rework affiliation

affiliation.smk

-rule affiliation:
+rule blastn:
 	input:
-		biom = "work/dada/dada.biom",
 		fasta = "work/dada/seqtab.fasta"
 	output:
-		html = "work/FROGS/affiliation.html",
-		biom = "work/FROGS/affiliation.biom"
+		blast = "work/BLAST/seqtab.fasta.blast"
 	threads:
 		config["THREADS"]
 	params:
-		mem_tot = config["THREADS"]*MEM,
 		database = config["DATABASE"]
 	shell:
-		"affiliation_OTU.py "
-		"--nb-cpu {threads} "
-		"--java-mem {params.mem_tot} "
+		"blastn "
+		"-num_threads {threads} "
+		"-task megablast "
+		"-word_size 38 "
+		"-max_target_seqs 500 "
+		"-outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen' "
+		"-query {input.fasta} "
+		"-out {output.blast} "
+		"-db {params.database} "
+
+rule addAffi:
+	input:
+		biom = "work/dada/dada.biom",
+		fasta = "work/dada/seqtab.fasta",
+		blast = "work/BLAST/seqtab.fasta.blast"
+	output:
+		biom = "work/FROGS/affiliation.biom"
+	params:
+		database = config["DATABASE"]
+	shell:
+		"addAffiliation2biom.py "
 		"--reference {params.database} "
-		"--input-biom {input.biom} "
-		"--input-fasta {input.fasta} "
-		"--summary {output.html} "
-		"--output-biom {output.biom}"
+		"--blast-file {input.blast} "
+		"--biom-in {input.biom} "
+		"--biom-out {output.biom} "
 
 rule stats:
 	input: