Added bam_color_by_tag option

Author: simondrue

src/sessionizer/create_igv_session.py

@@ -103,6 +103,7 @@ def generate_igv_session(
     genome_path: Path,
     bam_group_by: List[AllignmentGroupByOption],
     bam_color_by: List[AllignmentColorByOption],
+    bam_color_by_tag: List[str],
     bam_display_mode: List[AllignmentDisplayModeOption],
     bam_hide_small_indels: List[bool],
     bam_small_indel_threshold: List[int],
@@ -138,6 +139,7 @@ def generate_igv_session(
     if alignment_files:
         bam_group_by = hanlde_attribute("bam_group_by", bam_group_by, alignment_files, "alignment files")
         bam_color_by = hanlde_attribute("bam_color_by", bam_color_by, alignment_files, "alignment files")
+        bam_color_by_tag = hanlde_attribute("bam_color_by_tag", bam_color_by_tag, alignment_files, "alignment files")
         bam_display_mode = hanlde_attribute("bam_display_mode", bam_display_mode, alignment_files, "alignment files")
         bam_hide_small_indels = hanlde_attribute("bam_hide_small_indels", bam_hide_small_indels, alignment_files, "alignment files")
         bam_small_indel_threshold = hanlde_attribute("bam_small_indel_threshold", bam_small_indel_threshold, alignment_files, "alignment files")
@@ -170,6 +172,7 @@ def generate_igv_session(
     # Allignment files
     bam_group_by_cycle = cycle(bam_group_by)
     bam_color_by_cycle = cycle(bam_color_by)
+    bam_color_by_tag_cycle = cycle(bam_color_by_tag)
     bam_display_mode_cycle = cycle(bam_display_mode)
     bam_hide_small_indels_cycle = cycle(bam_hide_small_indels)
     bam_small_indel_threshold_cycle = cycle(bam_small_indel_threshold)
@@ -202,6 +205,7 @@ def generate_igv_session(
                     height=height,
                     group_by=next(bam_group_by_cycle),
                     color_by=next(bam_color_by_cycle),
+                    color_by_tag=next(bam_color_by_tag_cycle),
                     hide_small_indels=next(bam_hide_small_indels_cycle),
                     small_indel_threshold=next(bam_small_indel_threshold_cycle),
                     display_mode=next(bam_display_mode_cycle),

src/sessionizer/main.py

@@ -107,6 +107,13 @@ def run(
             rich_help_panel=ALIGNMENT_OPTIONS,
         ),
     ] = [AllignmentColorByOption.NONE],
+    bam_color_by_tag: Annotated[
+        List[str],
+        typer.Option(
+            help="Parameter to color bams by tag.",
+            rich_help_panel=ALIGNMENT_OPTIONS,
+        ),
+    ] = [""],
     bam_display_mode: Annotated[
         List[AllignmentDisplayModeOption],
         typer.Option(
@@ -251,6 +258,7 @@ def run(
         genome_path=genome_path,
         bam_group_by=bam_group_by,
         bam_color_by=bam_color_by,
+        bam_color_by_tag=bam_color_by_tag,
         bam_display_mode=bam_display_mode,
         bam_hide_small_indels=bam_hide_small_indels,
         bam_small_indel_threshold=bam_small_indel_threshold,

src/sessionizer/track_elements.py

@@ -50,7 +50,6 @@ class AllignmentColorByOption(str, Enum):
     ZMW = "zmw"
     BISULFITE = "bisulfite"
     NOMESEQ = "nomeseq"
-    TAG = "tag"
     UNEXPECTED_PAIR = "unexpected_pair"
     MAPPED_SIZE = "mapped_size"
     LINK_STRAND = "link_strand"
@@ -63,6 +62,7 @@ class AllignmentColorByOption(str, Enum):
     SMRT_CCS_FWD_PW = "smrt_ccs_fwd_pw"
     SMRT_CCS_REV_IPD = "smrt_ccs_rev_ipd"
     SMRT_CCS_REV_PW = "smrt_ccs_rev_pw"
+    TAG = "tag"  # Special case - needs to be acompained by tag value
 
     def __str__(self):
         return self.value
@@ -122,6 +122,7 @@ def add_track(self, session_panel: ET.Element):
 class AllignmentTrack(DataTrack):
     group_by: AllignmentGroupByOption
     color_by: AllignmentColorByOption
+    color_by_tag: str
     display_mode: AllignmentDisplayModeOption
 
     hide_small_indels: bool
@@ -159,6 +160,8 @@ def add_track(self, session_panel: ET.Element):
             "RenderOptions",
         )
         render_options.set("colorOption", str(self.color_by.name))
+        if self.color_by == AllignmentColorByOption.TAG:
+            render_options.set("colorByTag", self.color_by_tag)
         render_options.set("groupByOption", str(self.group_by.name))
         render_options.set("hideSmallIndels", str(self.hide_small_indels).lower())
         render_options.set("smallIndelThreshold", str(self.small_indel_threshold))

tests/test_create_igv_session.py

@@ -46,6 +46,7 @@ def test_attribute_handling(self):
             genome=GENOME.HG38,
             genome_path="",
             bam_color_by=[AllignmentColorByOption.NONE],
+            bam_color_by_tag=[""],
             bam_display_mode=[AllignmentDisplayModeOption.COLLAPSED],
             bam_hide_small_indels=[False],
             bam_small_indel_threshold=[0],
@@ -73,6 +74,35 @@ def test_attribute_handling(self):
             genome=GENOME.HG38,
             genome_path="",
             bam_color_by=[AllignmentColorByOption.NONE],
+            bam_color_by_tag=[""],
+            bam_display_mode=[AllignmentDisplayModeOption.COLLAPSED],
+            bam_hide_small_indels=[False],
+            bam_small_indel_threshold=[0],
+            bam_show_coverage=[False],
+            bam_show_junctions=[False],
+            bw_ranges=[BigWigRangeOption(minimum=0.0, baseline=0.0, maximum=0.0)],
+            bw_color=[RGBColorOption.NONE],
+            bw_negative_color=[RGBColorOption.NONE],
+            bw_plot_type=[BigWigPlotTypeOption.NONE],
+            bw_auto_scale=[False],
+            vcf_show_genotypes=[False],
+            vcf_feature_visibility_window=[0],
+            gtf_display_mode=[GtfDisplayModeOption.COLLAPSED],
+        )
+
+        self.assertRaises(
+            ValueError,
+            generate_igv_session,
+            # Relevant arguments
+            files=[self.input_bam],
+            bam_color_by=[AllignmentColorByOption.TAG],
+            bam_color_by_tag=["PS"],
+            # Other arguments
+            names=[],
+            heights=[],
+            genome=GENOME.HG38,
+            genome_path="",
+            bam_group_by=[AllignmentGroupByOption.NONE],
             bam_display_mode=[AllignmentDisplayModeOption.COLLAPSED],
             bam_hide_small_indels=[False],
             bam_small_indel_threshold=[0],
@@ -101,6 +131,7 @@ def test_attribute_handling(self):
             genome=GENOME.HG38,
             genome_path="",
             bam_color_by=[AllignmentColorByOption.NONE],
+            bam_color_by_tag=[""],
             bam_display_mode=[AllignmentDisplayModeOption.COLLAPSED],
             bam_group_by=[AllignmentGroupByOption.NONE],
             bam_hide_small_indels=[False],
@@ -128,6 +159,7 @@ def test_attribute_handling(self):
             genome=GENOME.HG38,
             genome_path="",
             bam_color_by=[AllignmentColorByOption.NONE],
+            bam_color_by_tag=[""],
             bam_display_mode=[AllignmentDisplayModeOption.COLLAPSED],
             bam_group_by=[False],
             bam_hide_small_indels=[False],
@@ -154,6 +186,7 @@ def test_attribute_handling(self):
             genome=GENOME.HG38,
             genome_path="",
             bam_color_by=[AllignmentColorByOption.NONE],
+            bam_color_by_tag=[""],
             bam_display_mode=[AllignmentDisplayModeOption.COLLAPSED],
             bam_group_by=[False],
             bam_hide_small_indels=[False],
@@ -181,6 +214,7 @@ def test_attribute_handling(self):
             genome=GENOME.HG38,
             genome_path="",
             bam_color_by=[AllignmentColorByOption.NONE],
+            bam_color_by_tag=[""],
             bam_display_mode=[AllignmentDisplayModeOption.COLLAPSED],
             bam_group_by=[False],
             bam_hide_small_indels=[False],