analysis: added fastani (issue #80)

workflow/envs/fastani.yaml

+channels:
+    - conda-forge
+    - bioconda
+    - defaults
+  dependencies:
+    - fastani=1.32
+  
\ No newline at end of file

workflow/rules/analysis.smk

@@ -39,7 +39,7 @@ rule analysis_mashmap_one2one:
         out1=os.path.join(RESULTS_DIR, "analysis/mashmap/{rtype1}_{tool1}__{rtype2}_{tool2}.one2one.out")
         out2=os.path.join(RESULTS_DIR, "analysis/mashmap/{rtype2}_{tool2}__{rtype1}_{tool1}.one2one.out")
     log:
-        "logs/analysis.mashmap.one2on2.{rtype1}.{tool1}.{rtype2}.{tool2}.log"
+        "logs/analysis.mashmap.one2one2.{rtype1}.{tool1}.{rtype2}.{tool2}.log"
     wildcard_constraints:
         rtype1="|".join(READ_TYPES),
         rtype2="|".join(READ_TYPES),
@@ -59,6 +59,34 @@ rule analysis_mashmap_one2one:
         "mashmap -r ${asm2} -q ${asm1} {params.params} -t {threads} -o {output.out2} && "
         "date) &> {log}"
 
+##################################################
+# FastANI
+
+rule analysis_fastani_one2one:
+    input:
+        expand(
+            os.path.join(RESULTS_DIR, "assembly/{rtype_tool}/ASSEMBLY.POLISHED.fasta"),
+            rtype_tool=["%s/%s" % (rtype, tool) for rtype, tool in READ_ASSEMBLERS],
+        )
+    output:
+        out=os.path.join(RESULTS_DIR, "analysis/fastani/many2many.out"),
+        qlrl=temp(os.path.join(RESULTS_DIR, "analysis/fastani/input.txt"))
+    log:
+        "logs/analysis.fastani.many2many.log"
+    threads:
+        config["fastani"]["threads"]
+    params:
+        params="-s 1000 -pi 95 -f one-to-one --noSplit"
+    conda:
+        os.path.join(ENV_DIR, "fastani.yaml")
+    message:
+        "fastani: one-to-one: {input}"
+    shell:
+        "(date && "
+        "echo \"{input}\" | sed 's/\s\+/\\n/g' > {output.qlrl} && "
+        "fastANI --ql {output.qlrl} --rl {output.qlrl} -o {output.out} --threads {threads} && "
+        "date) &> {log}"
+
 ##################################################
 # CD-HIT
 # https://github.com/weizhongli/cdhit/wiki/3.-User's-Guide#CDHIT2D