fix intervals loading and plotting

ygidtu · Jun 13, 2024 · b7e6da3 · b7e6da3
1 parent 4cfee59
commit b7e6da3
Show file tree

Hide file tree

Showing 8 changed files with 85 additions and 84 deletions.
diff --git a/AppImageBuilder.yml b/AppImageBuilder.yml
@@ -11,7 +11,7 @@ AppDir:
   app_info:
     id: org.appimage-crafters.trackplot
     name: trackplot
-    version: 0.3.8
+    version: 0.4.0
     # Set the python executable as entry point
     exec: "bin/python3"
     # Set the application main script path as argument. Use '$@' to forward CLI parameters

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "trackplot"
-version = "0.3.8"
+version = "0.4.0"
 description = "The trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets. https://sashimi.readthedocs.io/"
 authors = ["ygidtu <[email protected]>"]
 license = "BSD-3"

diff --git a/requirements.txt b/requirements.txt
@@ -3,7 +3,7 @@ asciitree==0.3.3 ; python_version >= "3.8" and python_version < "3.12"
 blinker==1.8.2 ; python_version >= "3.8" and python_version < "3.12"
 blosc2==2.0.0 ; python_version >= "3.8" and python_version < "3.12"
 cairocffi==1.7.0 ; python_version >= "3.8" and python_version < "3.12"
-certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.12"
+certifi==2024.6.2 ; python_version >= "3.8" and python_version < "3.12"
 cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.12"
 charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.12"
 click-option-group==0.5.6 ; python_version >= "3.8" and python_version < "3.12"
@@ -17,7 +17,7 @@ cytoolz==0.12.3 ; python_version >= "3.8" and python_version < "3.12"
 dill==0.3.8 ; python_version >= "3.8" and python_version < "3.12"
 filetype==1.2.0 ; python_version >= "3.8" and python_version < "3.12"
 flask==2.3.3 ; python_version >= "3.8" and python_version < "3.12"
-fonttools==4.52.4 ; python_version >= "3.8" and python_version < "3.12"
+fonttools==4.53.0 ; python_version >= "3.8" and python_version < "3.12"
 h5py==3.11.0 ; python_version >= "3.8" and python_version < "3.12"
 hicmatrix==15 ; python_version >= "3.8" and python_version < "3.12"
 idna==3.7 ; python_version >= "3.8" and python_version < "3.12"
@@ -34,7 +34,7 @@ msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.12"
 multiprocess==0.70.16 ; python_version >= "3.8" and python_version < "3.12"
 numexpr==2.8.6 ; python_version >= "3.8" and python_version < "3.12"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.12"
-packaging==24.0 ; python_version >= "3.8" and python_version < "3.12"
+packaging==24.1 ; python_version >= "3.8" and python_version < "3.12"
 pandas==1.5.3 ; python_version >= "3.8" and python_version < "3.12"
 pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.12"
 py-cpuinfo==9.0.0 ; python_version >= "3.8" and python_version < "3.12"
@@ -46,7 +46,7 @@ pysam==0.21.0 ; python_version >= "3.8" and python_version < "3.12"
 python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.12"
 pytz==2024.1 ; python_version >= "3.8" and python_version < "3.12"
 pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.12"
-requests==2.32.2 ; python_version >= "3.8" and python_version < "3.12"
+requests==2.32.3 ; python_version >= "3.8" and python_version < "3.12"
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.12"
 seaborn==0.12.2 ; python_version >= "3.8" and python_version < "3.12"
 setuptools==70.0.0 ; python_version >= "3.8" and python_version < "3.12"
@@ -59,4 +59,4 @@ urllib3==2.2.1 ; python_version >= "3.8" and python_version < "3.12"
 werkzeug==3.0.3 ; python_version >= "3.8" and python_version < "3.12"
 win32-setctime==1.1.0 ; python_version >= "3.8" and python_version < "3.12" and sys_platform == "win32"
 xmltodict==0.13.0 ; python_version >= "3.8" and python_version < "3.12"
-zipp==3.19.0 ; python_version >= "3.8" and python_version < "3.12"
+zipp==3.19.2 ; python_version >= "3.8" and python_version < "3.12"
diff --git a/trackplot/file/Annotation.py b/trackplot/file/Annotation.py
@@ -538,15 +538,9 @@ def __load_interval(self):
                         strand = "*"
                         rec_name = ""
 
-                    interval_target.append(
-                        GenomicLoci(
-                            chromosome=rec.contig,
-                            start=rec.start,
-                            end=rec.end,
-                            strand=strand,
-                            name=rec_name
-                        )
-                    )
+                    interval_target.append(GenomicLoci(
+                        chromosome=rec.contig, start=start, end=end, strand=strand, name=rec_name
+                    ))
 
                 if len(interval_target) != 0 and rec is not None:
                     self.data.append(Transcript(

diff --git a/trackplot/plot.py b/trackplot/plot.py
@@ -29,7 +29,7 @@
 faulthandler.enable()
 
 
-__version__ = "0.3.8"
+__version__ = "0.4.0"
 __author__ = "ygidtu & Ran Zhou"
 __email__ = "[email protected]"
 

diff --git a/trackplot/plot_func.py b/trackplot/plot_func.py
@@ -147,17 +147,21 @@ def init_graph_coords(region: GenomicLoci, exons: Optional[List[List[int]]] = No
                 intron = [exons[i - 1][1], exons[i][0]]
 
                 for j in range(intron[0], intron[1]):
-                    graph_coords[j - region.start] = graph_coords[intron[0] - region.start - 1] + (
-                            j - intron[0] + 1) * intron_scale
+                    if j >= region.start:
+                        graph_coords[j - region.start] = graph_coords[intron[0] - region.start - 1] + (
+                                j - intron[0] + 1) * intron_scale
 
             for j in range(exon[0], exon[1] + 1):
-                graph_coords[j - region.start] = graph_coords[exon[0] - region.start - 1] + (
-                        j - exon[0] + 1) * exon_scale
+                if j >= region.start:
+                    graph_coords[j - region.start] = graph_coords[exon[0] - region.start - 1] + (
+                            j - exon[0] + 1) * exon_scale
 
         intron = [exons[-1][-1], region.end]
         for i in range(intron[0], intron[1]):
-            graph_coords[i - region.start] = graph_coords[intron[0] - region.start - 1] + (
-                    i - intron[0] + 1) * intron_scale
+            if i >= region.start:
+                graph_coords[i - region.start] = graph_coords[intron[0] - region.start - 1] + (
+                        i - intron[0] + 1) * intron_scale
+
     else:
         # if there is not any exons, just init graph_coords by region
         for i, j in enumerate(range(region.start, region.end + 1)):
@@ -450,8 +454,11 @@ def plot_annotation(
         # @2022.05.13
         # add index to avoid label overlapping of neighbor exon
         for ind, exon in enumerate(transcript.exons):
-            s, e, strand = region.relative(
-                exon.start), region.relative(exon.end), exon.strand
+            s, e, strand = (region.relative(exon.start),
+                            region.relative(exon.end), exon.strand)
+
+            if s < 0 or e < 0:
+                continue
 
             patches.append(plt.Rectangle(
                 (graph_coords[s], y_loc - exon_width / 2),

diff --git a/web/package.json b/web/package.json
@@ -1,7 +1,7 @@
 {
   "name": "trackplot",
   "private": true,
-  "version": "0.3.8",
+  "version": "0.4.0",
   "type": "module",
   "scripts": {
     "dev": "vite",