base score | |
| score_list = [ | |
| cutoff - (10 ** (qual / -10.0)) | |
| for qual in seq_record.letter_annotations["phred_quality"] | |
| ] | |
| # calculate cumulative score | |
| # if cumulative value < 0, set it to 0 | |
| # first value is set to 0, because of the assumption that | |
| # the first base will always be trimmed out | |
| cummul_score = [0] | |
| for i in range(1, len(score_list)): | |
| score = cummul_score[-1] + score_list[i] | |
| if score < 0: | |
| cummul_score.append(0) | |
| else: | |
| cummul_score.append(score) | |
| if not start: | |
| # trim_start = value when cumulative score is first > 0 | |
| trim_start = i | |
| start = True | |
| # trim_finish = index of highest cumulative score, | |
| # marking the end of sequence segment with highest cumulative score | |
| trim_finish = cummul_score.index(max(cummul_score)) | |
| return seq_record[trim_start:trim_finish] | |
| def _parse_tag_data(elem_code, elem_num, raw_data): | |
| """Return single data value (PRIVATE). | |
| Arguments: | |
| - elem_code - What kind of data | |
| - elem_num - How many data points | |
| - raw_data - abi file object from which the tags would be unpacked | |
| """ | |
| if elem_code in _BYTEFMT: | |
| # because '>1s' unpack differently from '>s' | |
| if elem_num == 1: | |
| num = "" | |
| else: | |
| num = str(elem_num) | |
| fmt = ">" + num + _BYTEFMT[elem_code] | |
| assert len(raw_data) == struct.calcsize(fmt) | |
| data = struct.unpack(fmt, raw_data) | |
| # no need to use tuple if len(data) == 1 | |
| # also if data is date / time | |
| if elem_code not in [10, 11] and len(data) == 1: | |
| data = data[0] | |
| # account for different data types | |
| if elem_code == 2: | |
| return data | |
| elif elem_code == 10: | |
| return str(datetime.date(*data)) | |
| elif elem_code == 11: | |
| return str(datetime.time(*data[:3])) | |
| elif elem_code == 13: | |
| return bool(data) | |
| elif elem_code == 18: | |
| return data[1:] | |
| elif elem_code == 19: | |
| return data[:-1] | |
| else: | |
| return data | |
| else: | |
| return None | |
| if __name__ == "__main__": | |
| pass | |