Commit 822454f4 authored by peguerin's avatar peguerin

alternative spygen ref database

parent 2ba262e6
......@@ -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
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