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Minor output formatting #282

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merged 1 commit into from
Dec 20, 2023
Merged

Minor output formatting #282

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6 changes: 3 additions & 3 deletions vamb/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -610,6 +610,7 @@ def calc_rpkm(
else:
assert isinstance(path, list)
logger.info(f"\tParsing {len(path)} BAM files with {nthreads} threads")
logger.info(f"\tMin identity: {abundance_options.min_alignment_id}")

abundance = vamb.parsebam.Abundance.from_files(
path,
Expand All @@ -621,10 +622,9 @@ def calc_rpkm(
)
abundance.save(outdir.joinpath("abundance.npz"))

logger.info(f"\tMin identity: {abundance.minid}")
logger.info("\tOrder of columns is:")
for samplename in abundance.samplenames:
logger.info(f"\t\t{samplename}")
for i, samplename in enumerate(abundance.samplenames):
logger.info(f"\t{i:>6}: {samplename}")

elapsed = round(time.time() - begintime, 2)
logger.info(f"\tProcessed RPKM in {elapsed} seconds.\n")
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2 changes: 1 addition & 1 deletion vamb/encode.py
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Original file line number Diff line number Diff line change
Expand Up @@ -411,7 +411,7 @@ def trainepoch(
epoch_absseloss += ab_sse.data.item()

logger.info(
"\t\tEpoch: {:>3} Loss: {:.5e} CE: {:.5e} AB: {:.5e} SSE: {:.5e} KLD: {:.5e} Batchsize: {}".format(
"\t\tEpoch: {:>3} Loss: {:.5e} CE: {:.5e} AB: {:.5e} SSE: {:.5e} KLD: {:.5e} Batchsize: {:>4}".format(
epoch + 1,
epoch_loss / len(data_loader),
epoch_celoss / len(data_loader),
Expand Down