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picrust
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mv databases /usr/local/lib/python2.7/dist-packages/picrust/data
step1:
Normalize the OTU abundances for a given OTU table picked against the newest version of Greengenes
normalize_by_copy_number.py -i closed_picked_otus.biom -o normalized_otus.biom
Input tab-delimited OTU table
normalize_by_copy_number.py -f -i closed_picked_otus.tab -o normalized_otus.biom
Change the version of Greengenes used for OTU picking
normalize_by_copy_number.py -g 18may2012 -i closed_picked_otus.biom -o normalized_otus.biom
step2:
Predict KO abundances for a given OTU table picked against the newest version of GreenGenes.
predict_metagenomes.py -i normalized_otus.biom -o predicted_metagenomes.biom
Change output format to plain tab-delimited
predict_metagenomes.py -f -i normalized_otus.biom -o predicted_metagenomes.txt
Predict COG abundances for a given OTU table.
predict_metagenomes.py -i normalized_otus.biom -t cog -o cog_predicted_metagenomes.biom
Predict RFAM abundances for a given OTU table.
predict_metagenomes.py -i normalized_otus.biom -t rfam -o rfam_predicted_metagenomes.biom
Output confidence intervals for each prediction.
predict_metagenomes.py -i normalized_otus.biom -o predicted_metagenomes.biom --with_confidence
Predict metagenomes using a custom trait table in tab-delimited format.
predict_metagenomes.py -i otu_table_for_custom_trait_table.biom -c custom_trait_table.tab -o output_metagenome_from_custom_trait_table.biom
Predict metagenomes,variances,and 95% confidence intervals for each gene category using a custom trait table in tab-delimited format.
predict_metagenomes.py -i otu_table_for_custom_trait_table.biom --input_variance_table custom_trait_table_variances.tab -c custom_trait_table.tab -o output_metagenome_from_custom_trait_table.biom --with_confidence
step3
categorize_by_function.py -i predicted_metagenomes.biom -c KEGG_Pathways -l 3 -o predicted_metagenomes.L3.biom
categorize_by_function.py -f -i predicted_metagenomes.biom -c KEGG_Pathways -l 3 -o predicted_metagenomes.L3.txt
categorize_by_function.py -i observation_table.biom -c taxonomy -l 1 -o observation_table.L1.biom