Xf3UdZddlmZddlmZddlmZddlmZddlm Z ddlm Z Gdd eZ d Z d Z d Zd ZdZdZdZdZdZdZdZGdde ZdS)aImplementations of Biopython-like Seq objects on top of BioSQL. This allows retrieval of items stored in a BioSQL database using a biopython-like SeqRecord and Seq interface. Note: Currently we do not support recording per-letter-annotations (like quality scores) in BioSQL. )Optional) SeqFeature)Seq)SequenceDataAbstractBaseClass)_RestrictedDict) SeqRecordc4eZdZdZdZdfd ZdZdZxZS)_BioSQLSequenceDataz9Retrieves sequence data from a BioSQL database (PRIVATE).) primary_idadaptor_lengthstartrc||_||_||_||_t dS)aUCreate a new _BioSQLSequenceData object referring to a BioSQL entry. You wouldn't normally create a _BioSQLSequenceData object yourself, this is done for you when retrieving a DBSeqRecord object from the database, which creates a Seq object using a _BioSQLSequenceData instance as the data provider. N)r r r rsuper__init__)selfr r rlength __class__s -lib/python3.11/site-packages/BioSQL/BioSeq.pyrz_BioSQLSequenceData.__init__#s=%    c|jS)z"Return the length of the sequence.)r rs r__len__z_BioSQLSequenceData.__len__1s |rcdt|trE||j\}}}t t |||}|dkrdSn|}|dkr ||jz }|dkrt |n||jkrt ||j|j |j |z|j |zdz}t|S|dkr}|dkrS||jkrH|j|j |j |j |jz}| dSt|j |j|j |z|S|j|j |j |z|j |z} | dd| dS)z@Return a subsequence as a bytes or a _BioSQLSequenceData object.rrASCIIN) isinstancesliceindicesr lenrange IndexErrorr get_subseq_as_stringr rordencoder ) rkeyrendstepsizeicsequencefulls r __getitem__z_BioSQLSequenceData.__getitem__5s c5 ! ! "{{4<88 E3uUC..//DqyysA1uuT\!q55$S//)dl"" oo% 11aa!1CAq66M 199zzddl22<<<OTZdl1J w///+OT\4:3Et <44e!3TZ#5ED$<&&w// /r)rr) __name__ __module__ __qualname____doc__ __slots__rrr. __classcell__)rs@rr r sfCC=I      &0&0&0&0&0&0&0rr c|d|f}|sdSt|dkr tdt|d|d\}t|S)Nz5SELECT length FROM biosequence WHERE bioentry_id = %srExpected 1 response, got .r)execute_and_fetchallr ValueErrorint)r r seqs given_lengths r_retrieve_seq_lenr=^su  ' '?*  D t 4yyA~~ASYYAAABBB1gO\ |  rc|d|f}|sdSt|dkr tdt|d|d\}}} t|}t|}||krtd|d|d}n#t$r|td |d|d |f}t|dkr tdt|d|d\}}}|rtd |dt|}d }~YnwxYw~|r"t ||d| }t |St d|S)NzLSELECT alphabet, length, length(seq) FROM biosequence WHERE bioentry_id = %srr6r7rz''length' differs from sequence length, z, Tz$Expected 'length' to be 'None', got zDSELECT alphabet, length, seq FROM biosequence WHERE bioentry_id = %sz*Expected 'seq' to have a falsy value, got F)rrr)r8r r9r: TypeErrorr r) r r r;moltyper<rhave_seqseqdatas r _retrieve_seqrEks  ' 'V    D  4yyA~~ASYYAAABBB$(G!G\6V<(( \ ! !R,RR&RR    MFMMMNN N++ R M   t99>>ETEEEFF F%)!W"s  RP#PPPQQ Q\"" CC (":waOOO4yy4''''s;BBD76D7cg}|d|f}|D]2\}}}|r|dkr|d|}n|}||d|3|S)zBRetrieve the database cross references for the sequence (PRIVATE).z{SELECT dbname, accession, version FROM bioentry_dbxref join dbxref using (dbxref_id) WHERE bioentry_id = %s ORDER BY "rank"0r7:)r8append)r r _dbxrefsdbxrefsdbname accessionversionvs r_retrieve_dbxrefsrPsH**   G'.))" 7  w#~~((w((AAA6A(((( Orc rd}|||f}g}|D]\}}}|d|f}i} |D].\} } | | g| /|d|f}|D]5\} } | d| } | dg| 6|d|f}g} |D]\}}}}|r|dz}|dkrd}|d vrtd |d ||.|,||kr&ddl}dd lm}|d |||fz||tj }|tj }| ||||f|d|f}i}|D](\}}}}|r|dkr|d|}n|}|dkrd}||f||<)tj|}||_ | |_ t| dkrn(t| dkrz| d\}}}}t|||_||d\}}tj|||_||j_||j_||j_ng}| D]N}|\}}}}||d\}}|tj|||||Od|D}t|dkrd|vr |ddd}tj|d|_|||S)NzSELECT seqfeature_id, type.name, "rank" FROM seqfeature join term type on (type_term_id = type.term_id) WHERE bioentry_id = %s ORDER BY "rank"zvSELECT name, value FROM seqfeature_qualifier_value join term using (term_id) WHERE seqfeature_id = %s ORDER BY "rank"zSELECT dbxref.dbname, dbxref.accession FROM dbxref join seqfeature_dbxref using (dbxref_id) WHERE seqfeature_dbxref.seqfeature_id = %s ORDER BY "rank"rHdb_xrefzeSELECT location_id, start_pos, end_pos, strand FROM location WHERE seqfeature_id = %s ORDER BY "rank"rr)rNzInvalid strand z% found in database for seqfeature_id )BiopythonWarningzz%_retrieve_features..,s...Aqx...rrSjoin)r8 setdefaultrIr9warningsBiorTwarnrUnknownPosition_seqfeature_id qualifiersr "_retrieve_location_qualifier_valuelocation_operatorgetSimpleLocationlocationrWrYrXCompoundLocation)r r sqlresultsseq_feature_list seqfeature_idseqfeature_typeseqfeature_rankqvsrfqv_nameqv_valuevalue locations location_idrr'rWrarTremote_resultslookuprLrMrNrOfeaturelocsrkstrandss r_retrieve_featuresr~s  **3 >>G;B~)~)7 **      !$ @ @ GX  ! !'2 . . 5 5h ? ? ? ?**     "% ? ? GX++++E  ! !)R 0 0 7 7 > > > >..      07 @ @ +KV  {{^++ j*0&&--A S_u000000 '*/m)DE$}"244{ 022   k5#v> ? ? ? ? 55 (     7E . . 3KG 7c>> ,,7,,||#)1+F;  '_===!.' y>>Q    ^^q .7l +KV)K))G %%jjlCCOFG)8DDG &,G  #&,G  ##*G  D%  2:/ UC"(**[,"G"G -s6wv/....G7||q  R7]]DDbDz):4HHG  (((( rcd|d|f} |dS#t$rYdSwxYw)NzASELECT value FROM location_qualifier_value WHERE location_id = %srrU)execute_and_fetch_col0r")r rxrvs rrgrg:sO  * *K   EQx rrs ! //cji}|t|||t|||t|||t ||||t |||SN)update_retrieve_alphabet_retrieve_qualifier_value_retrieve_reference_retrieve_taxon_retrieve_comment)r r taxon_id annotationss r_retrieve_annotationsrEsK)':>>???0*EEFFF*7J??@@@w HEEFFF(*==>>> rcf|d|f}t|dkr tdt|d|d}t|dkr tdt|d|d}|dkrd}n|d krd }n |d krd }nd}|d |iSiS) Nz7SELECT alphabet FROM biosequence WHERE bioentry_id = %srr6r7rz%Expected 1 alphabet in response, got dnaDNArnaRNAprotein molecule_type)r8r r9)r r rn alphabetsalphabetrs rrrOs**AJ=G 7||qDS\\DDDEEE I 9~~RYRRRSSS|H5 U   Y  !   // rc|d|f}i}|D]H\}}|dkrd}n|dkrd}n|dkrd}||g|I|S)NzqSELECT name, value FROM bioentry_qualifier_value JOIN term USING (term_id) WHERE bioentry_id = %s ORDER BY "rank"keywordkeywords date_changeddatesecondary_accession accessions)r8r`rI)r r rsrfnamervs rrrgs  & &     CJ66 e 9  DD ^ # #DD * * *DdB''..u5555 rcb|d|f}g}|D]\}}}}}} } tj} ||"||dz}tj||g| _|r|| _|r|| _|| _| dkr| | _n | dkr| | _ | | |rd|iSiS)NzSELECT start_pos, end_pos, location, title, authors, dbname, accession FROM bioentry_reference JOIN reference USING (reference_id) LEFT JOIN dbxref USING (dbxref_id) WHERE bioentry_id = %s ORDER BY "rank"rPUBMEDMEDLINE references) r8r Referencerjrkauthorstitlejournal pubmed_id medline_idrI) r r refsrrr'rkrrrLrM references rrr|s  ' '     DJCG%%?sHeWfi(**  3?  ",";E3"G"G!HI   ( 'I   $#IO$  X  "+I   y #,I )$$$$j)) rci}|d|f}|r |d|d<|d|f}|r |d|d<|d|f}|r|dr|ddkr |d|d<g}|r<|d |f\}} } || krn|d|| }|<|r||d <|S) NzVSELECT name FROM taxon_name WHERE taxon_id = %s AND name_class = 'genbank common name'rsourcezRSELECT name FROM taxon_name WHERE taxon_id = %s AND name_class = 'scientific name'organismz3SELECT ncbi_taxon_id FROM taxon WHERE taxon_id = %srG ncbi_taxidzSELECT taxon_name.name, taxon.node_rank, taxon.parent_taxon_id FROM taxon, taxon_name WHERE taxon.taxon_id=taxon_name.taxon_id AND taxon_name.name_class='scientific name' AND taxon.taxon_id = %staxonomy)r execute_oneinsert) r r ra common_namesscientific_names ncbi_taxidsrrrankparent_taxon_ids rrrsE A11 2  L &"1o( 55 .   ,(+* 00={K){1~)+a.C*?*?%a.,H #&-&9&9 ' K ' ' #dO  & & 4   "! #$! * HrcX|d|f}d|D}|rd|iSiS)NzESELECT comment_text FROM comment WHERE bioentry_id=%s ORDER BY "rank"cg|] }|d S)rr[)r\comms r z%_retrieve_comment..s(((DQ(((rcomment)r8)r r rscommentss rrrsL  & &O    C)(C(((H8$$ rc|eZdZdZdZdZdZdZeeeedZ ede e fdZ e j d e e dd fd Z e jdd Z d ZdZdZeeeedZedejfdZej d eejdd fdZejddZd S) DBSeqRecordz4BioSQL equivalent of the Biopython SeqRecord object.c 4||_||_|jd|jf\|_|_|_}}|_|_|_|r|dkr |d||_ n||_ t||}t||_ dS)a8Create a DBSeqRecord object. Arguments: - adaptor - A BioSQL.BioSeqDatabase.Adaptor object - primary_id - An internal integer ID used by BioSQL You wouldn't normally create a DBSeqRecord object yourself, this is done for you when using a BioSeqDatabase object zSELECT biodatabase_id, taxon_id, name, accession, version, identifier, division, description FROM bioentry WHERE bioentry_id = %srGr7r?N) _adaptor _primary_idr_biodatabase_id _taxon_idr _identifier _division descriptionidr=r_per_letter_annotations)rr r rMrNrs rrzDBSeqRecord.__init__s  % M % % &       N I     N    w#~~"..W..DGGDG #7J77'6f'E'E'E$$$rcnt|dst|j|j|_|jS)N_seq)hasattrrErrrrs r __get_seqzDBSeqRecord.__get_seqs3tV$$ G%dmT5EFFDIyrc||_dSrr)rrCs r __set_seqzDBSeqRecord.__set_seqs  rc |`dSrrrs r __del_seqzDBSeqRecord.__del_seqs IIIrz Seq objectreturncnt|dst|j|j|_|jS)zDatabase cross references.rJ)rrPrrrJrs rrKzDBSeqRecord.dbxrefs s5tZ(( O-dmT=MNNDM}rrvNc||_dSrrJrrvs rrKzDBSeqRecord.dbxrefs's  rc |`dSrrrs rrKzDBSeqRecord.dbxrefs+s MMMrcnt|dst|j|j|_|jS)N _features)rr~rrrrs r__get_featureszDBSeqRecord.__get_features/s3t[)) Q/ t?OPPDN~rc||_dSrr)rfeaturess r__set_featureszDBSeqRecord.__set_features4s !rc |`dSrrrs r__del_featureszDBSeqRecord.__del_features7s NNNrFeaturesct|dsQt|j|j|j|_|jr|j|jd<|jr|j|jd<|jS)z Annotations. _annotationsgidata_file_division)rrrrrrrrrs rrzDBSeqRecord.annotations<sxt^,, I 5 t/!!D  ;*.*:!$'~ I:>.!"67  rc*|r ||_dSi|_dSrrrs rrzDBSeqRecord.annotationsIs&  # %D    "D   rc |`dSrrrs rrzDBSeqRecord.annotationsPs    r)rN)r/r0r1r2r_DBSeqRecord__get_seq_DBSeqRecord__set_seq_DBSeqRecord__del_seqpropertyrCliststrrKsetterdeleter_DBSeqRecord__get_features_DBSeqRecord__set_features_DBSeqRecord__del_featuresrr_AnnotationsDictrrr[rrrrs>>&F&F&FP  (9iL A AC cX  ^T#Y4^ __ """x SSH  !Y7 ! ! !X !#)*D!E#$#### rrN)r2typingrrbrBio.Seqrr Bio.SeqRecordrrr r=rErPr~rgrrrrrrrr[rrrs111111))))))######=0=0=0=0=07=0=0=0@   .(.(.(b&HHHV0*$$$N4 4 4 n   kkkkk)kkkkkr