Commit 34a3025c authored by Midoux Cedric's avatar Midoux Cedric
Browse files

rework affiliation

parent ea533335
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:
......
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