feat!: Use only a single minimum coverage level

RIVM-bioinformatics · Apr 14, 2022 · cdd29b7 · cdd29b7
1 parent d156599
commit cdd29b7
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Showing 2 changed files with 49 additions and 51 deletions.
diff --git a/TrueConsense/Outputs.py b/TrueConsense/Outputs.py
@@ -10,8 +10,8 @@
 from .Sequences import BuildConsensus
 
 
-def WriteGFF(gffheader, gffdict, outdir, name, cov):
-    with open(f"{outdir}/{name}_cov_ge_{cov}.gff", "w") as out:
+def WriteGFF(gffheader, gffdict, outdir, name):
+    with open(f"{outdir}/{name}.gff", "w") as out:
         out.write(gffheader)
 
         for k, v in gffdict.items():
@@ -24,7 +24,7 @@ def WriteGFF(gffheader, gffdict, outdir, name, cov):
 
 
 def WriteOutputs(
-    cov,
+    mincov,
     iDict,
     uGffDict,
     inputbam,
@@ -44,16 +44,16 @@ def WriteOutputs(
     today = date.today().strftime("%Y%m%d")
 
     bam = Readbam(inputbam)
-    consensus, newgff = BuildConsensus(cov, iDict, uGffDict, IncludeAmbig, bam, True)
-    consensus_noinsert = BuildConsensus(cov, iDict, uGffDict, IncludeAmbig, bam, False)[
-        0
-    ]
+    consensus, newgff = BuildConsensus(mincov, iDict, uGffDict, IncludeAmbig, bam, True)
+    consensus_noinsert = BuildConsensus(
+        mincov, iDict, uGffDict, IncludeAmbig, bam, False
+    )[0]
 
     if gffout is not None:
-        WriteGFF(gffheader, newgff, gffout, name, cov)
+        WriteGFF(gffheader, newgff, gffout, name)
 
     if WriteVCF is not None:
-        hasinserts, insertpositions = ListInserts(iDict, cov, bam)
+        hasinserts, insertpositions = ListInserts(iDict, mincov, bam)
 
         q = 0
         for record in SeqIO.parse(ref, "fasta"):
@@ -65,7 +65,7 @@ def WriteOutputs(
 
         seqlist = list(consensus_noinsert.upper())
 
-        with open(f"{os.path.abspath(WriteVCF)}/{name}_cov_ge_{cov}.vcf", "w") as out:
+        with open(f"{os.path.abspath(WriteVCF)}/{name}.vcf", "w") as out:
             out.write(
                 f"""##fileformat=VCFv4.3
 ##fileDate={today}
@@ -117,7 +117,7 @@ def WriteOutputs(
                     for lposition in insertpositions:
                         if i == lposition:
                             currentcov = GetCoverage(iDict, i + 1)
-                            if currentcov > cov:
+                            if currentcov > mincov:
                                 for y in insertpositions.get(lposition):
                                     to_insert = str(
                                         insertpositions.get(lposition).get(y)
@@ -130,5 +130,5 @@ def WriteOutputs(
                                     else:
                                         continue
 
-    with open(f"{os.path.abspath(outdir)}/{name}_cov_ge_{cov}.fa", "w") as out:
-        out.write(f">{name}_cov_ge_{cov}\n{consensus}\n")
+    with open(f"{os.path.abspath(outdir)}/{name}.fa", "w") as out:
+        out.write(f">{name} mincov={mincov}\n{consensus}\n")
diff --git a/TrueConsense/TrueConsense.py b/TrueConsense/TrueConsense.py
@@ -127,13 +127,12 @@ def currentpath():
     )
 
     reqs.add_argument(
-        "--coverage-levels",
+        "--coverage-level",
         "-cov",
         type=int,
-        nargs="+",
-        default=1,
-        metavar="1 5 10",
-        help="List of one or multiple 'levels' that will be used as the minimum coverage",
+        default=30,
+        metavar="100",
+        help="The minimum coverage level of the consensus and variant calls",
         required=True,
     )
 
@@ -251,9 +250,8 @@ def main():
     elif args.noambiguity is True:
         IncludeAmbig = False
 
-    parallel(
-        WriteOutputs,
-        args.coverage_levels,
+    WriteOutputs(
+        args.coverage_level,
         indexDict,
         GffDict,
         args.input,
@@ -268,33 +266,33 @@ def main():
     )
 
 
-def parallel(
-    function,
-    covlist,
-    indexDict,
-    GffDict,
-    inputbam,
-    IncludeAmbig,
-    WriteVCF,
-    name,
-    ref,
-    gffoutdir,
-    gffheader,
-    outdir,
-    workers,
-):
-    parmap.map(
-        function,
-        covlist,
-        indexDict,
-        GffDict,
-        inputbam,
-        IncludeAmbig,
-        WriteVCF,
-        name,
-        ref,
-        gffoutdir,
-        gffheader,
-        outdir,
-        pm_processes=workers,
-    )
+# def parallel(
+#     function,
+#     covlist,
+#     indexDict,
+#     GffDict,
+#     inputbam,
+#     IncludeAmbig,
+#     WriteVCF,
+#     name,
+#     ref,
+#     gffoutdir,
+#     gffheader,
+#     outdir,
+#     workers,
+# ):
+#     parmap.map(
+#         function,
+#         covlist,
+#         indexDict,
+#         GffDict,
+#         inputbam,
+#         IncludeAmbig,
+#         WriteVCF,
+#         name,
+#         ref,
+#         gffoutdir,
+#         gffheader,
+#         outdir,
+#         pm_processes=workers,
+#     )