Error in importing my_SNP.tar.gz

Hi, I was trying to import my SNP file and I followed your instruction here. However, I got the error message as follows: Importing polymorphism set: my/path/to/my_SNP.tar.gz... (This may take a while) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "pyGeno/importation/SNPs.py", line 65, in importSNPs return _importSNPs_dbSNPSNP(setName, species, genomeSource, snpsFile) File "pyGeno/importation/SNPs.py", line 192, in _importSNPs_dbSNPSNP snpData = VCFFile(snpsFile, gziped = True, stream = True) File "pyGeno/tools/parsers/VCFTools.py", line 89, in __init__ self.parse(filename, gziped, stream) File "pyGeno/tools/parsers/VCFTools.py", line 106, in parse ll = self.f.readline() File "/usr/lib/python2.7/gzip.py", line 464, in readline c = self.read(readsize) File "/usr/lib/python2.7/gzip.py", line 268, in read self._read(readsize) File "/usr/lib/python2.7/gzip.py", line 303, in _read self._read_gzip_header() File "/usr/lib/python2.7/gzip.py", line 197, in _read_gzip_header raise IOError, 'Not a gzipped file' IOError: Not a gzipped file

I zipped both manifest.ini and snps.txt to my_SNP.tar.gz using tar -cvzf.

Do you have any idea why this issue comes up and how I could fix this?

Thanks

[Yiming-Shen]

Thanks, I would look into the Agnostic SNP format and try to find a proper way to convert VCF files. Just a quick question. Since the position in VCF file is 1 based and Agnostic SNP is 0 based, does that mean the number of positions in VCF file needs to minus 1 when converted to Agnostic?

[tariqdaouda]

You’re welome, I’m here to help.