arq5x / cyvcf Goto Github PK

Hello, cyvcf seems to have the same problem as jamescasbon/PyVCF#108:

>>> import cyvcf
>>> import cPickle
>>> f = open(path)
>>> r = cyvcf.Reader(f)
>>> cPickle.dumps(next(r))
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/user/.virtualenvs/bio-env/lib64/python2.6/copy_reg.py", line 70, in _reduce_ex
    raise TypeError, "can't pickle %s objects" % base.__name__
TypeError: can't pickle _Record objects

I:cyvcf xing$ python setup.py build
running build
running build_py
running build_ext
building 'cyvcf.parser' extension
cc -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c cyvcf/parser.c -o build/temp.macosx-10.11-intel-2.7/cyvcf/parser.o
clang: error: no such file or directory: 'cyvcf/parser.c'
clang: error: no input files
error: command 'cc' failed with exit status 1

Hi,

I would like to use your cyvcf parser, but had problems with setup. It appears that the parser.c file is missing from this repo. Could you please upload it?

Thank you,
Emily

Some of the VCF files from dbSNP exclude any sample information and use VCF as a container for a "generic variant". That appears to be the source of this error:

/usr/local/Cellar/python/2.7.1/lib/python2.7/site-packages/cyvcf/parser.so in cyvcf.parser.Reader.__next__ (cyvcf/parser.c:13509)()
/usr/local/Cellar/python/2.7.1/lib/python2.7/site-packages/cyvcf/parser.so in cyvcf.parser._Record.__cinit__ (cyvcf/parser.c:4232)()
TypeError: expected string or Unicode object, NoneType found

Is there a possibility of supporting these (arguably malformed) VCF files?

Thanks,
Sean

Although I actually found the issue in the
https://github.com/sein-tao/cyvcf
fork, that one doesn't allow issues, while this one seems no longer active.

issue occurs when 2 files are being walked, and both have values at the same position. They are returned in 2 different yields ie
yield (rec1, None)
yield (None,rec2)

instead of being a single yield of
yield (rec1, rec2)

When there are missing genotypes (./.) in the VCF, they get assigned the value 2 in gt_types. I think this probably calls for some convention to represent missing genotypes -- will -1 be appropriate?

Example:

>>> import cyvcf
>>>
>>> vcf_reader = cyvcf.Reader(open('test.vcf', 'rb'))
>>> for record in vcf_reader:
...     print record
... 
1       10014   .       A       C       .       .       .     GT:AD:DP:DP4:FREQ:RD    0/0:9,0:8:8,0,0,0:0.0:8 ./.     0/1:13,3:15:12,0,3,0:0.2:12
1       10043   .       T       TAA     .       .       .    GT:AD:DP:DP4:FREQ:RD    0/0:0:13:12,1,0,0:0.0:13        0/1:2:10:8,0,2,0:0.2:8  ./.
>>> 
>>> vcf_reader = cyvcf.Reader(open('test.vcf', 'rb'))
>>> 
>>> for record in vcf_reader:
...     print record.alleles
... 
['A', 'C']
['T', 'TAA']
>>>
>>> vcf_reader = cyvcf.Reader(open('test.vcf', 'rb'))
>>> for record in vcf_reader:
...     print record.gt_types
... 
[0, 2, 1]
[0, 1, 2]

Hi,

I've used cyvcf for a long time, and really enjoy the speed compared to PyVCF. Lately I've discovered some discrepancies however that make analysis somewhat cumbersome. It specifically deals with parsing the FILTER column. It seems as if cyvcf treats an undefined filter (i.e. '.', often provided with raw,unfiltered calls from GATK) and variants that are deemed reliable after filtering (i.e. 'PASS') in the same way. Both '.' and 'PASS' in the VCF filter column are parsed into None objects by cyvcf. PyVCF treats them differently (None and an empty list, respectively). I discovered this with cyvcf 0.1.11 and PyVCF 0.6.7.

Hi
How is it possible to to get "NA00001 NA00002 NA00003" out of this vcf file
https://github.com/arq5x/cyvcf/blob/master/test/walk_left.vcf ?

Thank you in advance.

Mic

Hi,

I am installing cyvcf on my new Mac, but ran into trouble I have not experienced before. Cython v0.20.1 is used here. Do you have any idea why I get this error?

best,
Sigve

python setup.py build
running build
running build_py
creating build
creating build/lib.macosx-10.9-intel-2.7
creating build/lib.macosx-10.9-intel-2.7/cyvcf
copying cyvcf/init.py -> build/lib.macosx-10.9-intel-2.7/cyvcf
copying cyvcf/filters.py -> build/lib.macosx-10.9-intel-2.7/cyvcf
copying cyvcf/utils.py -> build/lib.macosx-10.9-intel-2.7/cyvcf
copying cyvcf/version.py -> build/lib.macosx-10.9-intel-2.7/cyvcf
running build_ext
cythoning cyvcf/parser.pyx to cyvcf/parser.c
warning: cyvcf/parser.pyx:352:37: cdef variable 'gt_bases' declared after it is used

Error compiling Cython file:

...
raise StopIteration

    #CHROM
    cdef bytes chrom = row[0]
    if self._prepend_chr:
        chrom = 'chr' + chrom
                     ^

cyvcf/parser.pyx:1172:26: Cannot convert 'str' to 'bytes' implicitly. This is not portable.

Error compiling Cython file:

...
cdef list row = line.split('\t')

    #CHROM
    cdef bytes chrom = row[0]
    if other._prepend_chr:
        chrom = 'chr' + chrom
                     ^

cyvcf/parser.pyx:1232:26: Cannot convert 'str' to 'bytes' implicitly. This is not portable.