added new consensus identity mini alignment function

KatyBrown · May 14, 2024 · 752c415 · 752c415
1 parent 5aff1a6
commit 752c415
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diff --git a/CIAlign/argP.py b/CIAlign/argP.py
@@ -512,6 +512,12 @@ def getParser():
                        rows which have been removed by each function marked \
                        up in corresponding colours. Default: %(default)s")
 
+    optional.add("--plot_consensus_identity", dest="plot_consensus_identity",
+                 action="store_true",
+                 help="""Plot a mini alignment showing positions which are \
+                 identical to or differ from the consensus. \
+                 Default: %(default)s""")
+
     optional.add("--plot_dpi", dest="plot_dpi",
                  type=int, default=300, metavar="(int)",
                  help="DPI for mini alignments. Default: %(default)s")

diff --git a/CIAlign/runCIAlign.py b/CIAlign/runCIAlign.py
@@ -161,6 +161,7 @@ def whichFunctions(args):
     if any([args.plot_input,
             args.plot_output,
             args.plot_markup,
+            args.plot_consensus_identity,
             args.visualise,
             args.all_options]):
         which_functions.append("mini_alignments")
@@ -884,6 +885,20 @@ def runMiniAlignments(args, log, orig_arr, orig_nams, arr, nams,
                                          markupdict=markupdict,
                                          force_numbers=fn,
                                          palette=args.palette)
+    if args.plot_consensus_identity:
+        log.info("Plotting identity to consensus")
+        if not args.silent:
+            print("Plotting identity to consensus")
+        outf = "%s_consensus_identity.%s" % (args.outfile_stem,
+                                             args.plot_format)
+        miniAlignments.drawMiniAlignment(arr, nams, log,
+                                         outf, typ,
+                                         plot_type='boolean',
+                                         dpi=args.plot_dpi,
+                                         width=args.plot_width,
+                                         height=args.plot_height,
+                                         force_numbers=fn,
+                                         palette=args.palette)
 
 
 def runConsensus(args, log, orig_arr, orig_nams, arr, nams, removed_seqs):