Re: [Samtools-help] Tabix issues

[Heng Li <lh...@sa...>]

Sorry, I do not know enough about Windows. You may consider pysam.

Heng

On Jun 23, 2011, at 3:35 PM, Jake Christiansen wrote:

> When attempting to run tabix from a python program in eclipse ide, my program throws errors.  Python version is 2.6, tabix version is 0.2.5, running on Windows 7.  The errors thrown are as follows:
>  File "C:\Users\jcc7\workspace\GeneZoom\src\genezoom.py", line 113, in main
>     vcf = vcfReader( options.vcf_file )
>   File "C:\Users\jcc7\workspace\GeneZoom\src\vcfutils.py", line 75, in __init__
>     self._vcf = tabix.Tabix(filename)
>   File "C:\Python26\lib\tabix.py", line 50, in __init__
>     self.tabix = tabix_init();
>   File "C:\Python26\lib\tabix.py", line 32, in tabix_init
>     tabix = load_shared_library('tabix')
>   File "C:\Python26\lib\tabix.py", line 22, in load_shared_library
>     candidates = glob.glob(_path+'/lib'+lib+suf);
> UnboundLocalError: local variable 'suf' referenced before assignment
> Exception AttributeError: "Tabix instance has no attribute 'tabix'" in <bound method Tabix.__del__ of <tabix.Tabix instance at 0x034A91C0>> ignored
> 
> genezoom.py is my own program, which attempts to define a vcfReader through vcfutils, by using tabix.  But the error is within tabix itself, in the following code:
> def load_shared_library(lib, _path='.', ver='*'):
>     """Search for and load the tabix library. The
>     expectation is that the library is located in
>     the current directory (ie. "./")
>     """
>     # find from the system path
>     path = find_library(lib)
>     if (path == None): # if fail, search in the custom directory
>         s = platform.system()
>         if (s == 'Darwin'): suf = ver+'.dylib'
>         elif (s == 'Linux'): suf = '.so'+ver
>         candidates = glob.glob(_path+'/lib'+lib+suf);
>         if (len(candidates) == 1): path = candidates[0]
>         else: return None
>     cdll.LoadLibrary(path)
>     return CDLL(path)
> 
> The error thrown is due to the fact that I am running Windows 7, and not using a Darwin or Linux operating system, thus "suf" is never initialized.  Is there a way to get this to work, or is there a link to a Windows-viable version (did I just accidentally download the Mac/Linux version instead of the Windows version)?
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