-
I posted a version here:
https://gist.github.com/1870749
Otherwise it goes wrong after a certain number of open connections.
-
on python < 2.7 sys.version_info is a tuple, so this line:
https://github.com/jamescasbon/PyVCF/blob/0ff01c4a83b6ecd2b21e1208e8c1d1f67e06ed15/setup.py#L8
fails.
-
The file test/null_genotype_mono.vcf which is referenced in the latest code was not added to the repository. This breaks the unit tests.
> python -m unittest test.test_vcf.TestRegression
> ./full/pa…
-
As expected, looping through the samples in _parse_samples is rather slow for files with many samples (e.g., [1]). It seems that the main bottlenecks are Python's split() and the fact that looping in…
arq5x updated
12 years ago
-
Currently, we can do the following:
```
>>> for sample in record.samples:
... print sample['GT']
'1|2'
'2|1'
'2/2'
```
It would be nice to have a built in method that looks at the ref and alt al…
arq5x updated
12 years ago
-
This is likely owing to my naivete, but I am working on another tool that depends upon PyVcf. As such, in my `setup.py` I have:
```
install_requires=['numpy', 'pyparsing', 'pysam', 'pyvcf>=0.4.0'],
…
arq5x updated
12 years ago
-
Updating to biopython-1.52, which was released September 22, 2009. Main improvements were to alignment and sequence file conversion, population genetics statistics, and the Bio.SeqIO.indexed_dict()…