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_${i}/PROFILE.db \
-C ALL_CONTIGS -o 10_GENE_TABLES/${i} --init-gene-coverages \
--report-aa-seqs-for-gene-calls; done

3. Collect relevant output tables.

# Gene coverages w. unique gene call number:
/export/dahlefs/work/Metagenomes_chimneys_2020_workfolder/10_GENE_TABLES/${sample}/bin_by_bin/ALL_CONTIGS/ALL_CONTIGS-gene_coverages.txt

# Gene calls w. unique gene call number found at:
/export/dahlefs/work/Metagenomes_chimneys_2020_workfolder/10_GENE_TABLES/${sample}/bin_by_bin/ALL_CONTIGS/ALL_CONTIGS-gene_calls.txt

# header like so:
gene_callers_id	contig	start	stop	direction	KEGG_Class	KEGG_Class (ACCESSION)	KOfam	KOfam (ACCESSION)	KEGG_ModuleKEGG_Module (ACCESSION)	Pfam	Pfam (ACCESSION)	dna_sequence	aa_sequence

4. Edit the tables to include sample names as columns, and then to only consist of columns you want to process.

# add filename as a column
for i in `cat AMOR_2020_Good`; do  words=$(wc -l < ${i}/bin_by_bin/ALL_CONTIGS/ALL_CONTIGS-gene_calls.txt); 
yes ${i} | head -n ${words} > ${i}_out.txt; 
paste ${i}_out.txt ${i}/bin_by_bin/ALL_CONTIGS/ALL_CONTIGS-gene_calls.txt > ${i}_gene_calls.txt ; 
done


# get rid of the filepath info behind sample name.
for i in `cat AMOR_2020_Good`; 
do sed -i 's#/bin_by_bin/ALL_CONTIGS/ALL_CONTIGS-gene_calls.txt##g' ${i}_gene_calls.txt ; 
done

# replace the header with SampleName instead of the name of the individual sample
for i in `cat AMOR_2020_Good`; 
do sed '/'"${i}"'/{s//SampleName/;:p;n;bp}' ${i}_gene_calls.txt >> ${i}_short.txt; 
done

# Fill blank fields with "NaN"
for j in `cat AMOR_2020_Good`; 
do awk 'BEGIN { FS = OFS = "\t" } { for(i=1; i<=NF; i++) if($i ~ /^ *$/) $i = "NaN" }; \
1' ${j}_short.txt > ${j}_full.txt; 
done

# Join all the tables into one large table
awk '
    FNR==1 && NR!=1 { while (/^<header>/) getline; }
    1 {print}
' *full.txt >all_genes.txt

5. Similar process for coverage files

# put samplename as first column
for i in `cat AMOR_2020_Good`; do awk '{print FILENAME (NF?" ":"") $0}' \
${i}/bin_by_bin/ALL_CONTIGS/ALL_CONTIGS-gene_coverages.txt > ${i}_gene_coveragenew.txt ; done

# get rid of filepath
for i in `cat AMOR_2020_Good`;  do sed -i 's#/bin_by_bin/ALL_CONTIGS/ALL_CONTIGS-gene_coverages.txt##g' \
${i}_gene_coveragenew.txt ;  done

# replace the header with column names
for i in `cat AMOR_2020_Good`; do sed -i '1s/.*/SampleName gene_callers_id coverage/'\
 ${i}_coverage_short.txt; done

6. Merge the gene annotation and coverage info

paste all_gene.txt all_gene_coverages.txt > all_all.txt