PIc@sdZddlmZmZddlmZddlmZddlmZddl m Z dfdYZ d fd YZ d S( s'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. i(tgmtimetstrftime(tAlphabet(tcrc64(tEntrez(t UnknownSeqtDatabaseLoadercBseZdZedZdZddZddddZdZ dZ dZ dddZ d Z d Zd Zd Zd ZdZdZdZdZdZdZdZdZdZdZdZdZdZdZRS(s=Object used to load SeqRecord objects into a BioSQL database.cCs||_||_||_dS(s!Initialize 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(tadaptortdbidtfetch_NCBI_taxonomy(tselfRRR ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyt__init__s  cCs|j|}|j|||j|||j|||j|||jjdd}x<t|tt |D]\}}|j |||qW|j ||x=tt |j D]&}|j |}|j |||qWdS(s6Load a Biopython SeqRecord into the database. t referencesN((t_load_bioentry_tablet_load_bioentry_datet_load_biosequencet _load_commentt _load_dbxrefst annotationstgettziptrangetlent_load_referencet_load_annotationstfeaturest_load_seqfeature(R trecordt bioentry_idR t referencetranktseq_feature_numt seq_feature((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pytload_seqrecord/s( cCsO|jjd|f}|r&|dS|jjd||f|jjdS(s}Returns the 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. s0SELECT ontology_id FROM ontology WHERE name = %sis6INSERT INTO ontology(name, definition) VALUES (%s, %s)tontology(Rtexecute_and_fetch_col0texecutetlast_id(R tnamet definitiontoids((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyt_get_ontology_id?s    cCsd}|g}|r/|d7}|j|n|jj||}t|dkrotd||fnSt|dkr|ddSd}|jj|||||f|jjdSdS( sGet 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. s(SELECT term_id FROM term WHERE name = %ss AND ontology_id = %sisMultiple term ids for %s: %risTINSERT INTO term (name, definition, identifier, ontology_id) VALUES (%s, %s, %s, %s)ttermN(tappendRtexecute_and_fetchallRt ValueErrorR$R%(R R&t ontology_idR't identifiertsqltfieldst id_results((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyt _get_term_idSs    cCs,|jjd|||f|jjdS(s"Insert a dbxref and return its id.sBINSERT INTO dbxref(dbname, accession, version) VALUES (%s, %s, %s)tdbxref(RR$R%(R tdbnamet accessiontversion((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyt _add_dbxrefxs cCsd}d|jkrkt|jdtr[t|jddkrh|jdd}qhqk|jd}n|sx|jD]~}|jdkrt|di}d|krx;|jdD])}|j drt |d}PqqWqn|r{Pq{q{Wny|jd d }Wnt k r.d}nXy|jdd }Wnt k r]d}nX|rw|j |||S| r| rdS|r|j jd |f}|r|dSn|r|j jd |f}t|dkrtd t||fn|r|dSng} x3|jjdgD]} | jdd| gq4W| rkd| dd "scientific name", "EquivalentName" -> "equivalent name", "Synonym" -> "synonym", cSs"|jrd|jS|SdS(Nt (tisuppertlower(tletter((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyt add_space;s t(tjointstripR_tAssertionError(R t entrez_nameRaR`tanswer((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyt_fix_name_class's .c Cs|s t|jjd|f}|r2|dSd}d}d}d}g} |rl| jd|fn|r| jd|fn|jr tjddd|d d } tj| } t | d kr | dd t |kstd | dd |f|j | dd}| dd}| ddd}| ddd}d| ddfg} yx| ddj D]l\} } |j | } t| ts| g} nx3| D]+}t|tr| j| |fqqWqWWqtk rqXq n|jjd|||||ddf|jjd}x4| D],\} }|jjd||d | fqLW|S(sGet the taxon id for this record from the NCBI taxon ID (PRIVATE). 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). s3SELECT taxon_id FROM taxon WHERE ncbi_taxon_id = %siR@sscientific names common nametdbR>tidtretmodetXMLitTaxIds %s versus %st LineageExtRankt GeneticCodetGCIdtMitoGeneticCodetMGCIdtScientificNamet OtherNamessINSERT 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)RDsFINSERT INTO taxon_name(taxon_id, name, name_class) VALUES (%s, %s, %s)iN(ReRR#RER+R RtefetchtreadRtstrt_get_taxon_id_from_ncbi_lineaget iteritemsRhRFRGt basestringRLR$R%(R RORRRSR[RZRt genetic_codetmito_genetic_codet species_namesthandlettaxonomic_recordt name_classtnamesR&((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyRMDsp     !  "    cCsr|dd}|jjd|}|r`t|trYt|dksQt|dS|Snt|dkr|j|d }t|tst|tstt |nd }|dj dd }|jj d|||f|jj d}t|ts2t|ts2tt ||dj d d }|rn|jj d ||d fn|S( sHThis is recursive! (PRIVATE). taxonomic_lineage - list of taxonomy dictionaries from Bio.Entrez First dictionary in list is the taxonomy root, highest would be the species. Each dictionary includes: - TaxID (string, NCBI taxon id) - Rank (string, e.g. "species", "genus", ..., "phylum", ...) - ScientificName (string) (and that is all at the time of writing) This method will record all the lineage given, returning the the taxon id (database key, not NCBI taxon id) of the final entry (the species). iRms1SELECT taxon_id FROM taxon WHERE ncbi_taxon_id=%siiRosPINSERT INTO taxon(ncbi_taxon_id, parent_taxon_id, node_rank) VALUES (%s, %s, %s)RDRtsUINSERT INTO taxon_name(taxon_id, name, name_class) VALUES (%s, %s, 'scientific name')iN(RR#RFRGRReRyRKtlongtreprRERR$R%(R ttaxonomic_lineageROR[RZRRR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyRys4  3 0 c Csf|jjddkrf|jjd\}}yt|}Wqutk rb|j}d}quXn|j}d}d|jkrt|jdtr|jdr|jdd}n|j|}d|jkr|jd}n |j}t |dd }|jj dd }d}|j j ||j||j|||||f|j jd } | S( sFill the bioentry table with sequence information (PRIVATE). record - SeqRecord object to add to the database. t.iit accessionstgit descriptiontdata_file_divisions7 INSERT INTO bioentry ( biodatabase_id, taxon_id, name, accession, identifier, division, description, version) VALUES ( %s, %s, %s, %s, %s, %s, %s, %s)tbioentryN(RjtcounttsplitRKR-RRFRGR\RIRERRR$RR&R%( R RR6R7R[R/RtdivisionR0R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyR s<       cCsn|jjdtdtj}|jd}|jd|}d}|jj||||fdS(sAdd the effective date of the entry into the database. record - a SeqRecord object with an annotated date bioentry_id - corresponding database identifier tdates%d-%b-%YsAnnotation Tagst date_changeds_INSERT INTO bioentry_qualifier_value (bioentry_id, term_id, value, rank) VALUES (%s, %s, %s, 1)N( RRRRtupperR)R3RR$(R RRRtannotation_tags_idtdate_idR0((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyR3s  cCs|jdkrdSt|jjtjr4d}nHt|jjtjrUd}n't|jjtjrvd}nd}t|jtrd}nt |j}d}|j j ||t |j||fdS(sRecord a SeqRecord's sequence and alphabet in the database (PRIVATE). record - a SeqRecord object with a seq property bioentry_id - corresponding database identifier Ntdnatrnatproteintunknowns`INSERT INTO biosequence (bioentry_id, version, length, seq, alphabet) VALUES (%s, 0, %s, %s, %s)( tseqRERFtalphabetRt DNAAlphabett RNAAlphabettProteinAlphabetRRxRR$R(R RRRtseq_strR0((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyRDs"     cCs|jjd}|sdSt|ts7|g}nxRt|D]D\}}|jdd}d}|jj||||dfqDWdS(sRecord a SeqRecord's annotated comment in the database (PRIVATE). record - a SeqRecord object with an annotated comment bioentry_id - corresponding database identifier tcommentNs R]sIINSERT INTO comment (bioentry_id, comment_text, rank) VALUES (%s, %s, %s)i(RRRFRGt enumeratetreplaceRR$(R RRtcommentstindexRR0((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyRfs c Cs"d}d}|jd}x|jjD]\}}|d krIq+n|j|d|}t|trd} x|D]V} t| tst| trz| d 7} |jj |||t| | fqzqzWq+t|tst|tr+|jj |||t|fq+q+Wd S( sRecord 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. record - a SeqRecord object with an annotations dictionary bioentry_id - corresponding database identifier sUINSERT INTO bioentry_qualifier_value(bioentry_id, term_id, value) VALUES (%s, %s, %s)s_INSERT INTO bioentry_qualifier_value(bioentry_id, term_id, value, rank) VALUES (%s, %s, %s, %s)sAnnotation TagsR RR9R.iiN(R RR9( R)RRzR3RFRGRxRKRR$( R RRtmono_sqltmany_sqlttag_ontology_idtkeytvaluetterm_idRtentry((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyR{s&      cCsd }|jr-|jjd|jf}n| r[|jr[|jjd|jf}n|sg}x3|j|j|jfD]}|j|pdqWt dj |}|jjd|f}n|s|jr|j d|jd}n*|jr|j d|jd}nd }|jp-d } |jp<d } |jpKd} |jj d || | | |f|jj d } n |d} |jrd tt|jdj} tt|jdj}n d } d }d }|jj ||| | ||d fd S(sRecord a SeqRecord's annotated references in the database (PRIVATE). record - a SeqRecord object with annotated references bioentry_id - corresponding database identifier smSELECT reference_id FROM reference JOIN dbxref USING (dbxref_id) WHERE dbname = 'MEDLINE' AND accession = %sslSELECT reference_id FROM reference JOIN dbxref USING (dbxref_id) WHERE dbname = 'PUBMED' AND accession = %ssRbs1SELECT reference_id FROM reference WHERE crc = %stMEDLINEitPUBMEDs\INSERT INTO reference (dbxref_id, location, title, authors, crc) VALUES (%s, %s, %s, %s, %s)RispINSERT INTO bioentry_reference (bioentry_id, reference_id, start_pos, end_pos, rank) VALUES (%s, %s, %s, %s, %s)N(REt medline_idRR#t pubmed_idtauthorsttitletjournalR+RRcR8R$R%tlocationRKRxtstarttend(R RRRtrefstsRPtcrct dbxref_idRRRt reference_idRRR0((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyRsT              cCs?|j|j||}|j|||j|j|dS(sALoad a biopython SeqFeature into the database (PRIVATE). N(t_load_seqfeature_basicRHt_load_seqfeature_locationst_load_seqfeature_qualifiersR;(R tfeaturet feature_rankRt seqfeature_id((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyRs c Cs|jd}|j|d|}|jd}|jdd|}d}|jj|||||df|jjd} | S(sLoad the first tables of a seqfeature and returns the id (PRIVATE). This loads the "key" of the seqfeature (ie. CDS, gene) and the basic seqfeature table itself. sSeqFeature KeysR.sSeqFeature SourcessEMBL/GenBank/SwissProts`INSERT INTO seqfeature (bioentry_id, type_term_id, source_term_id, rank) VALUES (%s, %s, %s, %s)it seqfeature(R)R3RR$R%( R t feature_typeRRR.tseqfeature_key_idt source_cat_idtsource_term_idR0R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyRs    cCsZ|js|j|d|n7x4t|jD]#\}}|j||d|q/WdS(s1Load all of the locations for a SeqFeature into tables (PRIVATE). This adds the locations related to the SeqFeature into the seqfeature_location table. Fuzzies are not handled right now. For a simple location, ie (1..2), we have a single table row with seq_start = 1, seq_end = 2, location_rank = 1. For split locations, ie (1..2, 3..4, 5..6) we would have three row tables with: start = 1, end = 2, rank = 1 start = 3, end = 4, rank = 2 start = 5, end = 6, rank = 3 iN(t sub_featurest_insert_seqfeature_locationR(R RRRt cur_feature((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyRs   c Cs|jjd}|jj}|jp(d}d}|jr[|j|jpLd|j}nd}d} |jj | |||||||fdS(sAdd a location of a SeqFeature to the seqfeature_location table (PRIVATE). TODO - Add location_operators to location_qualifier_value. iiRbs}INSERT INTO location (seqfeature_id, dbxref_id, term_id,start_pos, end_pos, strand, rank) VALUES (%s, %s, %s, %s, %s, %s, %s)N( Rt nofuzzy_startt nofuzzy_endtstrandREtreft_get_dbxref_idtref_dbRR$( R RRRRRRt loc_term_idRR0((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyR!s  !c Cs|jd}x|jD]}|dkr|j|d|}||}t|tsh|g}nxdtt|D]9}||}d} |jj| |||d|fq{Wq|j |||qWdS(sInsert the (key, value) pair qualifiers relating to a feature (PRIVATE). Qualifiers should be a dictionary of the form: {key : [value1, value2]} sAnnotation TagsR<R.seINSERT INTO seqfeature_qualifier_value (seqfeature_id, term_id, rank, value) VALUES (%s, %s, %s, %s)iN( R)tkeysR3RFRGRRRR$t_load_seqfeature_dbxref( R R;RRt qualifier_keytqualifier_key_idtentriestqual_value_ranktqualifier_valueR0((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyRWs"       c Csxt|D]\}}y?|jddjddjd}|d}|d}Wntd|nXx7|D]/}|j||} |j|| |dqyWq WdS( sAdd database crossreferences of a SeqFeature to the database (PRIVATE). o dbxrefs List, dbxref data from the source file in the format : o 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 R]Rbs t:iisParsing of db_xref failed: '%s'N(RRRR-Rt_get_seqfeature_dbxref( R tdbxrefsRRRt dbxref_dataRiRR6R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyR~s'  cCsBd}|jj|||f}|r/|dS|j||dS(s _get_dbxref_id(self, db, accession) -> Int o db String, the name of the external database containing the accession number o 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. sASELECT dbxref_id FROM dbxref WHERE dbname = %s AND accession = %si(RR#R8(R RiR6R0R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyRs cCs>d}|jj|||f}|r+|S|j|||S(s Check for a pre-existing seqfeature_dbxref entry with the passed seqfeature_id and dbxref_id. If one does not exist, insert new data sfSELECT seqfeature_id, dbxref_id FROM seqfeature_dbxref WHERE seqfeature_id = '%s' AND dbxref_id = '%s'(RR#t_add_seqfeature_dbxref(R RRRR0tresult((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyRs  cCs,d}|jj||||f||fS(s_ Insert a seqfeature_dbxref row and return the seqfeature_id and dbxref_id sQINSERT INTO seqfeature_dbxref (seqfeature_id, dbxref_id, rank) VALUES(%s, %s, %s)(RR$(R RRRR0((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyRscCsxt|jD]\}}|jddks7ty4|jdd\}}|j}|j}Wntd|nX|j||}|j|||dqWdS(siLoad any sequence level cross references into the database (PRIVATE). See table bioentry_dbxref.s iRis$Parsing of dbxrefs list failed: '%s'N( RRRReRRdR-Rt_get_bioentry_dbxref(R RRRRRiR6R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyRs cCs>d}|jj|||f}|r+|S|j|||S(s Check for a pre-existing bioentry_dbxref entry with the passed seqfeature_id and dbxref_id. If one does not exist, insert new data s`SELECT bioentry_id, dbxref_id FROM bioentry_dbxref WHERE bioentry_id = '%s' AND dbxref_id = '%s'(RR#t_add_bioentry_dbxref(R RRRR0R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyRs  cCs,d}|jj||||f||fS(s] Insert a bioentry_dbxref row and return the seqfeature_id and dbxref_id sLINSERT INTO bioentry_dbxref (bioentry_id,dbxref_id,rank) VALUES (%s, %s, %s)(RR$(R RRRR0((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyRsN( t__name__t __module__t__doc__tFalseR R!RER)R3R8R\RhRMRyR RRRRRRRRRRRRRRRRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyRs>    !   m 7 I  "  , A    6 ' %    tDatabaseRemovercBs eZdZdZdZRS(s;Complement 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. YB: now use the cascaded deletions cCs||_||_dS(s>Initialize with a database id and adaptor connection. N(RR(R RR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyR s cCsBd}|jj||jfd}|jj||jfdS(s<Remove everything related to the given database id. s.DELETE FROM bioentry WHERE biodatabase_id = %ss1DELETE FROM biodatabase WHERE biodatabase_id = %sN(RR$R(R R0((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pytremoves(RRRR R(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyRs  N( RttimeRRtBioRtBio.SeqUtils.CheckSumRRtBio.SeqRRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/BioSQL/Loader.pyts