def build(self, clobber=False, separator='!'):
"""Build index file.
@keyword clobber: Overwrite existing index file (default=False)
"""
if clobber:
try:
self.cursor.execute('drop table Offsets;')
except:
pass
if not self.isIndexed():
schema = """
CREATE TABLE Offsets (
id INTEGER,
accession TEXT,
offset INTEGER
);
create index idx_offsets_id on Offsets (id);
create index idx_offsets_accession on Offsets (accession);
"""
self.connection.executescript(schema)
tmpFile = tempfile.NamedTemporaryFile()
for i,(accession,offset) in enumerate(self._byteOffsetGenerator()):
print >> tmpFile, "%i%s%s%s%i" % (i,separator,accession,separator,offset)
if i % 1000==0:
progressMessage("Sequences: %s", i+1)
progressMessage("Sequences: %s\n", i+1)
tmpFile.flush()
cmd = """sqlite3 -separator '%s' %s '.import "%s" Offsets'""" \
% (separator, self.idxFilename, tmpFile.name)
os.system(cmd)
tmpFile.close()
def build(self, clobber=False, separator='!'):
"""Build index file.
@keyword clobber: Overwrite existing index file (default=False)
"""
if clobber:
try:
self.cursor.execute('drop table Offsets;')
except:
pass
if not self.isIndexed():
schema = """
CREATE TABLE Offsets (
id INTEGER,
accession TEXT,
offset INTEGER
);
create index idx_offsets_id on Offsets (id);
create index idx_offsets_accession on Offsets (accession);
"""
self.connection.executescript(schema)
tmpFile = tempfile.NamedTemporaryFile()
for i, (accession,
offset) in enumerate(self._byteOffsetGenerator()):
print >> tmpFile, "%i%s%s%s%i" % (i, separator, accession,
separator, offset)
if i % 1000 == 0:
progressMessage("Sequences: %s", i + 1)
progressMessage("Sequences: %s\n", i + 1)
tmpFile.flush()
cmd = """sqlite3 -separator '%s' %s '.import "%s" Offsets'""" \
% (separator, self.idxFilename, tmpFile.name)
os.system(cmd)
tmpFile.close()
-Sanger format can encode a Phred quality score from 0 to 93 using ASCII 33 to 126 (although in raw read data the Phred quality score rarely exceeds 60, higher scores are possible in assemblies or read maps).
-Solexa/Illumina 1.0 format can encode a Solexa/Illumina quality score from -5 to 62 using ASCII 59 to 126 (although in raw read data Solexa scores from -5 to 40 only are expected)
-Illumina 1.3+ format can encode a Phred quality score from 0 to 62 using ASCII 64 to 126 (although in raw read data Phred scores from 0 to 40 only are expected).
"""
import os, sys
from srt.fastq import FastqFile
from srt.useful import progressMessage
iFilename = sys.argv[1]
oFilename = sys.argv[2]
if oFilename=="-":
oFilename = sys.stdout
iFile = FastqFile(iFilename)
oFile = FastqFile(oFilename, "w")
i = 0
for header,seq,qual in iFile:
i += 1
if (i % 1000)==0:
progressMessage("# lines %s", i)
qual2 = "".join([chr(ord(q)-64+33) for q in qual])
oFile.write(header, seq, qual2)
progressMessage("# lines %s\n", i)
oFile.close()
Author: Tony Papenfuss
Date: Fri Nov 6 15:44:08 EST 2009
-Sanger format can encode a Phred quality score from 0 to 93 using ASCII 33 to 126 (although in raw read data the Phred quality score rarely exceeds 60, higher scores are possible in assemblies or read maps).
-Solexa/Illumina 1.0 format can encode a Solexa/Illumina quality score from -5 to 62 using ASCII 59 to 126 (although in raw read data Solexa scores from -5 to 40 only are expected)
-Illumina 1.3+ format can encode a Phred quality score from 0 to 62 using ASCII 64 to 126 (although in raw read data Phred scores from 0 to 40 only are expected).
"""
import os, sys
from srt.fastq import FastqFile
from srt.useful import progressMessage
iFilename = sys.argv[1]
oFilename = sys.argv[2]
if oFilename == "-":
oFilename = sys.stdout
iFile = FastqFile(iFilename)
oFile = FastqFile(oFilename, "w")
i = 0
for header, seq, qual in iFile:
i += 1
if (i % 1000) == 0:
progressMessage("# lines %s", i)
qual2 = "".join([chr(ord(q) - 64 + 33) for q in qual])
oFile.write(header, seq, qual2)
progressMessage("# lines %s\n", i)
oFile.close()
