# $PATH represents the location of the files.
split_libraries.py -f $PATH/SEQUENCE-full.fasta -q $PATH/SEQUENCE-full.qual -m $PATH/Mapping.txt -b 8 -o $PATH/split_lib/
pick_open_reference_otus.py -i $PATH/split_lib/seqs.fna -o $PATH/otus
#For below: ID chimeras - a is for the alignment reference path. This was copied from the config file and included to ensure the script requirements were met.
identify_chimeric_seqs.py -i $PATH/otus/pynast_aligned_seqs/rep_set_aligned.fasta
-o $PATH/otus/chimeric_seqs.txt -m ChimeraSlayer
-a
/macqiime/anaconda/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta
filter_fasta.py -f $PATH/otus/pynast_aligned_seqs/rep_set_aligned.fasta -o $PATH/otus/pynast_aligned_seqs/rep_set_aligned-nochimera.fasta -s $PATH/otus/chimeric_seqs.txt --negate
filter_alignment.py -i $PATH/otus/pynast_aligned_seqs/rep_set_aligned-nochimera.fasta -o $PATH/otus/
make_phylogeny.py -i $PATH/otus/pynast_aligned_seqs/rep_set_aligned-nochimera_pfiltered.fasta -o $PATH/otus/rep_set_aligned-nochimera.tre
make_otu_table.py -i #PATH/otus/final_otu_map_mc2.txt -o $PATH/otus/otu_table_nochimera.biom -t $PATH/otus/uclust_assigned_taxonomy/rep_set_tax_assignments.txt -e $PATH/otus/chimeric_seqs.txt
##Remove Choloroplasts, Mitochondria, Archeae, & Unclassified
filter_taxa_from_otu_table.py -i $PATH/otus/otu_table_nochimera.biom -o $PATH/otus/otu_table_mc2_w_tax_nochimera_noChloroMitoUnID.biom -n Unassigned,k__Archaea,c__Chloroplast,f__mitochondria