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Fix Issues with Microsetta-Processing Scripts for American Gut Project Data #19

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Fix Issues with Microsetta-Processing Scripts for American Gut Project Data #19

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2 changes: 1 addition & 1 deletion scripts/05c.beta.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ if [[ ! -z "${TMI_WEIGHTED_UNIFRAC}" ]]; then
echo "${d}/beta/weighted_normalized_unifrac.qza" >> $SAFE_TO_DROP

python k_neighbors.py neighbors \
--distance-matrix ${d}/beta/weighted_unifrac.qza \
--distance-matrix ${d}/beta/weighted_normalized_unifrac.qza \
--output ${d}/beta/weighted_unifrac_neighbors.tsv \
--k 100 \
--mask-study-id 10317
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4 changes: 2 additions & 2 deletions scripts/metadata_operations.py
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Expand Up @@ -200,8 +200,8 @@ def anonymize_sample_ids(input_output_md, input_output_tab):

mapping.update(_anonymize_sample_and_study(random_studies, study_grp,
md))

tab.update_ids(mapping, inplace=True, strict=False)
if len(mapping) > 0:
tab.update_ids(mapping, inplace=True, strict=False)
with biom.util.biom_open(input_output_tab, 'w') as fp:
tab.to_hdf5(fp, 'asd')

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