Support reading and writing to/from file-like objects #148
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| try: | ||
| from pathlib import Path | ||
| except ImportError: | ||
| from pathlib2 import Path # python 2 backport |
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I suppose for python2 this makes pathlib or pathlib2 a dependency? Can we just not support python2 after a certain version of cyvcf2? It would make things so much nicer, especially if we can use the typing library for python 3?
| cdef htsFile *hts | ||
| cdef bytes fname | ||
| cdef bytes mode | ||
| cdef bint from_path |
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there's probably more in VCF that's needed across both VCF and Writer that we can move here.
| @@ -2155,6 +2214,7 @@ cdef from_bytes(s): | |||
| return s | |||
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| # TODO: make Writer extend HTSFile not VCF by moving common methods into HTSFile | |||
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^this should be a tech-debt issue
Also: - "/dev/stdin" works as an input to the VCF (reader) class - writing supported from a file descriptor
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I kind of wish the |
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| # file-like object | ||
| with open(VCF_PATH) as fp: | ||
| run_writer(Writer(fp, v), f, rec) |
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I'm all ears for having a regression test for stdin/stdout support in the reader/writer, but I don't have a good solution
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@brentp fixed up based on your comments, can you resolve my comments? I am particularly interested in python2 support, and if we can get rid of it! |
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@brentp I also noticed that tests are running on travis for this PR, any ideas why not? |
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they are running. not sure why they aren't linked: https://travis-ci.org/github/brentp/cyvcf2/jobs/674073923 |
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@brentp I had PR in another repo where travis wasn't posting its results. Very odd. |
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Build is passing: https://travis-ci.org/github/brentp/cyvcf2/builds/674079601 |
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thank you! |
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