&hxdZddlmZddlmZddlmZddlmZddlm Z ddl m Z Gdd Z Gd d Z y ) a'Load biopython objects into a BioSQL database for persistent storage. This code makes it possible to store biopython objects in a relational database and then retrieve them back. You shouldn't use any of the classes in this module directly. Rather, call the load() method on a database object. )gmtime)strftime)Entrez)UndefinedSequenceError)UnknownPosition)crc64ceZdZdZddZdZd dZd!dZdZdZ d Z d Z d"d Z d Z d ZdZdZdZdZdZdZ d#dZdZdZdZdZdZdZdZdZdZdZy)$DatabaseLoaderz=Object used to load SeqRecord objects into a BioSQL database.c.||_||_||_y)aInitialize with connection information for the database. Creating a DatabaseLoader object is normally handled via the BioSeqDatabase DBServer object, for example:: from BioSQL import BioSeqDatabase server = BioSeqDatabase.open_database(driver="MySQLdb", user="gbrowse", passwd="biosql", host="localhost", db="test_biosql") try: db = server["test"] except KeyError: db = server.new_database("test", description="For testing GBrowse") N)adaptordbidfetch_NCBI_taxonomy)selfr r rs \/mounts/lovelace/software/anaconda3/envs/py312/lib/python3.12/site-packages/BioSQL/Loader.py__init__zDatabaseLoader.__init__$s&  #6 c  |j|}|j|||j|||j|||j |||j j dd}t|ttt|D]\}}|j||||j||tt|jD]$}|j|}|j|||&y)z-Load a Biopython SeqRecord into the database. referencesN)_load_bioentry_table_load_bioentry_date_load_biosequence _load_comment _load_dbxrefs annotationsgetziplistrangelen_load_reference_load_annotationsfeatures_load_seqfeature)rrecord bioentry_idr referencerankseq_feature_num seq_features rload_seqrecordzDatabaseLoader.load_seqrecord;s//7    5 v{3 6;/ 6;/''++L"= ":tE#j/4J/KL ?OIt  D+ > ? v{3$S%9: MO ///:K  ! !+ L MrNc|jjd|f}|r|dS|jjd||f|jjdS)axReturn identifier for the named ontology (PRIVATE). This looks through the onotology table for a the given entry name. If it is not found, a row is added for this ontology (using the definition if supplied). In either case, the id corresponding to the provided name is returned, so that you can reference it in another table. z0SELECT ontology_id FROM ontology WHERE name = %srz6INSERT INTO ontology(name, definition) VALUES (%s, %s)ontology)r execute_and_fetch_col0executelast_id)rname definitionoidss r_get_ontology_idzDatabaseLoader._get_ontology_idJs`||22 >  7N  DtZFX ||##J//rcXd}|g}|r|dz }|j||jj||}t|dkDrt d|d|t|dk(r|ddSd}|jj |||||f|jj dS) aGet the id that corresponds to a term (PRIVATE). This looks through the term table for a the given term. If it is not found, a new id corresponding to this term is created. In either case, the id corresponding to that term is returned, so that you can reference it in another table. The ontology_id should be used to disambiguate the term. z(SELECT term_id FROM term WHERE name = %sz AND ontology_id = %szMultiple term ids for z: rzTINSERT INTO term (name, definition, identifier, ontology_id) VALUES (%s, %s, %s, %s)term)appendr execute_and_fetchallr ValueErrorr/r0)rr1 ontology_idr2 identifiersqlfields id_resultss r _get_term_idzDatabaseLoader._get_term_id]s9  * *C MM+ &\\66sFC z?Q 5dV2j^LM M _ !a=# #+  LL tZ[&Q R<<''/ /rcv|jjd|||f|jjdS)z,Insert a dbxref and return its id (PRIVATE).zBINSERT INTO dbxref(dbname, accession, version) VALUES (%s, %s, %s)dbxref)r r/r0)rdbname accessionversions r _add_dbxrefzDatabaseLoader._add_dbxref|s8  P Y ( ||##H--rc d}d|jvrZt|jdtr.t|jddk(r"|jdd}n|jd}|sj|jD][}|j dk(rFt |di}d|vr5|jdD]#}|jdst|d d}n|s[n |jd dd } |jddd }|r|j|||S|s|sy|r$|jjd |f}|r|dS|rK|jjd |f}t|dkDrtdt||fz|r|dSg} |jjdgD]} | j!dd| g| rd| dd<| j!dd|jd gd|jvr!| j!dd|jdgd|jvr!| j!dd|jdg|| dd<|jj#dd} | sd} | dz } |jj#dd} | sd} | dt| zzdz } d}| D]t}|jj%d||d|d| | f|jj'd}|jj%d||ddd f| dz } | dz} |}v|r|jj%d|fS#t$rd}YpwxYw#t$rd}YowxYw)a!Get the taxon id for this record (PRIVATE). Arguments: - record - a SeqRecord object This searches the taxon/taxon_name tables using the NCBI taxon ID, scientific name and common name to find the matching taxon table entry's id. If the species isn't in the taxon table, and we have at least the NCBI taxon ID, scientific name or common name, at least a minimal stub entry is created in the table. Returns the taxon id (database key for the taxon table, not an NCBI taxon ID), or None if the taxonomy information is missing. See also the BioSQL script load_ncbi_taxonomy.pl which will populate and update the taxon/taxon_name tables with the latest information from the NCBI. N ncbi_taxidr6rsource qualifiersdb_xrefztaxon:organismzRSELECT taxon_id FROM taxon_name WHERE name_class = 'scientific name' AND name = %sz8SELECT DISTINCT taxon_id FROM taxon_name WHERE name = %szTaxa: %d species have name %rtaxonomygenusspecies subspeciesvariantvarietas!SELECT MAX(left_value) FROM taxonz"SELECT MAX(right_value) FROM taxonzqINSERT INTO taxon(parent_taxon_id, ncbi_taxon_id, node_rank, left_value, right_value) VALUES (%s, %s, %s, %s, %s)taxonzTINSERT INTO taxon_name(taxon_id, name, name_class)VALUES (%s, %s, 'scientific name')zPINSERT INTO taxon_name(taxon_id, name, name_class)VALUES (%s, %s, 'common name'))r isinstancerr r#typegetattrrJ startswithintKeyError _get_taxon_id_from_ncbi_taxon_idr r.r:rr8 execute_oner/r0)rr% ncbi_taxon_idfqualsrKscientific_name common_nametaxalineagec left_valueright_start_value right_valueparent_taxon_idrXtaxon_ids r _get_taxon_idzDatabaseLoader._get_taxon_ids. 6-- -&,,\:DAv)),78A=$*$6$6|$DQ$GM & 2 2< @ __ 66X%#A|R8E E)'(||I'>&G&11(;03GABK0@ %&!  #$00  'E LL /!%(E!Hj+N   ||++G4H LL 558DS>*  !OJ 1 K&O# '$  LL 1;'  o #"O # K s$M +M MM M-,M-cddjfd|Dj}||jk7rtd|d|S)ajMap Entrez name terms to those used in taxdump (PRIVATE). We need to make this conversion to match the taxon_name.name_class values used by the BioSQL load_ncbi_taxonomy.pl script. e.g.:: "ScientificName" -> "scientific name", "EquivalentName" -> "equivalent name", "Synonym" -> "synonym", cL|jrd|jzS|S)z$Add a space before a capital letter. )isupperlower)letters r add_spacez1DatabaseLoader._fix_name_class..add_spaceAs"~~V\\^++ rc3.K|] }|ywNr).0rtrus r z1DatabaseLoader._fix_name_class..HsEv6*Esz!Expected processed entrez_name, 'z"' to only have lower case letters.)joinstriprsr:)r entrez_nameanswerrus @r_fix_name_classzDatabaseLoader._fix_name_class+sV, EEEKKM V\\^ #3F8;]^  rc|sy|jjd||f}g}g}|D]L}|d}|d}||k\r|dz }||kDr|dz }|j||df|j||dfNt|dd}t|d d}|jj d ||jj d |y) z>Update the left and right taxon values in the table (PRIVATE).Nz^SELECT left_value, right_value, taxon_id FROM taxon WHERE right_value >= %s or left_value > %sr6rrWc |dSNrrxs rz@DatabaseLoader._update_left_right_taxon_values..qs adrT)keyreversec |dSrrrs rrz@DatabaseLoader._update_left_right_taxon_values..rs AaDrz4UPDATE taxon SET left_value = %s WHERE taxon_id = %sz5UPDATE taxon SET right_value = %s WHERE taxon_id = %s)r r9r8sorted executemany)rrirows right_rows left_rowsrow new_rightnew_lefts r_update_left_right_taxon_valuesz.DatabaseLoader._update_left_right_taxon_valuesOs ||00 9  $     1CAI1vHJ&Q *$A    y#a&1 2   hA/ 0 1JNDI 9.$G    BI    CZ rc |s td|jjdt|f}|r|dSd}d}d}d}d} d} d} d} g} |r| j d|f|r| j d|f|j rEt jd|d }t j|}t|d k(r |dd t|k7rtd |d|dd |j|dd\}} } | } | d z} t|dd}t|ddd}t|ddd}dt|ddfg} |ddjD]T\}}|j|}t|ts|g}|D]&}t|ts| j ||f(Vn |j#| |jj%d|||||| | f|jj'd}| D]'\}}|jj%d||dd|f)|S#t $rYwxYw)aGet the taxon id for record from NCBI taxon ID (PRIVATE). Arguments: - ncbi_taxon_id - string containing an NCBI taxon id - scientific_name - string, used if a stub entry is recorded - common_name - string, used if a stub entry is recorded This searches the taxon table using ONLY the NCBI taxon ID to find the matching taxon table entry's ID (database key). If the species isn't in the taxon table, and the fetch_NCBI_taxonomy flag is true, Biopython will attempt to go online using Bio.Entrez to fetch the official NCBI lineage, recursing up the tree until an existing entry is found in the database or the full lineage has been fetched. Otherwise the NCBI taxon ID, scientific name and common name are recorded as a minimal stub entry in the taxon and taxon_name tables. Any partial information about the lineage from the SeqRecord is NOT recorded. This should mean that (re)running the BioSQL script load_ncbi_taxonomy.pl can fill in the taxonomy lineage. Returns the taxon id (database key for the taxon table, not an NCBI taxon ID). z-Expected a non-empty value for ncbi_taxon_id.z3SELECT taxon_id FROM taxon WHERE ncbi_taxon_id = %srNrRzscientific namez common namerOXML)dbidretmoder6TaxIdz.ncbi_taxon_id different from parent taxon id. z versus LineageExRank GeneticCodeGCIdMitoGeneticCodeMGCIdScientificName OtherNameszINSERT INTO taxon(parent_taxon_id, ncbi_taxon_id, node_rank, genetic_code, mito_genetic_code, left_value, right_value) VALUES (%s, %s, %s, %s, %s, %s, %s)rXzFINSERT INTO taxon_name(taxon_id, name, name_class) VALUES (%s, %s, %s)rN)r:r r.r]r8rrefetchreadr str_get_taxon_id_from_ncbi_lineageitemsrrYrr^rr/r0)rrardrermrlr( genetic_codemito_genetic_codeparent_left_valueparent_right_valuerirk species_nameshandletaxonomic_record name_classnamesr1s rr_z/DatabaseLoader._get_taxon_id_from_ncbi_taxon_id{s8LM M<<66 AC DVCX  A;     !     "3_!E F   -!= >  # #]]j]ERF%{{62 #$)#A&w/3}3EE$HW_`pqr`st{`|_}~88$Q' 4 #%& 0 014 +A.v67"#3A#6}#Ef#MN $'(8(;t |j dtr!|j dr|j dd}|j|}d|j vr|j d}n |j}t|dd}|j jd}d }|jj||j||j|||||f|jjd S#t$r|j}d}YwxYw) zFill the bioentry table with sequence information (PRIVATE). Arguments: - record - SeqRecord object to add to the database. .r6r accessionsgi descriptionNdata_file_divisiona7 INSERT INTO bioentry ( biodatabase_id, taxon_id, name, accession, identifier, division, description, version) VALUES ( %s, %s, %s, %s, %s, %s, %s, %s)bioentry)rcountsplitr]r:rrYrrnr[rr r/r r1r0) rr%rDrErmr<rdivisionr=s rrz#DatabaseLoader._load_bioentry_table[sr 99??3 1 $!'!5 Iw g,  IG F.. .6--l;TB""<0**<8;I %%f- 6%% %++D1JJfmT: %%))*>?*      ||##J//A "II  s EE76E7c.|jjdtdtj }t |t r|d}|jd}|jd|}d}|jj||||fy)zAdd the effective date of the entry into the database (PRIVATE). record - a SeqRecord object with an annotated date bioentry_id - corresponding database identifier datez%d-%b-%YrAnnotation Tags date_changedzaINSERT INTO bioentry_qualifier_value (bioentry_id, term_id, value, "rank") VALUES (%s, %s, %s, 1)N) rrrrupperrYrr4r@r r/)rr%r&rannotation_tags_iddate_idr=s rrz"DatabaseLoader._load_bioentry_dates!!%%fhz68.L.R.R.TU dD !7D!223DE##N4FG & S;">?rc<|jy|jjdd}d|vrd}nd|vrd}n d|vrd}nd } t|j}d }|j j ||t|j||fy#t$rd}YCwxYw) zRecord SeqRecord's sequence and alphabet in DB (PRIVATE). Arguments: - record - a SeqRecord object with a seq property - bioentry_id - corresponding database identifier N molecule_typervDNAdnaRNArnaproteinunknownz`INSERT INTO biosequence (bioentry_id, version, length, seq, alphabet) VALUES (%s, 0, %s, %s, %s))seqrrrrr r/r )rr%r&ralphabetseq_strr=s rrz DatabaseLoader._load_biosequences ::  **..C M !H m #H - ' H H &**oG  ) S;FJJ("ST& G sB BBc|jjd}|syt|ts|g}t |D];\}}|j dd}d}|j j||||dzf=y)zRecord a SeqRecord's annotated comment in the database (PRIVATE). Arguments: - record - a SeqRecord object with an annotated comment - bioentry_id - corresponding database identifier commentN rqzKINSERT INTO comment (bioentry_id, comment_text, "rank") VALUES (%s, %s, %s)r6)rrrYr enumeratereplacer r/)rr%r&commentsindexrr=s rrzDatabaseLoader._load_comments%%)))4 (D) zH'1 INE7oodC0G'  LL {GUQY&G H Irc d}d}|jd}|jjD]\}}|dvr |j||}t |t t frOd} |D]G} t | ttfr/| dz } |jj|||t| | fHIt |ttfr)|jj|||t|fŒy) aRecord a SeqRecord's misc annotations in the database (PRIVATE). The annotation strings are recorded in the bioentry_qualifier_value table, except for special cases like the reference, comment and taxonomy which are handled with their own tables. Arguments: - record - a SeqRecord object with an annotations dictionary - bioentry_id - corresponding database identifier zUINSERT INTO bioentry_qualifier_value(bioentry_id, term_id, value) VALUES (%s, %s, %s)zaINSERT INTO bioentry_qualifier_value(bioentry_id, term_id, value, "rank") VALUES (%s, %s, %s, %s)r)rrrrHrr;rr6N) r4rrr@rYrtuplerr]r r/) rr%r&mono_sqlmany_sqltag_ontology_idrvalueterm_idr(entrys rr"z DatabaseLoader._load_annotationss #   '  //0AB ,,224 JCVV'''IG%$/"E!%#s4  ,,${GSZ&NEC:. $$X Wc%j/QR) rc |d}|jr'|jjd|jf}|s3|jr'|jjd|jf}|svg}|j|j |j fD]}|j|xsdtdj|}|jjd|f}|s|jr|jd|jd}n,|jr|jd |jd}nd}|jxsd} |j xsd} |j xsd} |jjd || | | f|jjd } n|d} |jrZd tt|jdj z} tt|jdj"}nd} d}d }|jj||| | ||d zfy)zRecord SeqRecord's annotated references in the database (PRIVATE). Arguments: - record - a SeqRecord object with annotated references - bioentry_id - corresponding database identifier NzlSELECT reference_id FROM reference JOIN dbxref USING (dbxref_id) WHERE dbname = 'MEDLINE' AND accession = %szkSELECT reference_id FROM reference JOIN dbxref USING (dbxref_id) WHERE dbname = 'PUBMED' AND accession = %szrvz1SELECT reference_id FROM reference WHERE crc = %sMEDLINErPUBMEDz\INSERT INTO reference (dbxref_id, location, title, authors, crc) VALUES (%s, %s, %s, %s, %s)r'r6zrINSERT INTO bioentry_reference (bioentry_id, reference_id, start_pos, end_pos, "rank") VALUES (%s, %s, %s, %s, %s)) medline_idr r. pubmed_idauthorstitlejournalr8rr{rFr/r0locationr]rstartend)rr'r(r&refssrbcrc dbxref_idrrr reference_idrrr=s rr!zDatabaseLoader._load_reference*s)   <<66?%%' D  ++<<66>$$& D A&& 9J9JJ )i( ) #C<<66CcVD## ,,Y 8L8LaP $$ ,,Xy7J7JAN  ''/4GOO+tE ''-2G LL /GUGS9    <<//   --l -T--.BC **6}*M >   +0.,QRBRS ||##L11rc |jjdk7r)ddl}ddlm}|j d|j z||jj}|r&|Dchc]}|jc}dhk(r|ddd}t|D]\}}|j||dz|y#t$rYswxYwcc}w)a4Load all of the locations for a SeqFeature into tables (PRIVATE). This adds the locations related to the SeqFeature into the seqfeature_location table. Fuzzies are not handled right now. For a simple location, ie (1..2), we have a single table row with seq_start = 1, seq_end = 2, location_rank = 1. For split locations, ie (1..2, 3..4, 5..6) we would have three row tables with:: start = 1, end = 2, rank = 1 start = 3, end = 4, rank = 2 start = 5, end = 6, rank = 3 r{rN)BiopythonWarningz-%s location operators are not fully supportedrQr6) roperatorwarningsBiorwarnlocation_operatorAttributeErrorpartsstrandr_insert_location)rrrrrrlocr(s rrz)DatabaseLoader._load_seqfeature_locationss$ ((F2 0 C//0$  && E2Scjj2rd:$B$KE"5) @ID#  ! !#tax ? @   3sAB, B;, B87B8c  t|jdz} t|j }|j xsd}d}|jr+|j|jxsd|j}nd}d} |jj| |||||||fy#t$r!t|jtrd}nYwxYw#t$r!t|j trd}nYwxYw)zAdd SeqFeature location to seqfeature_location table (PRIVATE). TODO - Add location operator to location_qualifier_value? r6NrrvzINSERT INTO location (seqfeature_id, dbxref_id, term_id,start_pos, end_pos, strand, "rank") VALUES (%s, %s, %s, %s, %s, %s, %s)) r]r TypeErrorrYrrrref_get_dbxref_idref_dbr r/) rrr(rrrr loc_term_idrr=s rrzDatabaseLoader._insert_locations '!+E hll#C%A  << ++HOO,Ar8<<PII 2  -KVTR  [ (../:  (,,8 s"B!C!'C  C 'C87C8c F|jd}|D]}|dk7ro|j||}||}t|ts|g}t t |D],}||}d} |j j| |||dz|f.w|j|||y)zInsert feature's (key, value) pair qualifiers (PRIVATE). Qualifiers should be a dictionary of the form:: {key : [value1, value2]} rrKrzgINSERT INTO seqfeature_qualifier_value (seqfeature_id, term_id, "rank", value) VALUES (%s, %s, %s, %s)r6N) r4r@rYrrr r r/_load_seqfeature_dbxref) rrJrr qualifier_keyqualifier_key_identriesqual_value_rankqualifier_valuer=s rrz*DatabaseLoader._load_seqfeature_qualifierss//0AB'$ WM  )#'#4#4!$5$ %]3!'40 'iG',S\':O&-o&>O, LL((),+a/+ *,,Z -F VI$ Wrc:t|D]p\}} |jddjddjd}|d}|dd}|D]*}|j ||} |j || |dz,ry#t$rt d|d dwxYw) aAdd SeqFeature's DB cross-references to the database (PRIVATE). Arguments: - dbxrefs - List, dbxref data from the source file in the format : - seqfeature_id - Int, the identifier for the seqfeature in the seqfeature table Insert dbxref qualifier data for a seqfeature into the seqfeature_dbxref and, if required, dbxref tables. The dbxref_id qualifier/value sets go into the dbxref table as dbname, accession, version tuples, with dbxref.dbxref_id being automatically assigned, and into the seqfeature_dbxref table as seqfeature_id, dbxref_id, and rank tuples. rqrvr:rr6NzParsing of db_xref failed: '')rrr Exceptionr:r_get_seqfeature_dbxref) rdbxrefsrr(r dbxref_datarrrDrs rr z&DatabaseLoader._load_seqfeature_dbxref=s(%W- PKD% T#mmC4< ++M9dQhO  P P T #?wa!HItS Ts ;BBcvd}|jj|||f}|r|dS|j||dS)aGet DB cross-reference for accession (PRIVATE). Arguments: - db - String, the name of the external database containing the accession number - accession - String, the accession of the dbxref data Finds and returns the dbxref_id for the passed data. The method attempts to find an existing record first, and inserts the data if there is no record. zASELECT dbxref_id FROM dbxref WHERE dbname = %s AND accession = %sr)r r.rF)rrrDr=rs rrzDatabaseLoader._get_dbxref_idbsHRLL77b)_M  Q< Iq11rcpd}|jj|||f}|r|S|j|||S)zGet DB cross-reference, creating it if needed (PRIVATE). Check for a pre-existing seqfeature_dbxref entry with the passed seqfeature_id and dbxref_id. If one does not exist, insert new data. zbSELECT seqfeature_id, dbxref_id FROM seqfeature_dbxref WHERE seqfeature_id = %s AND dbxref_id = %s)r r._add_seqfeature_dbxref)rrrr(r=results rrz%DatabaseLoader._get_seqfeature_dbxrefwsH : 44S=):TU M**=)TJJrcLd}|jj||||f||fS)zAdd DB cross-reference (PRIVATE). Insert a seqfeature_dbxref row and return the seqfeature_id and dbxref_id zSINSERT INTO seqfeature_dbxref (seqfeature_id, dbxref_id, "rank") VALUES(%s, %s, %s)r r/)rrrr(r=s rrz%DatabaseLoader._add_seqfeature_dbxrefs4  S=)T"BCy))rcvt|jD]\}}|jd}|dk7r td |j dd\}}|j }|j }|j||}|j|||dzy#t $rtd|ddwxYw) zrLoad any sequence level cross references into the database (PRIVATE). See table bioentry_dbxref. rrz;Expected a single line in value, got {newline_escape_count}rr6z!Parsing of dbxrefs list failed: 'rN) rrrr:rr|rr_get_bioentry_dbxref) rr%r&r(rnewline_escape_countrrDrs rrzDatabaseLoader._load_dbxrefss %V^^4 HKD%$);;t#4 #q( Q Y % C 3 IXXZ%OO- ++B :I  % %k9dQh G- H" Y #DUG1!MNTXX Ys 5BB8cpd}|jj|||f}|r|S|j|||S)zGet pre-existing db-xref, or create and return it (PRIVATE). Check for a pre-existing bioentry_dbxref entry with the passed seqfeature_id and dbxref_id. If one does not exist, insert new data z\SELECT bioentry_id, dbxref_id FROM bioentry_dbxref WHERE bioentry_id = %s AND dbxref_id = %s)r r._add_bioentry_dbxref)rr&rr(r=rs rr z#DatabaseLoader._get_bioentry_dbxrefsH 8 44S; :RS M((iFFrcLd}|jj||||f||fS)zlInsert a bioentry_dbxref row (PRIVATE). Returns the seqfeature_id and dbxref_id (PRIVATE). zNINSERT INTO bioentry_dbxref (bioentry_id,dbxref_id,"rank") VALUES (%s, %s, %s)r)rr&rr(r=s rr#z#DatabaseLoader._add_bioentry_dbxrefs4   S; 4"@AY''r)Frx)NNN)NN)zEMBL/GenBank/SwissProt) __name__ __module__ __qualname____doc__rr+r4r@rFrnrrr_rrrrrr"r!r$rrrrr rrrrr r#rrrr r !sG7. M0&0>.eN"H* Z@DJXR1hN0`@(!UFI2+^@UDL.?W2,(@TJ X-W^#PJ2*K& *H:G& (rr ceZdZdZdZdZy)DatabaseRemoveraComplement the Loader functionality by fully removing a database. This probably isn't really useful for normal purposes, since you can just do a:: DROP DATABASE db_name and then recreate the database. But, it's really useful for testing purposes. c ||_||_y)z5Initialize with a database id and adaptor connection.N)r r )rr r s rrzDatabaseRemover.__init__s  rcd}|jj||jfd}|jj||jfy)z3Remove everything related to the given database id.z.DELETE FROM bioentry WHERE biodatabase_id = %sz1DELETE FROM biodatabase WHERE biodatabase_id = %sN)r r/r )rr=s rremovezDatabaseRemover.removes@> S499,/A S499,/rN)r%r&r'r(rr-rrrr*r*s  0rr*N)r(timerrrrBio.SeqrBio.SeqFeaturerBio.SeqUtils.CheckSumrr r*rrrr2s7**(r(r(j%00r