alternative spygen ref database

main.sh

@@ -40,9 +40,26 @@ obiuniq -m sample $ALL_FAS > $dereplicated_all
 
 
 ###############################################################################
-#REF_DATABASE="/media/superdisk/edna/donnees/reference_database_teleo/"
-#base_pref="embl_std"
+REF_DATABASE="/media/superdisk/edna/donnees/reference_database_teleo/"
+base_pref="embl_std"
 
 ##Assign each sequence to a taxon
 all_sample_sequences_tag="${dereplicated_all/.fasta/.tag.fasta}"
 ecotag -d "$REF_DATABASE"/"${base_pref}" -R "$REF_DATABASE"/db_"${base_pref}".fasta $dereplicated_all > $all_sample_sequences_tag
+##The sequences can be sorted by decreasing order of count
+all_sample_sequences_sort="${all_sample_sequences_tag/.fasta/.sort.fasta}"
+obisort -k count -r $all_sample_sequences_tag > $all_sample_sequences_sort
+##generate a table final results
+obitab -o $all_sample_sequences_sort > final/all.csv
+
+## Assign each sequence to a taxon according to alternative SPYGEN fasta sequences
+
+spygen_bdr_fasta="/donnees/rhone_all/teleo_V1_0_VM.fasta"
+all_sample_sequences_tag-spygen="${dereplicated_all/.fasta/.tag-spygen.fasta}"
+ecotag -d "$REF_DATABASE"/"${base_pref}" -R "$spygen_bdr_fasta" $dereplicated_all > $all_sample_sequences_tag-spygen
+##The sequences can be sorted by decreasing order of count
+all_sample_sequences_sort="${all_sample_sequences_tag-spygen/.fasta/.sort.fasta}"
+obisort -k count -r $all_sample_sequences_tag > $all_sample_sequences_sort
+##generate a table final results
+obitab -o $all_sample_sequences_sort > final/all-spygen.csv
+