Commit 822454f4 authored by peguerin's avatar peguerin
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alternative spygen ref database

parent 2ba262e6

final/.gitkeep

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main.sh

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@@ -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

main/.gitkeep

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