I have no idea about it, but maybe something goes wrong during the
construction of pygr seqlen files
(pureseq has I think the correct size, but some length is wrong in
seqlen (chrM is a small file (17Ko) but its length in seqlen is huge).
First I concatenate the fasta files with this program :
import sys, os, string
def concatenate(inputFileDir, outputFile):
os.chdir(inputFileDir)
print 'processing ... %s' % os.getcwd()
fileList=os.listdir(inputFileDir)
outFile=open(outputFile,'w')
for fileName in fileList:
for lines in open(fileName,'r').xreadlines():
outFile.write(lines)
outFile.close()
print '%s is constructed' % os.getcwd()
if __name__=='__main__':
INPUTFILE_DIR='D:/data/ucsc/mm8'
OUTPUTFILE='D:/data/ucsc/genome/mm8'
concatenate(INPUTFILE_DIR,OUTPUTFILE)
then I construct pygr file with this program :
def make_blast_db(inputFileDir):
os.chdir(inputFileDir)
fileList=os.listdir(inputFileDir)
for fileName in fileList:
seqdb.BlastDB(fileName)
if __name__=='__main__':
#CREATE PYGR RESSOURCE
INPUTFILE_DIR='D:/data/ucsc/genome'
make_blast_db(INPUTFILE_DIR)
On May 12, 3:32 pm, Istvan Albert <istvan.alb...@gmail.com> wrote:
> On May 12, 6:08 am, michel bellis <fill.i...@9online.fr> wrote:
>
> > I tried your code and got a lot of file longer than 1 000 000. But I
> > do not undestand what is the limit exactly.
>
> The number refers the the length of the sequence not the size of the
> file. The limit of a 32 bit long signed integer is 2,147,483,647
>
> The point that Chris was making is that each human chromosome is at
> most 245 million bp long so how could you end up with sequences that
> are over 2 billion long?
>
> Istvan
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