Refactor sample loading code#104
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Codecov Report
@@ Coverage Diff @@
## master #104 +/- ##
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- Coverage 85.59% 84.86% -0.74%
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Files 31 31
Lines 1534 1526 -8
Branches 242 239 -3
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- Hits 1313 1295 -18
- Misses 170 178 +8
- Partials 51 53 +2
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| def main(args): | ||
| if (args.num_bands is None) is not (args.band is None): | ||
| raise ValueError('Must specify --num-bands and --band together') | ||
| myband = args.band - 1 if args.band else None |
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The human interface (CLI) expects the band to be 1-based (band \in {1..numbands}), whereas the Python and C++ APIs expect band to be 0-based (band \in {0..numbands-1}).
| for seqfile in seqfiles: | ||
| if mask: | ||
| if numbands: | ||
| nr, nk = sketch.consume_seqfile_banding_with_mask( |
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Bulk loading with mask now available from khmer master.
| print('[kevlar::counting] ', message, file=logfile) | ||
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| if outfile: | ||
| if not outfile.endswith(('.ct', '.counttable')): |
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This behavior (with respect to filename extensions for saved sketches) should be documented somewhere. A single function to handle reading/writing sketches would help. One already exists, but it isn't suited for all cases IIRC.
2 participants
Most of these changes were lumped together with (and are orthogonal to the main thrust of) a PR that likely will not be merged (#102).
The idea is to make the "sequentially diluted loading" strategy optional, and to generally clean things up a bit. Parallel loading should be handled in a separate PR.
Something to consider: there are functions that autodetects whether input files are Fastq/Fasta or sketches and invokes the appropriate command to load them. So far this has only applied to single file names, but it will clean up the code quite a bit in some places if this can handle file lists appropriately.