def __init__(self, inputFnameLs=None, **keywords):
"""
2008-07-27
use option_default_dict
2008-07-06
use the firstline (header) of the fasta file to extract which chromosome. using filename is unreliable.
"""
AbstractDBInteractingJob.__init__(self, inputFnameLs=inputFnameLs, **keywords)
#self.connectDB() called within its __init__()
self.FigureOutTaxID_ins = FigureOutTaxID(db_user=self.db_user,
db_passwd=self.db_passwd, hostname=self.hostname, dbname=self.dbname)
if self.organism is not None:
from annot.bin.codense.common import org_short2long, org2tax_id
if org_short2long(self.organism):
self.tax_id = org2tax_id(org_short2long(self.organism))
else:
self.tax_id = self.FigureOutTaxID_ins.returnTaxIDGivenSentence(self.organism)
#self.p_chromosome = re.compile(r'[a-zA-Z]+_chr(\w+).fa')
self.p_chromosome = re.compile(r'chromosome (\w+)[,\n\r]?') #the last ? means [,\n\r] is optional
self.p_acc_ver = re.compile(r'(\w+)\.(\d+)')
self.parseFastaDescriptionDict = {1: self.parseFastaDescriptionForGenBank, \
2: self.parseFastaDescriptionForWUSTLVervetScaffolds,\
3: self.parseFastaDescriptionForFullVervetBACs,\
4: self.parseFastaDescriptionForWUSTLVervetChromosomeGenome}
def __init__(self, inputFnameLs=None, **keywords):
"""
2008-07-27
use option_default_dict
2008-07-06
use the firstline (header) of the fasta file to extract which chromosome. using filename is unreliable.
"""
AbstractDBInteractingJob.__init__(self, inputFnameLs=inputFnameLs, **keywords)
#self.connectDB() called within its __init__()
self.FigureOutTaxID_ins = FigureOutTaxID(db_user=self.db_user,
db_passwd=self.db_passwd, hostname=self.hostname, dbname=self.dbname)
if self.organism is not None:
from annot.bin.codense.common import org_short2long, org2tax_id
if org_short2long(self.organism):
self.tax_id = org2tax_id(org_short2long(self.organism))
else:
self.tax_id = self.FigureOutTaxID_ins.returnTaxIDGivenSentence(self.organism)
#self.p_chromosome = re.compile(r'[a-zA-Z]+_chr(\w+).fa')
self.p_chromosome = re.compile(r'chromosome (\w+)[,\n\r]?') #the last ? means [,\n\r] is optional
self.p_acc_ver = re.compile(r'(\w+)\.(\d+)')
self.parseFastaDescriptionDict = {1: self.parseFastaDescriptionForGenBank, \
2: self.parseFastaDescriptionForWUSTLVervetScaffolds,\
3: self.parseFastaDescriptionForFullVervetBACs,\
4: self.parseFastaDescriptionForWUSTLVervetChromosomeGenome}
class chromosome_fasta2db(AbstractDBInteractingJob):
__doc__ = __doc__
option_default_dict = AbstractDBInteractingJob.option_default_dict.copy()
option_default_dict.update({
('organism', 0, ): [None, 'g', 1, '2-letter abbreviation for organism. Optional, if specified, only sequence from this organism would be extracted.'],\
('sequence_type_id', 0, int):[9, '', 1, 'column SequenceType.id in database GenomeDB'],\
('sequence_type_name', 0, ):[None, 's', 1, 'column SequenceType.short_name'],\
('tax_id', 0, int):[60711, '', 1, 'taxonomy ID, if not given, query argument organism against tax db'],\
('version', 0, int):[1, '', 1, 'which version'],\
('run_type', 1, int):[1, 'y', 1, 'run type. 1: genBank fasta files. \n\
2: scaffolds from WUSTL. \n\
3: fully sequenced vervet BACs. \n\
4: fully-assembled vervet ref genome from WUSTL. '],\
('maxNoOfFastaRecords', 1, int):[500, 'x', 1, 'maximum number of fasta records to be inserted (in the input file order)'],\
})
option_default_dict[('schema', 0, )][0] = 'genome'
option_default_dict.pop((('outputFname', 0, )))
def __init__(self, inputFnameLs=None, **keywords):
"""
2008-07-27
use option_default_dict
2008-07-06
use the firstline (header) of the fasta file to extract which chromosome. using filename is unreliable.
"""
AbstractDBInteractingJob.__init__(self, inputFnameLs=inputFnameLs, **keywords)
#self.connectDB() called within its __init__()
self.FigureOutTaxID_ins = FigureOutTaxID(db_user=self.db_user,
db_passwd=self.db_passwd, hostname=self.hostname, dbname=self.dbname)
if self.organism is not None:
from annot.bin.codense.common import org_short2long, org2tax_id
if org_short2long(self.organism):
self.tax_id = org2tax_id(org_short2long(self.organism))
else:
self.tax_id = self.FigureOutTaxID_ins.returnTaxIDGivenSentence(self.organism)
#self.p_chromosome = re.compile(r'[a-zA-Z]+_chr(\w+).fa')
self.p_chromosome = re.compile(r'chromosome (\w+)[,\n\r]?') #the last ? means [,\n\r] is optional
self.p_acc_ver = re.compile(r'(\w+)\.(\d+)')
self.parseFastaDescriptionDict = {1: self.parseFastaDescriptionForGenBank, \
2: self.parseFastaDescriptionForWUSTLVervetScaffolds,\
3: self.parseFastaDescriptionForFullVervetBACs,\
4: self.parseFastaDescriptionForWUSTLVervetChromosomeGenome}
def saveRawSequence(self, session, seq_to_db, passingdata, aa_attr_instance):
"""
2010-12-17
RawSequence.annot_assembly is a foreign key element now.
2008-07-29
to store one sequence segment
"""
passingdata.current_stop = passingdata.current_start+len(seq_to_db)-1
raw_sequence = RawSequence(start=passingdata.current_start, stop=passingdata.current_stop, sequence=seq_to_db)
raw_sequence.annot_assembly = aa_attr_instance
session.add(raw_sequence)
if not passingdata.raw_sequence_initiated:
session.flush() # 2010-12-17 to get raw_sequence.id
passingdata.raw_sequence_initiated = True
aa_attr_instance.raw_sequence_start_id = raw_sequence.id
passingdata.current_start += len(seq_to_db)
def parseFastaDescriptionForGenBank(self, descriptionLine=None, FigureOutTaxID_ins=None):
"""
2011-7-6
"""
"""
possible header lines:
>gi|51511461|ref|NC_000001.8|NC_000001 H**o sapiens chromosome 1, complete sequence
>gi|186497660|ref|NC_003070.6| Arabidopsis thaliana chromosome 1, complete sequence
>gi|26556996|ref|NC_001284.2| Arabidopsis thaliana mitochondrion, complete genome
>gi|115442598|ref|NC_008394.1| Oryza sativa (japonica cultivar-group) genomic DNA, chromosome 1
"""
header = descriptionLine[1:-1] #discard '>' and '\n'
header = header.split('|')
_tax_id = FigureOutTaxID_ins.returnTaxIDGivenSentence(header[4])
if self.p_chromosome.search(header[4]) is not None:
chromosome = self.p_chromosome.search(header[4]).groups()[0]
elif header[4].find('mitochondrion')!=-1:
chromosome = 'mitochondrion'
elif header[4].find('chloroplast')!=-1:
chromosome = 'chloroplast'
else: #something else, take the whole before ','
chromosome = header[4].split(',')[0]
gi = int(header[1])
acc_ver = header[3]
comment = header[4]
return PassingData(tax_id=_tax_id, gi=gi, comment=comment, acc_ver=acc_ver, chromosome=chromosome)
def parseFastaDescriptionForWUSTLVervetScaffolds(self, descriptionLine=None, FigureOutTaxID_ins=None):
"""
2011-7-6
"""
"""
possible header lines:
>Contig0 12652774 13406928
"""
header = descriptionLine[1:-1] #discard '>' and '\n'
header = header.split()
chromosome = header[0] #contig name is taken as chromosome
"""
p_chromosome = re.compile(r'Contig(\d+)')
if p_chromosome.search(header[0]) is not None:
chromosome = p_chromosome.search(header[0]).groups()[0]
else:
chromosome = None
"""
gi = None
acc_ver = None
comment = None
return PassingData(tax_id=None, gi=gi, comment=comment, acc_ver=acc_ver, chromosome=chromosome)
def parseFastaDescriptionForWUSTLVervetChromosomeGenome(self, descriptionLine=None, FigureOutTaxID_ins=None):
"""
2013.05.09 include 'CAE' in the chromosome ID name.
2013.04.12 header looks like, CAE stands for C. aethiops:
>CAE1
GTGAAAGAAGCCAAAAAG
"""
header = descriptionLine[1:-1] #discard '>' and '\n'
header = header.split()
p_chromosome = re.compile(r'(CAE[\dXYxy]+)')
if p_chromosome.search(header[0]) is not None:
chromosome = p_chromosome.search(header[0]).groups()[0]
else:
chromosome = None
gi = None
acc_ver = None
comment = None
return PassingData(tax_id=None, gi=gi, comment=comment, acc_ver=acc_ver, chromosome=chromosome)
def parseFastaDescriptionForFullVervetBACs(self, descriptionLine=None, FigureOutTaxID_ins=None):
"""
2011-7-6
possible header lines:
>gi|285026568|gb|AC239257.2| Chlorocebus aethiops chromosome UNK clone CH252-270J24, WORKING DRAFT SEQUENCE, 2 unordered pieces
>gi|281332227|gb|AC238852.3| Chlorocebus aethiops BAC clone CH252-133A18 from chromosome 3, complete sequence
>gi|285002488|gb|AC239185.3| Chlorocebus aethiops BAC clone CH252-404N12 from chromosome unknown, complete sequence
"""
header = descriptionLine[1:-1] #discard '>' and '\n'
header = header.split('|')
_tax_id = None
p_chromosome = re.compile(r'UNK clone ([^,]+),') # 1st type of clone description
p2_chromosome = re.compile(r'clone ([^,]+),') # 2nd type of clone description
if p_chromosome.search(header[4]) is not None:
chromosome = p_chromosome.search(header[4]).groups()[0]
else:
if p2_chromosome.search(header[4]) is not None:
chromosome = p2_chromosome.search(header[4]).groups()[0]
else:
chromosome = None
gi = int(header[1])
acc_ver = header[3]
comment = header[4]
return PassingData(tax_id=_tax_id, gi=gi, comment=comment, acc_ver=acc_ver, chromosome=chromosome)
def parse_chromosome_fasta_file(self, db=None, filename=None, tax_id=None, version=None, chunk_size=10000, \
sequence_type_name=None, sequence_type_id=None, run_type=1,
maxNoOfFastaRecords=500):
"""
2011-7-10
add argument maxNoOfFastaRecords: the max number of fasta records before quitting
2011-7-6
add argument run_type
1: chromosome sequences from NCBI genbank
2: vervet scaffolds from WUSTL
3: full vervet BACs from McGill
2010-12-15
fix a bug that _tax_id shall be used in query AnnotAssembly.
This bug caused the db redundancy check to fail.
2010-12-15
if entry already exists in AnnotAssembly, skip it.
2008-07-29
figure out tax_id via FigureOutTaxID
filename could contain multiple fasta blocks
2008-07-27
change to use data structures from GenomeDB.py
2008-07-06
use the firstline (header) of the fasta file to extract which chromosome. using filename is unreliable.
"""
inf = utils.openGzipFile(filename, openMode='r')
line = inf.readline()
new_fasta_block = 1 #'line' is not enough to stop the 'while' loop. after the file reading is exhausted by "for line in inf:", 'line' still contains the stuff from the last line.
no_of_fasta_blocks = 0
while line and new_fasta_block:
new_fasta_block = 0 #set it to 0, assuming only one fasta block, change upon new fasta block
if line[0]!='>': #not fasta block header
for line in inf: #exhaust this fasta block as it's not what's wanted.
if line[0]=='>':
new_fasta_block = 1
break #start from while again
continue
headerData = self.parseFastaDescriptionDict[run_type](line, self.FigureOutTaxID_ins)
if not headerData.chromosome:
sys.stderr.write("Error chromosome for header %s is empty %s.\n"%(line, headerData.chromosome))
import pdb
pdb.set_trace()
if tax_id is not None and headerData.tax_id and tax_id!=headerData.tax_id:
sys.stderr.write("tax_id (%s) not matching the one given (%s). Ignore.\n"%(headerData.tax_id, tax_id))
line = inf.readline()
new_fasta_block = 1
continue
chromosome = headerData.chromosome
sequence_type = db.getSequenceType(short_name=sequence_type_name, id=sequence_type_id)
start = 1
aa_attr_instance = db.checkAnnotAssembly(version=version, tax_id=tax_id, \
chromosome=chromosome, start=start, stop=None, \
sequence_type_id=sequence_type.id)
if aa_attr_instance and aa_attr_instance.raw_sequence_start_id is not None:
# if raw sequences have been associated with this AnnotAssembly and
sys.stderr.write("raw sequences have been associated with this AnnotAssembly (tax_id %s, chr=%s, start=%s). Ignore.\n"%\
(tax_id, chromosome, start))
line = inf.readline()
new_fasta_block = 1
continue
if aa_attr_instance is None:
aa_attr_instance = db.getAnnotAssembly(gi=headerData.gi, acc_ver=headerData.acc_ver, accession =None, \
version =None, tax_id=tax_id, chromosome =chromosome, \
start =start, stop =None, orientation=None, sequence = None,\
raw_sequence_start_id=None, original_path=os.path.abspath(filename),\
sequence_type_id=sequence_type.id, \
chromosome_type_id=None, chromosome_type_name=None, comment=headerData.comment)
if aa_attr_instance.acc_ver and self.p_acc_ver.search(aa_attr_instance.acc_ver):
aa_attr_instance.accession, aa_attr_instance.version = self.p_acc_ver.search(aa_attr_instance.acc_ver).groups()
aa_attr_instance.version = int(aa_attr_instance.version)
else:
aa_attr_instance.accession = None
aa_attr_instance.version = version
if self.debug:
sys.stderr.write("tax_id=%s for %s.\n"%(aa_attr_instance.tax_id, line))
#aa_attr_instance.raw_sequence_start_id = self.get_current_max_raw_sequence_id(curs, raw_sequence_table)+1
passingdata = PassingData()
passingdata.current_start = 1
passingdata.raw_sequence_initiated = False
seq = ''
for line in inf:
if line[0]=='>':
if seq: #last segment from the previous fasta block
self.saveRawSequence(db.session, seq, passingdata, aa_attr_instance)
seq = '' #set to nothing to avoid saving one more RawSequence
new_fasta_block = 1
break #start from while again
seq += line.strip()
if len(seq)>=chunk_size:
seq_to_db = seq[:chunk_size]
self.saveRawSequence(db.session, seq_to_db, passingdata, aa_attr_instance)
seq = seq[chunk_size:] #remove the one already in db
if self.report:
sys.stderr.write("%s\t%s\t%s"%('\x08'*20, no_of_fasta_blocks, passingdata.current_start/chunk_size+1))
if seq: # last segment from last line
self.saveRawSequence(db.session, seq, passingdata, aa_attr_instance)
aa_attr_instance.stop = passingdata.current_stop
db.session.add(aa_attr_instance)
db.session.flush()
no_of_fasta_blocks += 1
if no_of_fasta_blocks>=maxNoOfFastaRecords:
break
sys.stderr.write(" Number of fasta blocks/chromosomes: %s.\n"%(no_of_fasta_blocks))
del inf
def connectDB(self):
"""
2013.3.14
"""
db = GenomeDatabase(drivername=self.drivername, username=self.db_user,
password=self.db_passwd, hostname=self.hostname, database=self.dbname, schema=self.schema)
db.setup(create_tables=False)
self.db = db
def run(self):
"""
2008-07-27
--GenomeDatabase
--parse_chromosome_fasta_file()
"""
if self.debug:
import pdb
pdb.set_trace()
sys.stderr.write("\tTotally, %d files to be processed.\n"%(len(self.inputFnameLs)))
session = self.db.session
session.begin()
for filename in self.inputFnameLs:
sys.stderr.write("%d/%d:\t%s "%(self.inputFnameLs.index(filename)+1,\
len(self.inputFnameLs),filename))
self.parse_chromosome_fasta_file(db=self.db, filename=filename, tax_id=self.tax_id, version=self.version, \
chunk_size=10000, \
sequence_type_name=self.sequence_type_name, \
sequence_type_id=self.sequence_type_id,\
run_type=self.run_type, maxNoOfFastaRecords=self.maxNoOfFastaRecords)
if self.commit:
session.commit()
else:
session.rollback()
class chromosome_fasta2db(AbstractDBInteractingJob):
__doc__ = __doc__
option_default_dict = AbstractDBInteractingJob.option_default_dict.copy()
option_default_dict.update({
('organism', 0, ): [None, 'g', 1, '2-letter abbreviation for organism. Optional, if specified, only sequence from this organism would be extracted.'],\
('sequence_type_id', 0, int):[9, '', 1, 'column SequenceType.id in database GenomeDB'],\
('sequence_type_name', 0, ):[None, 's', 1, 'column SequenceType.short_name'],\
('tax_id', 0, int):[60711, '', 1, 'taxonomy ID, if not given, query argument organism against tax db'],\
('version', 0, int):[1, '', 1, 'which version'],\
('run_type', 1, int):[1, 'y', 1, 'run type. 1: genBank fasta files. \n\
2: scaffolds from WUSTL. \n\
3: fully sequenced vervet BACs. \n\
4: fully-assembled vervet ref genome from WUSTL. '],\
('maxNoOfFastaRecords', 1, int):[500, 'x', 1, 'maximum number of fasta records to be inserted (in the input file order)'],\
})
option_default_dict[('schema', 0, )][0] = 'genome'
option_default_dict.pop((('outputFname', 0, )))
def __init__(self, inputFnameLs=None, **keywords):
"""
2008-07-27
use option_default_dict
2008-07-06
use the firstline (header) of the fasta file to extract which chromosome. using filename is unreliable.
"""
AbstractDBInteractingJob.__init__(self, inputFnameLs=inputFnameLs, **keywords)
#self.connectDB() called within its __init__()
self.FigureOutTaxID_ins = FigureOutTaxID(db_user=self.db_user,
db_passwd=self.db_passwd, hostname=self.hostname, dbname=self.dbname)
if self.organism is not None:
from annot.bin.codense.common import org_short2long, org2tax_id
if org_short2long(self.organism):
self.tax_id = org2tax_id(org_short2long(self.organism))
else:
self.tax_id = self.FigureOutTaxID_ins.returnTaxIDGivenSentence(self.organism)
#self.p_chromosome = re.compile(r'[a-zA-Z]+_chr(\w+).fa')
self.p_chromosome = re.compile(r'chromosome (\w+)[,\n\r]?') #the last ? means [,\n\r] is optional
self.p_acc_ver = re.compile(r'(\w+)\.(\d+)')
self.parseFastaDescriptionDict = {1: self.parseFastaDescriptionForGenBank, \
2: self.parseFastaDescriptionForWUSTLVervetScaffolds,\
3: self.parseFastaDescriptionForFullVervetBACs,\
4: self.parseFastaDescriptionForWUSTLVervetChromosomeGenome}
def saveRawSequence(self, session, seq_to_db, passingdata, aa_attr_instance):
"""
2010-12-17
RawSequence.annot_assembly is a foreign key element now.
2008-07-29
to store one sequence segment
"""
passingdata.current_stop = passingdata.current_start+len(seq_to_db)-1
raw_sequence = RawSequence(start=passingdata.current_start, stop=passingdata.current_stop, sequence=seq_to_db)
raw_sequence.annot_assembly = aa_attr_instance
session.add(raw_sequence)
if not passingdata.raw_sequence_initiated:
session.flush() # 2010-12-17 to get raw_sequence.id
passingdata.raw_sequence_initiated = True
aa_attr_instance.raw_sequence_start_id = raw_sequence.id
passingdata.current_start += len(seq_to_db)
def parseFastaDescriptionForGenBank(self, descriptionLine=None, FigureOutTaxID_ins=None):
"""
2011-7-6
"""
"""
possible header lines:
>gi|51511461|ref|NC_000001.8|NC_000001 H**o sapiens chromosome 1, complete sequence
>gi|186497660|ref|NC_003070.6| Arabidopsis thaliana chromosome 1, complete sequence
>gi|26556996|ref|NC_001284.2| Arabidopsis thaliana mitochondrion, complete genome
>gi|115442598|ref|NC_008394.1| Oryza sativa (japonica cultivar-group) genomic DNA, chromosome 1
"""
header = descriptionLine[1:-1] #discard '>' and '\n'
header = header.split('|')
_tax_id = FigureOutTaxID_ins.returnTaxIDGivenSentence(header[4])
if self.p_chromosome.search(header[4]) is not None:
chromosome = self.p_chromosome.search(header[4]).groups()[0]
elif header[4].find('mitochondrion')!=-1:
chromosome = 'mitochondrion'
elif header[4].find('chloroplast')!=-1:
chromosome = 'chloroplast'
else: #something else, take the whole before ','
chromosome = header[4].split(',')[0]
gi = int(header[1])
acc_ver = header[3]
comment = header[4]
return PassingData(tax_id=_tax_id, gi=gi, comment=comment, acc_ver=acc_ver, chromosome=chromosome)
def parseFastaDescriptionForWUSTLVervetScaffolds(self, descriptionLine=None, FigureOutTaxID_ins=None):
"""
2011-7-6
"""
"""
possible header lines:
>Contig0 12652774 13406928
"""
header = descriptionLine[1:-1] #discard '>' and '\n'
header = header.split()
chromosome = header[0] #contig name is taken as chromosome
"""
p_chromosome = re.compile(r'Contig(\d+)')
if p_chromosome.search(header[0]) is not None:
chromosome = p_chromosome.search(header[0]).groups()[0]
else:
chromosome = None
"""
gi = None
acc_ver = None
comment = None
return PassingData(tax_id=None, gi=gi, comment=comment, acc_ver=acc_ver, chromosome=chromosome)
def parseFastaDescriptionForWUSTLVervetChromosomeGenome(self, descriptionLine=None, FigureOutTaxID_ins=None):
"""
2013.05.09 include 'CAE' in the chromosome ID name.
2013.04.12 header looks like, CAE stands for C. aethiops:
>CAE1
GTGAAAGAAGCCAAAAAG
"""
header = descriptionLine[1:-1] #discard '>' and '\n'
header = header.split()
p_chromosome = re.compile(r'(CAE[\dXYxy]+)')
if p_chromosome.search(header[0]) is not None:
chromosome = p_chromosome.search(header[0]).groups()[0]
else:
chromosome = None
gi = None
acc_ver = None
comment = None
return PassingData(tax_id=None, gi=gi, comment=comment, acc_ver=acc_ver, chromosome=chromosome)
def parseFastaDescriptionForFullVervetBACs(self, descriptionLine=None, FigureOutTaxID_ins=None):
"""
2011-7-6
possible header lines:
>gi|285026568|gb|AC239257.2| Chlorocebus aethiops chromosome UNK clone CH252-270J24, WORKING DRAFT SEQUENCE, 2 unordered pieces
>gi|281332227|gb|AC238852.3| Chlorocebus aethiops BAC clone CH252-133A18 from chromosome 3, complete sequence
>gi|285002488|gb|AC239185.3| Chlorocebus aethiops BAC clone CH252-404N12 from chromosome unknown, complete sequence
"""
header = descriptionLine[1:-1] #discard '>' and '\n'
header = header.split('|')
_tax_id = None
p_chromosome = re.compile(r'UNK clone ([^,]+),') # 1st type of clone description
p2_chromosome = re.compile(r'clone ([^,]+),') # 2nd type of clone description
if p_chromosome.search(header[4]) is not None:
chromosome = p_chromosome.search(header[4]).groups()[0]
else:
if p2_chromosome.search(header[4]) is not None:
chromosome = p2_chromosome.search(header[4]).groups()[0]
else:
chromosome = None
gi = int(header[1])
acc_ver = header[3]
comment = header[4]
return PassingData(tax_id=_tax_id, gi=gi, comment=comment, acc_ver=acc_ver, chromosome=chromosome)
def parse_chromosome_fasta_file(self, db=None, filename=None, tax_id=None, version=None, chunk_size=10000, \
sequence_type_name=None, sequence_type_id=None, run_type=1,
maxNoOfFastaRecords=500):
"""
2011-7-10
add argument maxNoOfFastaRecords: the max number of fasta records before quitting
2011-7-6
add argument run_type
1: chromosome sequences from NCBI genbank
2: vervet scaffolds from WUSTL
3: full vervet BACs from McGill
2010-12-15
fix a bug that _tax_id shall be used in query AnnotAssembly.
This bug caused the db redundancy check to fail.
2010-12-15
if entry already exists in AnnotAssembly, skip it.
2008-07-29
figure out tax_id via FigureOutTaxID
filename could contain multiple fasta blocks
2008-07-27
change to use data structures from GenomeDB.py
2008-07-06
use the firstline (header) of the fasta file to extract which chromosome. using filename is unreliable.
"""
inf = utils.openGzipFile(filename, openMode='r')
line = inf.readline()
new_fasta_block = 1 #'line' is not enough to stop the 'while' loop. after the file reading is exhausted by "for line in inf:", 'line' still contains the stuff from the last line.
no_of_fasta_blocks = 0
while line and new_fasta_block:
new_fasta_block = 0 #set it to 0, assuming only one fasta block, change upon new fasta block
if line[0]!='>': #not fasta block header
for line in inf: #exhaust this fasta block as it's not what's wanted.
if line[0]=='>':
new_fasta_block = 1
break #start from while again
continue
headerData = self.parseFastaDescriptionDict[run_type](line, self.FigureOutTaxID_ins)
if not headerData.chromosome:
sys.stderr.write("Error chromosome for header %s is empty %s.\n"%(line, headerData.chromosome))
import pdb
pdb.set_trace()
if tax_id is not None and headerData.tax_id and tax_id!=headerData.tax_id:
sys.stderr.write("tax_id (%s) not matching the one given (%s). Ignore.\n"%(headerData.tax_id, tax_id))
line = inf.readline()
new_fasta_block = 1
continue
chromosome = headerData.chromosome
sequence_type = db.getSequenceType(short_name=sequence_type_name, id=sequence_type_id)
start = 1
aa_attr_instance = db.checkAnnotAssembly(version=version, tax_id=tax_id, \
chromosome=chromosome, start=start, stop=None, \
sequence_type_id=sequence_type.id)
if aa_attr_instance and aa_attr_instance.raw_sequence_start_id is not None:
# if raw sequences have been associated with this AnnotAssembly and
sys.stderr.write("raw sequences have been associated with this AnnotAssembly (tax_id %s, chr=%s, start=%s). Ignore.\n"%\
(tax_id, chromosome, start))
line = inf.readline()
new_fasta_block = 1
continue
if aa_attr_instance is None:
aa_attr_instance = db.getAnnotAssembly(gi=headerData.gi, acc_ver=headerData.acc_ver, accession =None, \
version =version, tax_id=tax_id, chromosome =chromosome, \
start =start, stop =None, orientation=None, sequence = None,\
raw_sequence_start_id=None, original_path=os.path.abspath(filename),\
sequence_type_id=sequence_type.id, \
chromosome_type_id=None, chromosome_type_name=None, comment=headerData.comment)
if aa_attr_instance.acc_ver and self.p_acc_ver.search(aa_attr_instance.acc_ver):
aa_attr_instance.accession, aa_attr_instance.version = self.p_acc_ver.search(aa_attr_instance.acc_ver).groups()
aa_attr_instance.version = int(aa_attr_instance.version)
else:
aa_attr_instance.accession = None
aa_attr_instance.version = version
if self.debug:
sys.stderr.write("tax_id=%s for %s.\n"%(aa_attr_instance.tax_id, line))
#aa_attr_instance.raw_sequence_start_id = self.get_current_max_raw_sequence_id(curs, raw_sequence_table)+1
passingdata = PassingData()
passingdata.current_start = 1
passingdata.raw_sequence_initiated = False
seq = ''
for line in inf:
if line[0]=='>':
if seq: #last segment from the previous fasta block
self.saveRawSequence(db.session, seq, passingdata, aa_attr_instance)
seq = '' #set to nothing to avoid saving one more RawSequence
new_fasta_block = 1
break #start from while again
seq += line.strip()
if len(seq)>=chunk_size:
seq_to_db = seq[:chunk_size]
self.saveRawSequence(db.session, seq_to_db, passingdata, aa_attr_instance)
seq = seq[chunk_size:] #remove the one already in db
if self.report:
sys.stderr.write("%s\t%s\t%s"%('\x08'*20, no_of_fasta_blocks, passingdata.current_start/chunk_size+1))
if seq: # last segment from last line
self.saveRawSequence(db.session, seq, passingdata, aa_attr_instance)
aa_attr_instance.stop = passingdata.current_stop
db.session.add(aa_attr_instance)
db.session.flush()
no_of_fasta_blocks += 1
if no_of_fasta_blocks>=maxNoOfFastaRecords:
break
sys.stderr.write(" Number of fasta records/chromosomes: %s.\n"%(no_of_fasta_blocks))
del inf
def connectDB(self):
"""
2013.3.14
"""
db = GenomeDatabase(drivername=self.drivername, username=self.db_user,
password=self.db_passwd, hostname=self.hostname, database=self.dbname, schema=self.schema)
db.setup(create_tables=False)
self.db = db
def run(self):
"""
2008-07-27
--GenomeDatabase
--parse_chromosome_fasta_file()
"""
if self.debug:
import pdb
pdb.set_trace()
sys.stderr.write("\tTotally, %d files to be processed.\n"%(len(self.inputFnameLs)))
session = self.db.session
session.begin()
for filename in self.inputFnameLs:
sys.stderr.write("%d/%d:\t%s "%(self.inputFnameLs.index(filename)+1,\
len(self.inputFnameLs),filename))
self.parse_chromosome_fasta_file(db=self.db, filename=filename, tax_id=self.tax_id, version=self.version, \
chunk_size=10000, \
sequence_type_name=self.sequence_type_name, \
sequence_type_id=self.sequence_type_id,\
run_type=self.run_type, maxNoOfFastaRecords=self.maxNoOfFastaRecords)
if self.commit:
session.commit()
else:
session.rollback()