workflow: rm partial gene counts rule from analysis (issue #50)

workflow/rules/analysis.smk

@@ -26,23 +26,6 @@ rule analysis_quast:
 ##################################################
 # Proteins
 
-# Number of partial genes
-rule analysis_prodigal_partial:
-    input:
-        os.path.join(RESULTS_DIR, "annotation/prodigal/{rtype}/{tool}/proteins.faa")
-    output:
-        os.path.join(RESULTS_DIR, "annotation/prodigal/{rtype}/{tool}/partial_gene_counts.txt")
-    wildcard_constraints:
-        rtype="|".join(READ_TYPES),
-        tool="|".join(ASSEMBLERS)
-    threads: 1
-    message:
-        "Count partial genes in {input}"
-    shell:
-        "grep -E -o 'partial.{{0,3}}' {input} | grep '10\|01\|11' | wc -l > {output}"
-
-# TODO: summary for tables/figures: separate *.smk
-
 # for CD-HIT
 rule analysis_bbmap_rename:
     input:
@@ -93,15 +76,6 @@ rule analysis_cdhit:
         "cd-hit-2d -i {input.faa2} -i2 {input.faa1} -o {output.faa21} -c 0.9 -n 5 -d 0 -M 16000 -T 8 && "
         "date) 2> {log.err} > {log.out}"
 
-# TODO: summary for tables/figures: separate *.smk
-# """
-# cd-hit-2d -i {input.co1} -i2 {input.co2} -o {output.form1} -c 0.9 -n 5 -d 0 -M 16000 -T 8 &&\
-# cd-hit-2d -i {input.co2} -i2 {input.co1} -o {output.form2} -c 0.9 -n 5 -d 0 -M 16000 -T 8 &&\
-# echo {output.form1} > tmp && grep -c '>' {output.form1} >> tmp &&\
-# echo {output.form2} >> tmp && grep -c '>' {output.form2} >> tmp &&\
-# cat tmp | paste - - > {output.form3}
-# """
-
 ##################################################
 # MMseqs2
 

workflow/steps/analysis.smk

@@ -24,10 +24,6 @@ rule ANALYSIS_ASSEMBLY:
 
 rule ANALYSIS_PROTEINS:
     input:
-        expand(
-            os.path.join(RESULTS_DIR, "annotation/prodigal/{rtype_tool}/partial_gene_counts.txt"),
-            rtype_tool=["%s/%s" % (rtype, tool) for rtype, tool in READ_ASSEMBLERS]
-        ),
         expand(
             os.path.join(RESULTS_DIR, "analysis/cdhit/{combi}.faa"),
             combi=["%s_%s__%s_%s" % (p[0][0], p[0][1], p[1][0], p[1][1]) for p in READ_ASSEMBLER_PAIRS]