[pygr-notify] Issue 89 in pygr: Need for solexa seqdb with integer (64bit) ID which requires no hashing/indexing

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Updates:
	Summary: Need for solexa seqdb with integer (64bit) ID which requires no  
hashing/indexing

Comment #2 on issue 89 by deepreds: Need for solexa seqdb with integer  
(64bit) ID which requires no hashing/indexing
http://code.google.com/p/pygr/issues/detail?id=89

Extremely crude idea. 1 character for size of sequence + score (ordinal),  
then save
sequence + score.

outfile1 = open('test.ifa', 'w')
outfile2 = open('test.pfa', 'w')
infile = open('test.fq', 'r')
iCount = 0
while 1:
     line1 = infile.readline()
     line2 = infile.readline()
     line3 = infile.readline()
     line4 = infile.readline()
     if line1 == '' or line2 == '' or line3 == '' or line4 == '': break
     myacc = line1[1:].strip()
     myseq = '%s%s' % (line2.strip(), line4.strip())
     seqsize = chr(len(myseq))
     outfile1.write('%s%s' % (seqsize, myseq))
     outfile2.write('%s\t%d\n' % (myacc, iCount))
     iCount += 1 + len(myseq)
outfile1.close()
outfile2.close()

Two short .seek and .read operations. One for reading size of sequence and  
the other
for reading sequence + score. If we know integer sequence ID (position of  
file, we
can seek by .seek), we can read the sequence and score.

infile = open('test.ifa', 'r')
for lines in open('test.pfa', 'r').xreadlines():
     oldacc, intacc = lines.strip().split('\t')
     intacc = int(intacc)
     infile.seek(intacc)
     seqsize = ord(infile.read(1))
     infile.seek(intacc + 1)
     readseq = infile.read(seqsize)
     myseq, myscore = readseq[:seqsize/2], readseq[seqsize/2:]
     print oldacc, intacc, myseq, myscore

Let me know what you think.

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