Merge pull request #303 from LCoffion/edit_RGP_output

Edit regions output
labgem · Nov 26, 2024 · 4ec681f · 4ec681f
2 parents 583e0cb + f010295
commit 4ec681f
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diff --git a/docs/user/RGP/rgpOutputs.md b/docs/user/RGP/rgpOutputs.md
@@ -25,6 +25,7 @@ The file has the following format :
 | stop         | The stop position of the RGP in the contig.                                                                                                                                                                         |
 | length       | The length of the RGP in nucleotide                                                                                                                                                                                 |
 | coordinates  | The coordinates of the region. If the region overlap the contig edges will be right with join coordinates syntax (*i.e* 1523..1758,1..57)                                                                           |
+| score        | Score of the RGP.                                                                                                                                                                                                   |
 | contigBorder | This is a boolean column. If the RGP is on a contig border it will be True, otherwise, it will be False. This often can indicate that, if an RGP is on a contig border it is probably not complete.                 |
 | wholeContig  | This is a boolean column. If the RGP is an entire contig, it will be True, and False otherwise. If a RGP is an entire contig it can possibly be a plasmid, a region flanked with repeat sequences or a contaminant. |
 

diff --git a/ppanggolin/formats/writeFlatPangenome.py b/ppanggolin/formats/writeFlatPangenome.py
@@ -1096,6 +1096,7 @@ def write_rgp_table(regions: Set[Region], output: Path, compress: bool = False):
             "stop",
             "length",
             "coordinates",
+            "score",
             "contigBorder",
             "wholeContig",
         ]
@@ -1117,6 +1118,7 @@ def write_rgp_table(regions: Set[Region], output: Path, compress: bool = False):
                 "stop": region.stop,
                 "length": region.length,
                 "coordinates": region.string_coordinates(),
+                "score": region.score,
                 "contigBorder": region.is_contig_border,
                 "wholeContig": region.is_whole_contig,
             }

diff --git a/ppanggolin/workflow/all.py b/ppanggolin/workflow/all.py
@@ -602,6 +602,14 @@ def add_workflow_args(parser: argparse.ArgumentParser):
         "it will be assigned to its own unique cluster as a singleton.",
     )
 
+    optional.add_argument(
+        "--use_pseudo",
+        required=False,
+        action="store_true",
+        help="In the context of provided annotation, use this option to read pseudogenes. "
+        "(Default behavior is to ignore them)",
+    )
+
     optional.add_argument(
         "-K",
         "--nb_of_partitions",