/metagenomics_scripts

Primary LanguagePython

metagenomics_scripts

Miscellaneous scripts for metagenomics

checkM

add taxonomic lineage to checkM results

python add_tax.py checkm.txt > checkm_clean.tsv

Centrifuge

add taxonomic lineage to Centrifuge results

python add_tax.py centrifuge.tsv > centrifuge.plus.tsv

We can then generate some reports:

#
# $6 below is uniqueReads
# $5 would be totalReads
#

# superkingdom
awk -F"\t" '{a[$8] += $6} END{for (i in a) print i, a[i]}' centrifuge.plus.tsv | sort -n -k 2 -r

# phylum
awk -F"\t" '{a[$10] += $6} END{for (i in a) print i, a[i]}' centrifuge.plus.tsv | sort -n -k 2 -r

# class
awk -F"\t" '{a[$11] += $6} END{for (i in a) print i, a[i]}' centrifuge.plus.tsv | sort -n -k 2 -r