o RŀgY@sTdZddlZddlZddlmZddlmZddlmZddl m Z ddl m Z d Z d Z d Zd Zd ZdZddZddZddZddZddZedZ d8ddZddedDZd d!Zd"d#Zgd$Zd%d&Zd'd(Z d)d*Z!Gd+d,d,Z"Gd-d.d.e Z#d/d0Z$Gd1d2d2e#Z%Gd3d4d4e Z&e'd5krdd6l(m)Z)e)dd7dSdS)9a$Bio.SeqIO support for the binary Standard Flowgram Format (SFF) file format. SFF was designed by 454 Life Sciences (Roche), the Whitehead Institute for Biomedical Research and the Wellcome Trust Sanger Institute. SFF was also used as the native output format from early versions of Ion Torrent's PGM platform as well. You are expected to use this module via the Bio.SeqIO functions under the format name "sff" (or "sff-trim" as described below). For example, to iterate over the records in an SFF file, >>> from Bio import SeqIO >>> for record in SeqIO.parse("Roche/E3MFGYR02_random_10_reads.sff", "sff"): ... print("%s %i %s..." % (record.id, len(record), record.seq[:20])) ... E3MFGYR02JWQ7T 265 tcagGGTCTACATGTTGGTT... E3MFGYR02JA6IL 271 tcagTTTTTTTTGGAAAGGA... E3MFGYR02JHD4H 310 tcagAAAGACAAGTGGTATC... E3MFGYR02GFKUC 299 tcagCGGCCGGGCCTCTCAT... E3MFGYR02FTGED 281 tcagTGGTAATGGGGGGAAA... E3MFGYR02FR9G7 261 tcagCTCCGTAAGAAGGTGC... E3MFGYR02GAZMS 278 tcagAAAGAAGTAAGGTAAA... E3MFGYR02HHZ8O 221 tcagACTTTCTTCTTTACCG... E3MFGYR02GPGB1 269 tcagAAGCAGTGGTATCAAC... E3MFGYR02F7Z7G 219 tcagAATCATCCACTTTTTA... Each SeqRecord object will contain all the annotation from the SFF file, including the PHRED quality scores. >>> print("%s %i" % (record.id, len(record))) E3MFGYR02F7Z7G 219 >>> print("%s..." % record.seq[:10]) tcagAATCAT... >>> print("%r..." % (record.letter_annotations["phred_quality"][:10])) [22, 21, 23, 28, 26, 15, 12, 21, 28, 21]... Notice that the sequence is given in mixed case, the central upper case region corresponds to the trimmed sequence. This matches the output of the Roche tools (and the 3rd party tool sff_extract) for SFF to FASTA. >>> print(record.annotations["clip_qual_left"]) 4 >>> print(record.annotations["clip_qual_right"]) 134 >>> print(record.seq[:4]) tcag >>> print("%s...%s" % (record.seq[4:20], record.seq[120:134])) AATCATCCACTTTTTA...CAAAACACAAACAG >>> print(record.seq[134:]) atcttatcaacaaaactcaaagttcctaactgagacacgcaacaggggataagacaaggcacacaggggataggnnnnnnnnnnn The annotations dictionary also contains any adapter clip positions (usually zero), and information about the flows. e.g. >>> len(record.annotations) 12 >>> print(record.annotations["flow_key"]) TCAG >>> print(record.annotations["flow_values"][:10]) (83, 1, 128, 7, 4, 84, 6, 106, 3, 172) >>> print(len(record.annotations["flow_values"])) 400 >>> print(record.annotations["flow_index"][:10]) (1, 2, 3, 2, 2, 0, 3, 2, 3, 3) >>> print(len(record.annotations["flow_index"])) 219 Note that to convert from a raw reading in flow_values to the corresponding homopolymer stretch estimate, the value should be rounded to the nearest 100: >>> print("%r..." % [int(round(value, -2)) // 100 ... for value in record.annotations["flow_values"][:10]]) ... [1, 0, 1, 0, 0, 1, 0, 1, 0, 2]... If a read name is exactly 14 alphanumeric characters, the annotations dictionary will also contain meta-data about the read extracted by interpreting the name as a 454 Sequencing System "Universal" Accession Number. Note that if a read name happens to be exactly 14 alphanumeric characters but was not generated automatically, these annotation records will contain nonsense information. >>> print(record.annotations["region"]) 2 >>> print(record.annotations["time"]) [2008, 1, 9, 16, 16, 0] >>> print(record.annotations["coords"]) (2434, 1658) As a convenience method, you can read the file with SeqIO format name "sff-trim" instead of "sff" to get just the trimmed sequences (without any annotation except for the PHRED quality scores and anything encoded in the read names): >>> from Bio import SeqIO >>> for record in SeqIO.parse("Roche/E3MFGYR02_random_10_reads.sff", "sff-trim"): ... print("%s %i %s..." % (record.id, len(record), record.seq[:20])) ... E3MFGYR02JWQ7T 260 GGTCTACATGTTGGTTAACC... E3MFGYR02JA6IL 265 TTTTTTTTGGAAAGGAAAAC... E3MFGYR02JHD4H 292 AAAGACAAGTGGTATCAACG... E3MFGYR02GFKUC 295 CGGCCGGGCCTCTCATCGGT... E3MFGYR02FTGED 277 TGGTAATGGGGGGAAATTTA... E3MFGYR02FR9G7 256 CTCCGTAAGAAGGTGCTGCC... E3MFGYR02GAZMS 271 AAAGAAGTAAGGTAAATAAC... E3MFGYR02HHZ8O 150 ACTTTCTTCTTTACCGTAAC... E3MFGYR02GPGB1 221 AAGCAGTGGTATCAACGCAG... E3MFGYR02F7Z7G 130 AATCATCCACTTTTTAACGT... Looking at the final record in more detail, note how this differs to the example above: >>> print("%s %i" % (record.id, len(record))) E3MFGYR02F7Z7G 130 >>> print("%s..." % record.seq[:10]) AATCATCCAC... >>> print("%r..." % record.letter_annotations["phred_quality"][:10]) [26, 15, 12, 21, 28, 21, 36, 28, 27, 27]... >>> len(record.annotations) 4 >>> print(record.annotations["region"]) 2 >>> print(record.annotations["coords"]) (2434, 1658) >>> print(record.annotations["time"]) [2008, 1, 9, 16, 16, 0] >>> print(record.annotations["molecule_type"]) DNA You might use the Bio.SeqIO.convert() function to convert the (trimmed) SFF reads into a FASTQ file (or a FASTA file and a QUAL file), e.g. >>> from Bio import SeqIO >>> from io import StringIO >>> out_handle = StringIO() >>> count = SeqIO.convert("Roche/E3MFGYR02_random_10_reads.sff", "sff", ... out_handle, "fastq") ... >>> print("Converted %i records" % count) Converted 10 records The output FASTQ file would start like this: >>> print("%s..." % out_handle.getvalue()[:50]) @E3MFGYR02JWQ7T tcagGGTCTACATGTTGGTTAACCCGTACTGATT... Bio.SeqIO.index() provides memory efficient random access to the reads in an SFF file by name. SFF files can include an index within the file, which can be read in making this very fast. If the index is missing (or in a format not yet supported in Biopython) the file is indexed by scanning all the reads - which is a little slower. For example, >>> from Bio import SeqIO >>> reads = SeqIO.index("Roche/E3MFGYR02_random_10_reads.sff", "sff") >>> record = reads["E3MFGYR02JHD4H"] >>> print("%s %i %s..." % (record.id, len(record), record.seq[:20])) E3MFGYR02JHD4H 310 tcagAAAGACAAGTGGTATC... >>> reads.close() Or, using the trimmed reads: >>> from Bio import SeqIO >>> reads = SeqIO.index("Roche/E3MFGYR02_random_10_reads.sff", "sff-trim") >>> record = reads["E3MFGYR02JHD4H"] >>> print("%s %i %s..." % (record.id, len(record), record.seq[:20])) E3MFGYR02JHD4H 292 AAAGACAAGTGGTATCAACG... >>> reads.close() You can also use the Bio.SeqIO.write() function with the "sff" format. Note that this requires all the flow information etc, and thus is probably only useful for SeqRecord objects originally from reading another SFF file (and not the trimmed SeqRecord objects from parsing an SFF file as "sff-trim"). As an example, let's pretend this example SFF file represents some DNA which was pre-amplified with a PCR primers AAAGANNNNN. The following script would produce a sub-file containing all those reads whose post-quality clipping region (i.e. the sequence after trimming) starts with AAAGA exactly (the non- degenerate bit of this pretend primer): >>> from Bio import SeqIO >>> records = (record for record in ... SeqIO.parse("Roche/E3MFGYR02_random_10_reads.sff", "sff") ... if record.seq[record.annotations["clip_qual_left"]:].startswith("AAAGA")) ... >>> count = SeqIO.write(records, "temp_filtered.sff", "sff") >>> print("Selected %i records" % count) Selected 2 records Of course, for an assembly you would probably want to remove these primers. If you want FASTA or FASTQ output, you could just slice the SeqRecord. However, if you want SFF output we have to preserve all the flow information - the trick is just to adjust the left clip position! >>> from Bio import SeqIO >>> def filter_and_trim(records, primer): ... for record in records: ... if record.seq[record.annotations["clip_qual_left"]:].startswith(primer): ... record.annotations["clip_qual_left"] += len(primer) ... yield record ... >>> records = SeqIO.parse("Roche/E3MFGYR02_random_10_reads.sff", "sff") >>> count = SeqIO.write(filter_and_trim(records, "AAAGA"), ... "temp_filtered.sff", "sff") ... >>> print("Selected %i records" % count) Selected 2 records We can check the results, note the lower case clipped region now includes the "AAAGA" sequence: >>> for record in SeqIO.parse("temp_filtered.sff", "sff"): ... print("%s %i %s..." % (record.id, len(record), record.seq[:20])) ... E3MFGYR02JHD4H 310 tcagaaagaCAAGTGGTATC... E3MFGYR02GAZMS 278 tcagaaagaAGTAAGGTAAA... >>> for record in SeqIO.parse("temp_filtered.sff", "sff-trim"): ... print("%s %i %s..." % (record.id, len(record), record.seq[:20])) ... E3MFGYR02JHD4H 287 CAAGTGGTATCAACGCAGAG... E3MFGYR02GAZMS 266 AGTAAGGTAAATAACAAACG... >>> import os >>> os.remove("temp_filtered.sff") For a description of the file format, please see the Roche manuals and: http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=formats N)StreamModeError)Seq) SeqRecord)SequenceIterator)SequenceWriters.sffs.hshs.srts.mftc Csd}dt|ks J|d}|stdt|dkr tdzt||\ }}}}}}} } } } } }Wn ty@tddw|tt t fvrLtd|t krWtd|||||fd kritd ||||f|d krstd ||d k| d kArtd|| f||  d}||  d}| dd ksJ| | | d}d |krdksJ|J||| t|krd dl}d dlm}|d||| || | | ||fS)aRead in an SFF file header (PRIVATE). Assumes the handle is at the start of the file, will read forwards though the header and leave the handle pointing at the first record. Returns a tuple of values from the header (header_length, index_offset, index_length, number_of_reads, flows_per_read, flow_chars, key_sequence) >>> with open("Roche/greek.sff", "rb") as handle: ... values = _sff_file_header(handle) ... >>> print(values[0]) 840 >>> print(values[1]) 65040 >>> print(values[2]) 256 >>> print(values[3]) 24 >>> print(values[4]) 800 >>> values[-1] 'TCAG' z >4s4BQIIHHHBz Empty file.z*File too small to hold a valid SFF header.z(SFF files must be opened in binary mode.Nz0Handle seems to be at SFF index block, not startz#SFF file did not start '.sff', but )rrrrz.Unsupported SFF version in header, %i.%i.%i.%irz%Flowgram format code %i not supportedrz#Index offset %i but index length %iASCIIBiopythonParserWarningzQYour SFF file is invalid, post header %i byte null padding region contained data.)structcalcsizeread ValueErrorlenunpack TypeErrorr_hsh_srt_mft_sffdecodecount_nullwarningsBiorwarn)handlefmtdata magic_numberver0ver1ver2ver3 index_offset index_lengthnumber_of_reads header_length key_lengthnumber_of_flows_per_readflowgram_format flow_chars key_sequencepaddingrrr2C/var/www/html/myenv/lib/python3.10/site-packages/Bio/SeqIO/SffIO.py_sff_file_headersz%       $ r4ccs|dt|\}}}}}}}d}t|} d|} t| } dtdks*Jdtdks3Jdtdks2HI4H>%iHr>B>s>cr z,Malformed read header, says length is %i: %rNr IYour SFF file is invalid, post name %i byte padding region contained dataLYour SFF file is invalid, post quality %i byte padding region contained dataz4After scanning reads, did not end on a multiple of 8)seekr4rrrangetellrrrrrrrrrr)r r+r(r)r*r-r/r0read_header_fmtread_header_size read_flow_fmtread_flow_sizer record_offsetoffsetr"read_header_length name_lengthseq_lenclip_qual_leftclip_qual_rightclip_adapter_leftclip_adapter_rightnamer1rrsizer2r2r3_sff_do_slow_indexfs              rPc Cs|dt|\}}}}}}}||ksJ|r|s td||d}t|} || } | s;td||ft| | krJtd||| ft|| \} } } }}| t kr| | ||fdkrktd| | ||fd}t|}t|||\}}|| |||krtd || |||f|||||| |||| |||fS| t kr| | ||fdkrtd | | ||f|d } | t d krtd ||||dd|| d || d fS| t krtd td| d| )aLocate any existing Roche style XML meta data and read index (PRIVATE). Makes a number of hard coded assumptions based on reverse engineered SFF files from Roche 454 machines. Returns a tuple of read count, SFF "index" offset and size, XML offset and size, and the actual read index offset and size. Raises a ValueError for unsupported or non-Roche index blocks. rz!No index present in this SFF filez>4s4BzLPremature end of file? Expected index of size %i at offset %i, found nothingzGPremature end of file? Expected index of size %i at offset %i, found %r)1.0rSz5Unsupported version in .mft index header, %i.%i.%i.%iz>LLz@Problem understanding .mft index header, %i != %i + %i + %i + %iz5Unsupported version in .srt index header, %i.%i.%i.%iz3Did not find expected null four bytes in .srt indexzDHash table style indexes (.hsh) in SFF files are not (yet) supportedzUnknown magic number z in SFF index header: ) r>r4r@rrrrrrrrrr)r r+r(r)r*r-r/r0r!fmt_sizer"r#r$r%r&r'fmt2 fmt2_sizexml_size data_sizer2r2r3_sff_find_roche_indexs                 rZc Cs@t|\}}}}}}}}|r|std||||S)aRead any Roche style XML manifest data in the SFF "index". The SFF file format allows for multiple different index blocks, and Roche took advantage of this to define their own index block which also embeds an XML manifest string. This is not a publicly documented extension to the SFF file format, this was reverse engineered. The handle should be to an SFF file opened in binary mode. This function will use the handle seek/tell functions and leave the handle in an arbitrary location. Any XML manifest found is returned as a Python string, which you can then parse as appropriate, or reuse when writing out SFF files with the SffWriter class. Returns a string, or raises a ValueError if an Roche manifest could not be found. zNo XML manifest found)rZrr>rr) r r*r+r(r) xml_offsetrXread_index_offsetread_index_sizer2r2r3ReadRocheXmlManifest&s r^ccst|\}}}}}}}}||d} t|D]]} |d} |d} | s+td| | 7} | tkr4nq | ddtksEJ| dd| dd} t| | dd\}}}}}|d |d |d |}|rptd | |fVq| ||krtd | ||fdS)aRead any existing Roche style read index provided in the SFF file (PRIVATE). Will use the handle seek/tell functions. This works on ".srt1.00" and ".mft1.00" style Roche SFF index blocks. Roche SFF indices use base 255 not 256, meaning we see bytes in range the range 0 to 254 only. This appears to be so that byte 0xFF (character 255) can be used as a marker character to separate entries (required if the read name lengths vary). Note that since only four bytes are used for the read offset, this is limited to 255^4 bytes (nearly 4GB). If you try to use the Roche sfffile tool to combine SFF files beyond this limit, they issue a warning and omit the index (and manifest). z>5BTrzPremature end of file!Niz,Expected a null terminator to the read name.z#Problem with index length? %i vs %i) rZr>r?rr_flagrrrr@)r r*r+r(r)r[rXr\r]r!rr"morerNoff4off3off2off1off0rFr2r2r3_sff_read_roche_indexJsJ      rkz^[a-zA-Z0-9]{14}$Fc Csd}t|}d|}t|}t|||\} } } } } }}| r&| d8} |r,|d8}| dks6| ddkr%iBr<r=z9Overlapping clip values in SFF record, trimmed to nothingz%Overlapping clip values in SFF record) flow_values flow_indexr/flow_keyrJrKrLrMtimeregioncoordsDNA molecule_type)idrN description annotations phred_quality)rrrrrrrrrrrrlistmaxminupperlowerrematch_valid_UAN_read_name_get_read_time_get_read_region _get_read_xyrrdict __setitem___per_letter_annotations)r r-r/r0trimrArBrCrDrGrHrIrJrKrLrMrNr1rrrotemp_fmtrpseqquals clip_left clip_rightryrecordr2r2r3_sff_read_seq_records                     rcCsg|]}d|qS)$r2).0ir2r2r3 srr_cCsd}t|dddtD]K\}}dt|krdkr%nnt|d}n,dt|kr1dkr:nnt|d}nd t|krFd krOnnt|d }nd}|||7}q |S) zCInterpret a string as a base-36 number as per 454 manual (PRIVATE).rNr`rS9AZaz)zip _powers_of_36ord)stringtotalcpowervalr2r2r3_string_as_base_36srcCst|dd}t|dS)zBExtract coordinates from last 5 characters of read name (PRIVATE). Ni)rdivmod) read_namenumberr2r2r3r/s r)ip$i0*iQi<cCsTg}t|dd}tD]}t||\}}||q |||dd7<|S)zs  rcCs t|dS)z(Extract region from read name (PRIVATE).r )int)rr2r2r3rJs rcCs<d}t|}d|}t|}||}t||\}}} |dks(|ddkr.td|||d|7}||d|} || } | t| kr]ddl} ddlm } | d | | || 7}|||| d 7}|| d d} | rd| } || } | t| krddl} ddlm } | d | | || 7}|S) zDExtract the next read in the file as a raw (bytes) string (PRIVATE).z>2HIr6r:r rrlNr r;r<r=) rrrrrrrrrrr)r r-rArBrCrDrawrGrHrIr1padrrr2r2r3_sff_read_raw_recordOsN       rc@s8eZdZdZddZddZddZdd Zd d Zd S) _AddTellHandleaWrapper for handles which do not support the tell method (PRIVATE). Intended for use with things like network handles where tell (and reverse seek) are not supported. The SFF file needs to track the current offset in order to deal with the index block. cCs||_d|_dS)Nr)_handle_offset)selfr r2r2r3__init__s z_AddTellHandle.__init__cCs"|j|}|jt|7_|SN)rrrr)rlengthr"r2r2r3rs z_AddTellHandle.readcCs|jSr)rrr2r2r3r@sz_AddTellHandle.tellcCs(||jkr td|j||jdS)NzCan't seek backwards)r RuntimeErrorrr)rrFr2r2r3r>s z_AddTellHandle.seekcCs |jSr)rcloserr2r2r3rs z_AddTellHandle.closeN) __name__ __module__ __qualname____doc__rrr@r>rr2r2r2r3rs rcs2eZdZdZd fdd ZddZdd ZZS) SffIteratorz0Parser for Standard Flowgram Format (SFF) files.NFcs,|durtdtj|ddd||_dS)avIterate over Standard Flowgram Format (SFF) reads (as SeqRecord objects). - source - path to an SFF file, e.g. from Roche 454 sequencing, or a file-like object opened in binary mode. - alphabet - optional alphabet, unused. Leave as None. - trim - should the sequences be trimmed? The resulting SeqRecord objects should match those from a paired FASTA and QUAL file converted from the SFF file using the Roche 454 tool ssfinfo. i.e. The sequence will be mixed case, with the trim regions shown in lower case. This function is used internally via the Bio.SeqIO functions: >>> from Bio import SeqIO >>> for record in SeqIO.parse("Roche/E3MFGYR02_random_10_reads.sff", "sff"): ... print("%s %i" % (record.id, len(record))) ... E3MFGYR02JWQ7T 265 E3MFGYR02JA6IL 271 E3MFGYR02JHD4H 310 E3MFGYR02GFKUC 299 E3MFGYR02FTGED 281 E3MFGYR02FR9G7 261 E3MFGYR02GAZMS 278 E3MFGYR02HHZ8O 221 E3MFGYR02GPGB1 269 E3MFGYR02F7Z7G 219 You can also call it directly: >>> with open("Roche/E3MFGYR02_random_10_reads.sff", "rb") as handle: ... for record in SffIterator(handle): ... print("%s %i" % (record.id, len(record))) ... E3MFGYR02JWQ7T 265 E3MFGYR02JA6IL 271 E3MFGYR02JHD4H 310 E3MFGYR02GFKUC 299 E3MFGYR02FTGED 281 E3MFGYR02FR9G7 261 E3MFGYR02GAZMS 278 E3MFGYR02HHZ8O 221 E3MFGYR02GPGB1 269 E3MFGYR02F7Z7G 219 Or, with the trim option: >>> with open("Roche/E3MFGYR02_random_10_reads.sff", "rb") as handle: ... for record in SffIterator(handle, trim=True): ... print("%s %i" % (record.id, len(record))) ... E3MFGYR02JWQ7T 260 E3MFGYR02JA6IL 265 E3MFGYR02JHD4H 292 E3MFGYR02GFKUC 295 E3MFGYR02FTGED 277 E3MFGYR02FR9G7 256 E3MFGYR02GAZMS 271 E3MFGYR02HHZ8O 150 E3MFGYR02GPGB1 221 E3MFGYR02F7Z7G 130 Nz,The alphabet argument is no longer supportedbSFF)moder!)rsuperrr)rsourcealphabetr __class__r2r3rsA zSffIterator.__init__cCsJzd|krtd|Wn tyt|}Ynw||}|S)z9Start parsing the file, and return a SeqRecord generator.rzNot at start of file, offset %i)r@rAttributeErrorriterate)rr recordsr2r2r3parses    zSffIterator.parseccs|j}t|\}}}}}}} d} t| } d|} t| } dtdks(Jdtdks1Jdtdks:J| ddksBJt|D]2}|ro||kro||}|dr`|d|d7}|ddkshJ||d}t|||| |VqFt|||d S) z.Parse the file and generate SeqRecord objects.r5r6rr7r8r9r rN) rr4rrr?r@r>r _check_eof)rr rr+r(r)r*r-r/r0rArBrCrDrrFr2r2r3rs>      zSffIterator.iterate)NF)rrrrrrr __classcell__r2r2rr3rs F rcCs|}d}d}|r>||kr>||krtd||||f||||||}||kr>td|||||f|drMd|d}||}|dkra|ddtkratd ||f|ry|syddl}dd lm}|d ||dS|t |krddl}dd lm}|d ||f||}|ddkrtd ||df|d}|tkrtd||rtd|dS)zCheck final padding is OK (8 byte alignment) and file ends (PRIVATE). Will attempt to spot apparent SFF file concatenation and give an error. Will not attempt to seek, only moves the handle forward. rzHGap of %i bytes after final record end %i, before %i where index starts?z$Wanted %i, got %i, index is %i to %ir rTNzYour SFF file is invalid, post index %i byte null padding region ended '.sff' which could be the start of a concatenated SFF file? See offset %ir z]Your SFF file is technically invalid as it is missing a terminal %i byte null padding region.zSYour SFF file is invalid, post index %i byte null padding region contained data: %rz%Wanted offset %i %% 8 = %i to be zerozZAdditional data at end of SFF file, perhaps multiple SFF files concatenated? See offset %iz1Additional data at end of SFF file, see offset %i) r@rrrrrrrrr)r r(r)rFextrar1rrr2r2r3r$sv          rcs eZdZdZfddZZS)_SffTrimIteratorzFIterate over SFF reads (as SeqRecord objects) with trimming (PRIVATE).cstj|dddS)NT)r)rr)rrrr2r3rxsz_SffTrimIterator.__init__)rrrrrrr2r2rr3rusrcsBeZdZdZdfdd ZddZdd Zd d Zd d ZZ S) SffWriterzSFF file writer.TNcs,t|d||_|rg|_dSd|_dS)a~Initialize an SFF writer object. Arguments: - target - Output stream opened in binary mode, or a path to a file. - index - Boolean argument, should we try and write an index? - xml - Optional string argument, xml manifest to be recorded in the index block (see function ReadRocheXmlManifest for reading this data). wbN)rr_xml_index)rtargetindexxmlrr2r3rs    zSffWriter.__init__cCszt||_Wnty$d|_t|jdrt|jds"tddYnw|jdurBt|jdr6t|jdsBddl}|dd|_d|_ d|_ t|dsQt |}zt |}Wn t ybd}Ynw|durktdz|jd d |_|jd d |_t|j|_Wn tytd dw|||d }|D] }|||d 7}q|jdkr|j}|jd||_||j|n||jksJ|jdur||S)z>Use this to write an entire file containing the given records.rr>r@zA handle with a seek/tell methods is required in order to record the total record count in the file header (once it is known at the end).NzNA handle with a seek/tell methods is required in order to record an SFF index.nextzMust have at least one sequencerqr r/zMissing SFF flow informationr)r_number_of_readsrhasattrr rrrr _index_start _index_lengthiterr StopIterationryencode _key_sequence _flow_chars_number_of_flows_per_readKeyError write_header write_recordr@r> _write_index)rrrrrrFr2r2r3 write_filesp                zSffWriter.write_filec Csrt|j|jks J|j}|j||_|jdur"|j}nddl m }d|d}|d7}|d7}|}t|}d}t |}| t||d}d t |ksYJ|jd}|jD]v\} } | } | d } | | 8} | d } | | 8} | d }| |8} | | | || krtd | | | || f| d |d | d | f\} }} } | d kr| d kr|d kr| d kstd | | | || f| | t |d| || | d |t| d 7}qc||||_|jdrd|jd}| t|nd}|} | |j|j|krtd| |j|j|f||j| t |ddddd||||d||| dS)Nr) __version__z) zD zB z>I4BLLz>6Br_rarbrcz%i -> %i %i %i %ir z%i vs %i + %i + %iitfm.rQrRrS)rrrr sortr@rrrrrrrwriterrpackrr>r)rr rrxml_lenr!rUrV index_lenrNrFrgrjrirhr1r2r2r3rs              zSffWriter._write_indexcCst|j}d|j|f}t|ddkrd}n dt|d}t||}|ddks0Jt|ddddd|j|j|j|||jd|j |j}|j |t |dS)zWrite the SFF file header.z>I4BQIIHHHB%is%isr riffs.rN) rrrrrrrrrrr rr)rr,r!r1r+headerr2r2r3r(s2  zSffWriter.write_headerc Cs |j}t|}t|j}t|}z|jd}Wnty+td|jdwz$|j d}|j d}|j |j dksK|j |j dkrOtdWnty`td |jdt yktd dwzR|j d } | d kr~td |j| r| d7} |j d} | d krtd|j|j d} | d krtd|j| r| d7} |j d} | d krtd|jWntytd|jdw|j dur|j} | dkrd dl}|d|| fd|_ n |j ||jfd|}t|dd kr d }n dt|d}t||}|dd ks#Jt||||| | | | | t|}t||ks=Jd|j}t|}d|}|tj|g|Rtj|g|R|tj|g|R7}||dd}|ryd|}|j|t|dS)zmWrite a single additional record to the output file. This assumes the header has been done. rzz(Missing PHRED qualities information for Nrorprqr/z'Records have inconsistent SFF flow dataz!Missing SFF flow information for zHeader not written yet?rJrz&Negative SFF clip_qual_left value for rrKz'Negative SFF clip_qual_right value for rLz)Negative SFF clip_adapter_left value for rMz*Negative SFF clip_adapter_right value for z%Missing SFF clipping information for l| xzzRead %s has file offset %i, which is too large to store in the Roche SFF index structure. No index block will be recorded.z >2HI4H%isr r6rmr<)rwrrbytesrr~letter_annotationsrrryrrrrr r@rrrrrrrrr)rrrNname_lenrrIrrorprJrKrLrMrFrrAr1rGr"rCrDrr2r2r3rVs                     zSffWriter.write_record)TN) rrrrrrrrrrr2r2rr3r|s>Y.r__main__) run_doctest)verbose)F)*rrrrrBio.Seqr Bio.SeqRecordr Interfacesrrrrrrrrdr4rPrZr^rkcompilerrr?rrrrrrrrrrrrr Bio._utilsrr2r2r2r3sVd     j[e$ 9   3Q_