From c3490b2d933d443ed8a53009efa221cc519a7d93 Mon Sep 17 00:00:00 2001 From: alneberg Date: Thu, 15 Nov 2018 10:27:51 +0100 Subject: [PATCH] Use bin prefix when extracting bins as fasta --- bio/ngs/rules/binning/binning_eval.rules | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bio/ngs/rules/binning/binning_eval.rules b/bio/ngs/rules/binning/binning_eval.rules index 65e07bb..5c35148 100644 --- a/bio/ngs/rules/binning/binning_eval.rules +++ b/bio/ngs/rules/binning/binning_eval.rules @@ -176,10 +176,10 @@ rule binning_extract_16S_fasta_for_mag: all_approved_rrna_euk = "binning/{binning_alg}/{assembly}/output_{quant}/{binning_params}/metaxa_assignment/euk_rRNA.fasta" params: extract_script = config["binning_rules"]["extract_metaxa_mag_script"], - outdir = "binning/{binning_alg}/{assembly}/output_{quant}/{binning_params}/metaxa_assignment" - #bin_prefix = lambda wildcards: "{}_bin".format(wildcards.assembly.replace("meta-sensitive_", "")) + outdir = "binning/{binning_alg}/{assembly}/output_{quant}/{binning_params}/metaxa_assignment", + bin_prefix = lambda wildcards: "{}_bin".format("_".join(wildcards.assembly.split("_")[1:])) shell: - """python {params.extract_script} --clustering_file {input.clustering} --taxonomy_file {input.taxonomy} --rrna_prok_fasta_file <(cat {input.metaxa_arch} {input.metaxa_bac}) --rrna_euk_fasta_file {input.metaxa_euk} --all_approved_file {input.all_approved} --all_approved_euk_file {input.all_approved_euk} --outdir {params.outdir}""" + """python {params.extract_script} --clustering_file {input.clustering} --taxonomy_file {input.taxonomy} --rrna_prok_fasta_file <(cat {input.metaxa_arch} {input.metaxa_bac}) --rrna_euk_fasta_file {input.metaxa_euk} --all_approved_file {input.all_approved_prok} --all_approved_euk_file {input.all_approved_euk} --bin_prefix {params.bin_prefix} --outdir {params.outdir}""" rule binning_correctly_placed_16S: input: