10_GENE_TABLES

Switched back over to kjempefuru for this purpose. Creating a table of gene coverages from each sample assembly to itself. The idea here is to get the coverages from each sample for genes and later match up these gene calls based on the KO number annotated for each. This will require pandas dataframe joining.

1. Create a collection that encompasses all of your contigs to add to your profile

This will make one synthetic "bin".

for i in `cat AMOR_2020_Good`; do anvi-script-add-default-collection -c 03_INDIV_ASSEMBLY/${i}/${i}.prefixed.contigs.db -p 04_INDIV_PROFILES/06_PROFILES/${i}/${i}_to_${i}/PROFILE.db -C ALL_CONTIGS -b ALL_CONTIGS; done

2. Export gene coverage values from each of the 47 assemblies.

for i in `cat AMOR_2020_Good`; do anvi-summarize \
-c 03_INDIV_ASSEMBLY/${i}/${i}.prefixed.contigs.db \
-p 04_INDIV_PROFILES/06_PROFILES/${i}/${i}_to_${i}/PROFILE.db \
-o 10_GENE_TABLES --init-gene-coverages --report-aa-seqs-for-gene-calls; \
done