[Biopython-dev] BioSQL Loader.py patch .diff
Leighton Pritchard
lpritc at scri.sari.ac.uk
Tue Apr 4 14:19:01 UTC 2006
I'm not having much fun with mailing lists, this afternoon - my
attachment appears to have gone missing. The contents of the .diff are
inline below:
1c1
< """Load biopyton objects into a BioSQL database for persistant
storage.
---
> """Load biopython objects into a BioSQL database for persistant
storage.
9a10
> import sys
226c227
< taxon_id = "0" # inserted this because the taxon population
code is out of date
---
> #taxon_id = "0" # inserted this because the taxon population
code is out of date
231a233,235
> # removed taxon_id field, as it was causing difficulties with
the
> # schema - not inserting a value allows it to default to
NULL,
> # avoiding the foreign key constraint.
235d238
< taxon_id,
249d251
< %s,
252d253
< taxon_id,
450,451c451,543
< qualifier_key_id = self._get_term_id(qualifier_key,
< ontology_id =
tag_ontology_id)
---
> # Treat db_xref qualifiers differently to sequence
annotation
> # qualifiers by populating the seqfeature_dbxref and
dbxref
> # tables. Other qualifiers go into the
seqfeature_qualifier_value
> # and (if new) term tables.
> if qualifier_key != 'db_xref':
> qualifier_key_id = self._get_term_id(qualifier_key,
>
ontology_id=tag_ontology_id)
> # now add all of the values to their table
> for qual_value_rank in range(len(qualifiers
[qualifier_key])):
> qualifier_value = qualifiers
[qualifier_key][qual_value_rank]
> sql = r"INSERT INTO seqfeature_qualifier_value
VALUES" \
> r" (%s, %s, %s, %s)"
> self.adaptor.execute(sql, (seqfeature_id,
> qualifier_key_id,
> qual_value_rank + 1,
> qualifier_value))
> else:
> # 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
> self._load_seqfeature_dbxref(qualifiers
[qualifier_key],
> seqfeature_id)
>
>
> def _load_seqfeature_dbxref(self, dbxrefs, seqfeature_id):
> """ _load_seqfeature_dbxref(self, dbxrefs, seqfeature_id)
>
> o dbxrefs List, dbxref data from the source file
in the
> format <database>:<accession>
>
> 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
> """
> # Dictionary of database types, keyed by GenBank db_xref
abbreviation
> db_dict = {'GeneID': 'Entrez',
> 'GI': 'GeneIndex',
> 'COG': 'COG',
> 'CDD': 'CDD',
> 'DDBJ': 'DNA Databank of Japan',
> 'Entrez': 'Entrez',
> 'GeneIndex': 'GeneIndex',
> 'PUBMED': 'PubMed',
> 'taxon': 'Taxon',
> 'ATCC': 'ATCC',
> 'ISFinder': 'ISFinder',
> 'GOA': 'Gene Ontology Annotation',
> 'ASAP': 'ASAP',
> 'PSEUDO': 'PSEUDO',
> 'InterPro': 'InterPro',
> 'GEO': 'Gene Expression Omnibus',
> 'EMBL': 'EMBL',
> 'UniProtKB/Swiss-Prot': 'UniProtKB/Swiss-Prot',
> 'ECOCYC': 'EcoCyc',
> 'UniProtKB/TrEMBL': 'UniProtKB/TrEMBL'
> }
> for rank, value in enumerate(dbxrefs):
> # Split the DB:accession format string at colons. We have
to
> # account for multiple-line and multiple-accession entries
> try:
> dbxref_data = value.replace(' ','').replace
('\n','').split(':')
> key = dbxref_data[0]
> accessions = dbxref_data[1:]
> except:
> # Parsing fails - return
> # !!!!!!!!!!!!!!!!!!!!!!
> # !! IMPLEMENT RAISE ERROR MESSAGE HERE
> # !!!!!!!!!!!!!!!!!!!!!!
> print "Parsing of db_xref failed:", key, accession
> if key not in db_dict:
> # Database is currently unknown, so add it to the
db_dict
> # temporarily and print a message to stdout
> sys.stdout.write("%s not recognised as database type:
" % key+\
> "temporarily accepting key")
> db_dict[key] = key
> db = db_dict[key]
> # Loop over all the grabbed accessions, and attempt to
fill the
> # table
> for accession in accessions:
> # Get the dbxref_id value for the dbxref data
> dbxref_id = self._get_dbxref_id(db, accession)
> # Insert the seqfeature_dbxref data
> self._get_seqfeature_dbxref(seqfeature_id, dbxref_id,
rank+1)
>
> def _get_dbxref_id(self, db, accession):
> """ _get_dbxref_id(self, db, accession) -> Int
453,460c545,590
< # now add all of the values to their table
< for qual_value_rank in range(len(qualifiers
[qualifier_key])):
< qualifier_value = qualifiers
[qualifier_key][qual_value_rank]
< sql = r"INSERT INTO seqfeature_qualifier_value VALUES"
\
< r" (%s, %s, %s, %s)"
< self.adaptor.execute(sql, (seqfeature_id,
< qualifier_key_id, qual_value_rank + 1,
qualifier_value))
<
---
> 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.
> """
> # Check for an existing record
> sql = r'SELECT dbxref_id FROM dbxref WHERE dbname = %s ' \
> r'AND accession = %s'
> dbxref_id = self.adaptor.execute_and_fetch_col0(sql, (db,
accession))
> # If there was a record, return the dbxref_id, else create the
> # record and return the created dbxref_id
> if dbxref_id:
> return dbxref_id[0]
> return self._add_dbxref(db, accession, 0)
>
> def _get_seqfeature_dbxref(self, seqfeature_id, dbxref_id, rank):
> """ Check for a pre-existing seqfeature_dbxref entry with the
passed
> seqfeature_id and dbxref_id. If one does not exist,
insert new
> data
>
> """
> # Check for an existing record
> sql = r'SELECT seqfeature_id, dbxref_id FROM seqfeature_dbxref
' \
> r'WHERE seqfeature_id = "%s" AND dbxref_id = "%s"'
> result = self.adaptor.execute_and_fetch_col0(sql,
(seqfeature_id,
> dbxref_id))
> # If there was a record, return without executing anything,
else create
> # the record and return
> if result:
> return result
> return self._add_seqfeature_dbxref(seqfeature_id, dbxref_id,
rank)
>
> def _add_seqfeature_dbxref(self, seqfeature_id, dbxref_id, rank):
> """ Insert a seqfeature_dbxref row and return the
seqfeature_id and
> dbxref_id
> """
> sql = r'INSERT INTO seqfeature_dbxref VALUES' \
> r'(%s, %s, %s)'
> self.adaptor.execute(sql, (seqfeature_id, dbxref_id, rank))
> return (seqfeature_id, dbxref_id)
>
>
--
Dr Leighton Pritchard AMRSC
D131, Plant-Pathogen Interactions, Scottish Crop Research Institute
Invergowrie, Dundee, Scotland, DD2 5DA, UK
T: +44 (0)1382 562731 x2405 F: +44 (0)1382 568578
E: lpritc at scri.sari.ac.uk W: http://bioinf.scri.sari.ac.uk/lp
GPG/PGP: FEFC205C E58BA41B http://www.keyserver.net
(If the signature does not verify, please remove the SCRI disclaimer)
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