trackplot 0.5.4__tar.gz → 0.5.5__tar.gz

{trackplot-0.5.4/trackplot.egg-info → trackplot-0.5.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: trackplot
-Version: 0.5.4
+Version: 0.5.5
 Summary: 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/
 Author-email: ygidtu <ygidtu@gmail.com>
 License-Expression: BSD-3-Clause

{trackplot-0.5.4 → trackplot-0.5.5}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "trackplot"
-version = "0.5.4"
+version = "0.5.5"
 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 = [
     { name = "ygidtu", email = "ygidtu@gmail.com" }

{trackplot-0.5.4 → trackplot-0.5.5}/trackplot/base/Junction.py

@@ -145,7 +145,9 @@ class Junction(object):
             return str(self)
         return f"{self.chromosome}:{self.start}-{self.end}"
         
-        
+    def eq(self, other, with_strand: bool = False):
+        u""" 判断两个位点是否一致 """
+        return self.str(with_strand) == other.str(with_strand)
 
 
 if __name__ == '__main__':

{trackplot-0.5.4 → trackplot-0.5.5}/trackplot/file/Bam.py

@@ -9,7 +9,7 @@ changelog:
 """
 import gzip
 import os
-from typing import Optional, Set
+from typing import Optional, Set, List
 
 import numpy as np
 import pysam
@@ -23,6 +23,25 @@ from trackplot.conf.config import NORMALIZATION
 from trackplot.file.File import SingleCell  
 
 
+def check_junction_exists(ref: List[Junction], dst: Junction, with_strand: bool = False):
+    u"""
+    判断junction是否存在于included_junctions
+    """
+    
+    ref = sorted([Junction.create_junction(x) for x in ref])
+    
+    for i in ref:
+        if abs(i.start - dst.start) < 2 and abs(i.end - dst.end) < 2:
+            logger.warning(f"1 bp mismatch between {i} (from bam file) and {dst} (user input), please check the coordinates")
+        
+        if i.is_downstream(dst):
+            return False
+        if i.eq(dst, with_strand):
+            return True
+        
+    return False
+
+
 class Bam(SingleCell):
 
     __slots__ = "title", "label", "library", "density_by_strand"
@@ -283,24 +302,22 @@ class Bam(SingleCell):
                 
                 # if included_junctions is provided, then skip all junctions by default
                 if included_junctions:
-                    kept = False
-                
-                # check whether junctions should be kept
-                if k.str(with_strand = True) in included_junctions:
-                    logger.debug(f"{str(k)} is included")
-                    kept = True
-                elif k.str(with_strand = False) in included_junctions:
-                    logger.debug(f"{str(k)} is included, but strand is ignored")
-                    kept = True
+                    kept = check_junction_exists(included_junctions, k, with_strand=True)
+                    if kept:
+                        logger.debug(f"{str(k)} is included")
+                    else:
+                        kept = check_junction_exists(included_junctions, k, with_strand=False)
+                        logger.debug(f"{str(k)} is included, but strand is ignored")
 
-                if not kept:
-                    logger.debug(f"{str(k)} is not included")
-                else:
+                        if not kept:
+                            logger.debug(f"{str(k)} is not included")
+
+                if kept:
                     if k.strand == "+":
                         spanned_junctions_plus[k] = 1 + spanned_junctions_plus.get(k, v)
                     elif k.strand == "-":
                         spanned_junctions_minus[k] = -1 + spanned_junctions_minus.get(k, v)
-                        
+                            
         except IOError as err:
             logger.error('There is no .bam file at {0}'.format(self.path))
             logger.error(err)

{trackplot-0.5.4 → trackplot-0.5.5}/trackplot/plot.py

@@ -30,7 +30,7 @@ logging.getLogger('matplotlib.font_manager').setLevel(logging.ERROR)
 faulthandler.enable()
 
 
-__version__ = "0.5.4"
+__version__ = "0.5.5"
 __author__ = "ygidtu & Ran Zhou"
 __email__ = "ygidtu@gmail.com"
 

{trackplot-0.5.4 → trackplot-0.5.5/trackplot.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: trackplot
-Version: 0.5.4
+Version: 0.5.5
 Summary: 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/
 Author-email: ygidtu <ygidtu@gmail.com>
 License-Expression: BSD-3-Clause

{trackplot-0.5.4 → trackplot-0.5.5}/trackplot.egg-info/SOURCES.txt

@@ -43,6 +43,33 @@ trackplot/file/Junction.py
 trackplot/file/Motif.py
 trackplot/file/ReadSegments.py
 trackplot/file/__init__.py
+trackplot_issue/OA-452-DC.bam
+trackplot_issue/OA-452-DC.bam.bai
+trackplot_issue/OA-476-DC.bam
+trackplot_issue/OA-476-DC.bam.bai
+trackplot_issue/OA-479-DC.bam
+trackplot_issue/OA-479-DC.bam.bai
+trackplot_issue/OA-488-DC.bam
+trackplot_issue/OA-488-DC.bam.bai
+trackplot_issue/OA-500-DC.bam
+trackplot_issue/OA-500-DC.bam.bai
+trackplot_issue/OA-503-DC.bam
+trackplot_issue/OA-503-DC.bam.bai
+trackplot_issue/OA-506-DC.bam
+trackplot_issue/OA-506-DC.bam.bai
+trackplot_issue/OA-514-DC.bam
+trackplot_issue/OA-514-DC.bam.bai
+trackplot_issue/OA-515-DC.bam
+trackplot_issue/OA-515-DC.bam.bai
+trackplot_issue/OA-99-DC.bam
+trackplot_issue/OA-99-DC.bam.bai
+trackplot_issue/run_trackplot.sh
+trackplot_issue/samples.bam.tsv
+trackplot_issue/test.v051.pdf
+trackplot_issue/test.v053.included_junctions.log
+trackplot_issue/test.v053.included_junctions.pdf
+trackplot_issue/test.v053.included_junctions.png
+trackplot_issue/test.v053.pdf
 ui/index.html
 ui/vite.svg
 ui/assets/Home-7GzAh8lS.js

trackplot-0.5.5/trackplot.egg-info/top_level.txt

@@ -0,0 +1,3 @@
+trackplot
+trackplot_issue
+ui

trackplot-0.5.5/trackplot_issue/run_trackplot.sh

@@ -0,0 +1,42 @@
+#!/bin/bash
+
+gtf_file="/mnt/data1/ref/gencode/v49/human/gencode.v49.annotation.gtf.gz"
+
+../.venv/bin/python ../main.py \
+    -e chr16:89722829-89728948 \
+    -p 10 \
+    -r ${gtf_file} \
+    --density samples.bam.tsv \
+    --output test.v051.pdf \
+    --width 6 \
+    --height 3 \
+    --same-y \
+    --sites 89724829,89726948 \
+    --intron-scale 0.05
+
+
+# /home/TW/anaconda3/envs/trackplot_v0.5.3/bin/trackplot \
+#     -e chr16:89722829-89728948 \
+#     -p 10 \
+#     -r ${gtf_file} \
+#     --density samples.bam.tsv \
+#     --output test.v053.pdf \
+#     --width 6 \
+#     --height 3 \
+#     --same-y \
+#     --sites 89724829,89726948 \
+#     --intron-scale 0.05
+
+
+../.venv/bin/python ../main.py \
+    -e chr16:89722829-89728948 \
+    -p 10 \
+    -r ${gtf_file} \
+    --density samples.bam.tsv \
+    --output test.v053.included_junctions.png \
+    --width 6 \
+    --height 3 \
+    --same-y \
+    --sites 89724829,89726948 \
+    --intron-scale 0.05 \
+    --included-junctions chr16:89724829-89726948 

trackplot-0.5.5/trackplot_issue/samples.bam.tsv

@@ -0,0 +1,10 @@
+OA-488-DC.bam	bam	C_C
+OA-500-DC.bam	bam	C_C
+OA-503-DC.bam	bam	C_C
+OA-99-DC.bam	bam	C_T
+OA-476-DC.bam	bam	C_T
+OA-479-DC.bam	bam	C_T
+OA-514-DC.bam	bam	C_T
+OA-452-DC.bam	bam	T_T
+OA-506-DC.bam	bam	T_T
+OA-515-DC.bam	bam	T_T

trackplot-0.5.5/trackplot_issue/test.v053.included_junctions.log

@@ -0,0 +1,355 @@
+2025-11-12 14:41:04.301 | INFO     | trackplot.plot:__init__:210 - Create trackplot version: 0.5.4
+2025-11-12 14:41:04.301 | INFO     | trackplot.plot:set_region:266 - set region to chr16:89722829-89728948:+
+2025-11-12 14:41:04.301 | INFO     | trackplot.plot:set_annotation:435 - set annotation file to /mnt/data1/ref/gencode/v49/human/gencode.v49.annotation.gtf.gz
+2025-11-12 14:41:04.302 | INFO     | trackplot.file.Annotation:index_gtf:331 - Create index for /mnt/data1/ref/gencode/v49/human/gencode.v49.annotation.gtf.gz
+2025-11-12 14:41:04.303 | DEBUG    | trackplot.file.Annotation:index_gtf:340 - Guess gtf needs to be sorted: building of index for /mnt/data1/ref/gencode/v49/human/gencode.v49.annotation.gtf.gz failed
+2025-11-12 14:41:04.304 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_C /home/zym/code/trackplot/trackplot_issue/OA-488-DC.bam
+2025-11-12 14:41:04.304 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_C /home/zym/code/trackplot/trackplot_issue/OA-500-DC.bam
+2025-11-12 14:41:04.304 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_C /home/zym/code/trackplot/trackplot_issue/OA-503-DC.bam
+2025-11-12 14:41:04.305 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_T /home/zym/code/trackplot/trackplot_issue/OA-99-DC.bam
+2025-11-12 14:41:04.305 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_T /home/zym/code/trackplot/trackplot_issue/OA-476-DC.bam
+2025-11-12 14:41:04.305 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_T /home/zym/code/trackplot/trackplot_issue/OA-479-DC.bam
+2025-11-12 14:41:04.305 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_T /home/zym/code/trackplot/trackplot_issue/OA-514-DC.bam
+2025-11-12 14:41:04.305 | INFO     | trackplot.plot:__init_input_file__:495 - add bam T_T /home/zym/code/trackplot/trackplot_issue/OA-452-DC.bam
+2025-11-12 14:41:04.305 | INFO     | trackplot.plot:__init_input_file__:495 - add bam T_T /home/zym/code/trackplot/trackplot_issue/OA-506-DC.bam
+2025-11-12 14:41:04.305 | INFO     | trackplot.plot:__init_input_file__:495 - add bam T_T /home/zym/code/trackplot/trackplot_issue/OA-515-DC.bam
+2025-11-12 14:41:04.306 | INFO     | trackplot.plot:add_sites:279 - add sites: 89724829,89726948
+2025-11-12 14:41:04.306 | INFO     | trackplot.plot:plot:1094 - load annotation
+2025-11-12 14:41:04.320 | INFO     | trackplot.plot:plot:1108 - load data of 3 plots
+2025-11-12 14:41:04.389 | DEBUG    | trackplot.file.Bam:load:297 - chr16:89715906-89717977:+ is not included
+2025-11-12 14:41:04.389 | DEBUG    | trackplot.file.Bam:load:297 - chr16:89718055-89720312:+ is not included
+2025-11-12 14:41:04.390 | DEBUG    | trackplot.file.Bam:load:297 - chr16:89720332-89723990:+ is not included
+2025-11-12 14:41:04.390 | DEBUG    | trackplot.file.Bam:load:297 - chr16:89724244-89724656:+ is not included
+2025-11-12 14:41:04.390 | DEBUG    | trackplot.file.Bam:load:297 - chr16:89724357-89724656:+ is not included
+2025-11-12 14:41:04.390 | DEBUG    | trackplot.file.Bam:load:297 - chr16:89724618-89735694:+ is not included
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+2025-11-12 14:41:04.394 | DEBUG    | trackplot.file.Bam:load:297 - chr16:89715906-89717977:+ is not included
+2025-11-12 14:41:04.394 | DEBUG    | trackplot.file.Bam:load:297 - chr16:89718055-89720312:+ is not included
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+2025-11-12 14:41:04.442 | DEBUG    | trackplot.file.Bam:load:297 - chr16:89720332-89723990:+ is not included
+2025-11-12 14:41:04.442 | DEBUG    | trackplot.file.Bam:load:297 - chr16:89724618-89735696:+ is not included
+2025-11-12 14:41:04.442 | DEBUG    | trackplot.file.Bam:load:297 - chr16:89724618-89735694:+ is not included
+2025-11-12 14:41:04.442 | DEBUG    | trackplot.file.Bam:load:297 - chr16:89724830-89735694:+ is not included
+2025-11-12 14:41:04.442 | DEBUG    | trackplot.file.Bam:load:297 - chr16:89724830-89726948:+ is not included
+2025-11-12 14:41:04.442 | DEBUG    | trackplot.file.Bam:load:297 - chr16:89629652-90230653:+ is not included
+2025-11-12 14:41:04.442 | DEBUG    | trackplot.file.Bam:load:297 - chr16:89724830-89735696:+ is not included
+2025-11-12 14:41:04.442 | DEBUG    | trackplot.file.Bam:load:297 - chr16:89720429-89723990:+ is not included
+2025-11-12 14:41:04.462 | DEBUG    | trackplot.plot:plot:1160 - plots n_rows=7; n_cols = 1
+2025-11-12 14:41:04.463 | INFO     | trackplot.plot:plot:1161 - init graph_coords
+2025-11-12 14:41:04.493 | INFO     | trackplot.plot:plot:1203 - --same-y is enabled
+2025-11-12 14:41:04.539 | INFO     | trackplot.plot:plot:1272 - Set for C_C by global: max_y=125.33333333333333; min_y=0.0
+2025-11-12 14:41:04.539 | INFO     | trackplot.plot:plot:1291 - plotting density at idx: 0 with height_ratio: 1
+2025-11-12 14:41:04.701 | INFO     | trackplot.plot:plot:1272 - Set for C_T by global: max_y=125.33333333333333; min_y=0.0
+2025-11-12 14:41:04.701 | INFO     | trackplot.plot:plot:1291 - plotting density at idx: 1 with height_ratio: 1
+2025-11-12 14:41:04.842 | INFO     | trackplot.plot:plot:1272 - Set for T_T by global: max_y=125.33333333333333; min_y=0.0
+2025-11-12 14:41:04.842 | INFO     | trackplot.plot:plot:1291 - plotting density at idx: 2 with height_ratio: 1
+2025-11-12 14:41:04.986 | INFO     | trackplot.plot:plot:1409 - plotting x-axis ticks at idx: 3 with height_ratio: 1
+2025-11-12 14:41:05.080 | INFO     | trackplot.plot:plot:1419 - plotting annotation at idx: 4 with height_ratio: 1
+2025-11-12 14:41:05.194 | INFO     | trackplot.plot:plot:1439 - saving fig into test.v053.included_junctions.png
+2025-11-12 14:41:05.987 | INFO     | trackplot.plot:plot:1453 - Plot done
+2025-11-12 16:41:13.661 | INFO     | trackplot.plot:__init__:210 - Create trackplot version: 0.5.5
+2025-11-12 16:41:13.663 | INFO     | trackplot.plot:set_region:266 - set region to chr16:89722829-89728948:+
+2025-11-12 16:41:13.663 | INFO     | trackplot.plot:set_annotation:435 - set annotation file to /mnt/data1/ref/gencode/v49/human/gencode.v49.annotation.gtf.gz
+2025-11-12 16:41:13.664 | INFO     | trackplot.file.Annotation:index_gtf:331 - Create index for /mnt/data1/ref/gencode/v49/human/gencode.v49.annotation.gtf.gz
+2025-11-12 16:41:13.664 | DEBUG    | trackplot.file.Annotation:index_gtf:340 - Guess gtf needs to be sorted: building of index for /mnt/data1/ref/gencode/v49/human/gencode.v49.annotation.gtf.gz failed
+2025-11-12 16:41:13.664 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_C /home/zym/code/trackplot/trackplot_issue/OA-488-DC.bam
+2025-11-12 16:41:13.665 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_C /home/zym/code/trackplot/trackplot_issue/OA-500-DC.bam
+2025-11-12 16:41:13.665 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_C /home/zym/code/trackplot/trackplot_issue/OA-503-DC.bam
+2025-11-12 16:41:13.665 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_T /home/zym/code/trackplot/trackplot_issue/OA-99-DC.bam
+2025-11-12 16:41:13.665 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_T /home/zym/code/trackplot/trackplot_issue/OA-476-DC.bam
+2025-11-12 16:41:13.665 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_T /home/zym/code/trackplot/trackplot_issue/OA-479-DC.bam
+2025-11-12 16:41:13.665 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_T /home/zym/code/trackplot/trackplot_issue/OA-514-DC.bam
+2025-11-12 16:41:13.665 | INFO     | trackplot.plot:__init_input_file__:495 - add bam T_T /home/zym/code/trackplot/trackplot_issue/OA-452-DC.bam
+2025-11-12 16:41:13.666 | INFO     | trackplot.plot:__init_input_file__:495 - add bam T_T /home/zym/code/trackplot/trackplot_issue/OA-506-DC.bam
+2025-11-12 16:41:13.666 | INFO     | trackplot.plot:__init_input_file__:495 - add bam T_T /home/zym/code/trackplot/trackplot_issue/OA-515-DC.bam
+2025-11-12 16:41:13.666 | INFO     | trackplot.plot:add_sites:279 - add sites: 89724829,89726948
+2025-11-12 16:41:13.666 | INFO     | trackplot.plot:plot:1094 - load annotation
+2025-11-12 16:41:13.680 | INFO     | trackplot.plot:plot:1108 - load data of 3 plots
+2025-11-12 16:41:13.764 | ERROR    | __main__:<module>:15 - 'str' object has no attribute 'start'
+multiprocessing.pool.RemoteTraceback: 
+"""
+Traceback (most recent call last):
+  File "/home/zym/.local/share/uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/multiprocessing/pool.py", line 125, in worker
+    result = (True, func(*args, **kwds))
+                    ~~~~^^^^^^^^^^^^^^^
+  File "/home/zym/.local/share/uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/multiprocessing/pool.py", line 48, in mapstar
+    return list(map(*args))
+  File "/home/zym/code/trackplot/trackplot/plot.py", line 40, in __load__
+    p.load(*args, **kwargs)
+    ~~~~~~^^^^^^^^^^^^^^^^^
+  File "/home/zym/code/trackplot/trackplot/plot.py", line 140, in load
+    obj.load(region=region, *args, **kwargs)
+    ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/zym/code/trackplot/trackplot/file/Bam.py", line 305, in load
+    check_junction_exists(included_junctions, k)
+    ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/zym/code/trackplot/trackplot/file/Bam.py", line 34, in check_junction_exists
+    if abs(i.start - dst.start) < 2 and abs(i.end - dst.end) < 2:
+           ^^^^^^^
+AttributeError: 'str' object has no attribute 'start'
+"""
+
+
+The above exception was the direct cause of the following exception:
+
+
+Traceback (most recent call last):
+
+> File "/home/zym/code/trackplot/trackplot_issue/../main.py", line 13, in <module>
+    main()
+    └ <Command main>
+
+  File "/home/zym/code/trackplot/.venv/lib/python3.13/site-packages/click/core.py", line 1442, in __call__
+    return self.main(*args, **kwargs)
+           │    │     │       └ {}
+           │    │     └ ()
+           │    └ <function Command.main at 0x7f017a452ac0>
+           └ <Command main>
+  File "/home/zym/code/trackplot/.venv/lib/python3.13/site-packages/click/core.py", line 1363, in main
+    rv = self.invoke(ctx)
+         │    │      └ <click.core.Context object at 0x7f017a59c6e0>
+         │    └ <function Command.invoke at 0x7f017a4527a0>
+         └ <Command main>
+  File "/home/zym/code/trackplot/.venv/lib/python3.13/site-packages/click/core.py", line 1226, in invoke
+    return ctx.invoke(self.callback, **ctx.params)
+           │   │      │    │           │   └ {'event': 'chr16:89722829-89728948', 'process': 10, 'annotation': '/mnt/data1/ref/gencode/v49/human/gencode.v49.annotation.gt...
+           │   │      │    │           └ <click.core.Context object at 0x7f017a59c6e0>
+           │   │      │    └ <function main at 0x7f00218f9ee0>
+           │   │      └ <Command main>
+           │   └ <function Context.invoke at 0x7f017a4519e0>
+           └ <click.core.Context object at 0x7f017a59c6e0>
+  File "/home/zym/code/trackplot/.venv/lib/python3.13/site-packages/click/core.py", line 794, in invoke
+    return callback(*args, **kwargs)
+           │         │       └ {'event': 'chr16:89722829-89728948', 'process': 10, 'annotation': '/mnt/data1/ref/gencode/v49/human/gencode.v49.annotation.gt...
+           │         └ ()
+           └ <function main at 0x7f00218f9ee0>
+
+  File "/home/zym/code/trackplot/trackplot/cli.py", line 755, in main
+    p.plot(
+    │ └ <function Plot.plot at 0x7f0021b68540>
+    └ <trackplot.plot.Plot object at 0x7f00218b6d40>
+
+  File "/home/zym/code/trackplot/trackplot/plot.py", line 1137, in plot
+    self.plots = p.map(__load__, cmds)
+    │    │       │ │   │         └ [[<trackplot.plot.PlotInfo object at 0x7f002c79cd40>, (), {'intron_scale': 0.05, 'exon_scale': 1.0, 'same_y': True, 'same_y_s...
+    │    │       │ │   └ <function __load__ at 0x7f003332e980>
+    │    │       │ └ <function Pool.map at 0x7f0021736160>
+    │    │       └ <multiprocessing.pool.Pool state=TERMINATE pool_size=3>
+    │    └ <member 'plots' of 'Plot' objects>
+    └ <trackplot.plot.Plot object at 0x7f00218b6d40>
+
+  File "/home/zym/.local/share/uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/multiprocessing/pool.py", line 367, in map
+    return self._map_async(func, iterable, mapstar, chunksize).get()
+           │    │          │     │         │        └ None
+           │    │          │     │         └ <function mapstar at 0x7f00218df100>
+           │    │          │     └ [[<trackplot.plot.PlotInfo object at 0x7f002c79cd40>, (), {'intron_scale': 0.05, 'exon_scale': 1.0, 'same_y': True, 'same_y_s...
+           │    │          └ <function __load__ at 0x7f003332e980>
+           │    └ <function Pool._map_async at 0x7f0021736660>
+           └ <multiprocessing.pool.Pool state=TERMINATE pool_size=3>
+  File "/home/zym/.local/share/uv/python/cpython-3.13.3-linux-x86_64-gnu/lib/python3.13/multiprocessing/pool.py", line 774, in get
+    raise self._value
+          │    └ AttributeError("'str' object has no attribute 'start'")
+          └ <multiprocessing.pool.MapResult object at 0x7f002174cc20>
+
+AttributeError: 'str' object has no attribute 'start'
+2025-11-12 16:42:08.810 | INFO     | trackplot.plot:__init__:210 - Create trackplot version: 0.5.5
+2025-11-12 16:42:08.811 | INFO     | trackplot.plot:set_region:266 - set region to chr16:89722829-89728948:+
+2025-11-12 16:42:08.811 | INFO     | trackplot.plot:set_annotation:435 - set annotation file to /mnt/data1/ref/gencode/v49/human/gencode.v49.annotation.gtf.gz
+2025-11-12 16:42:08.812 | INFO     | trackplot.file.Annotation:index_gtf:331 - Create index for /mnt/data1/ref/gencode/v49/human/gencode.v49.annotation.gtf.gz
+2025-11-12 16:42:08.812 | DEBUG    | trackplot.file.Annotation:index_gtf:340 - Guess gtf needs to be sorted: building of index for /mnt/data1/ref/gencode/v49/human/gencode.v49.annotation.gtf.gz failed
+2025-11-12 16:42:08.812 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_C /home/zym/code/trackplot/trackplot_issue/OA-488-DC.bam
+2025-11-12 16:42:08.812 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_C /home/zym/code/trackplot/trackplot_issue/OA-500-DC.bam
+2025-11-12 16:42:08.812 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_C /home/zym/code/trackplot/trackplot_issue/OA-503-DC.bam
+2025-11-12 16:42:08.812 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_T /home/zym/code/trackplot/trackplot_issue/OA-99-DC.bam
+2025-11-12 16:42:08.813 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_T /home/zym/code/trackplot/trackplot_issue/OA-476-DC.bam
+2025-11-12 16:42:08.813 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_T /home/zym/code/trackplot/trackplot_issue/OA-479-DC.bam
+2025-11-12 16:42:08.813 | INFO     | trackplot.plot:__init_input_file__:495 - add bam C_T /home/zym/code/trackplot/trackplot_issue/OA-514-DC.bam
+2025-11-12 16:42:08.813 | INFO     | trackplot.plot:__init_input_file__:495 - add bam T_T /home/zym/code/trackplot/trackplot_issue/OA-452-DC.bam
+2025-11-12 16:42:08.813 | INFO     | trackplot.plot:__init_input_file__:495 - add bam T_T /home/zym/code/trackplot/trackplot_issue/OA-506-DC.bam
+2025-11-12 16:42:08.813 | INFO     | trackplot.plot:__init_input_file__:495 - add bam T_T /home/zym/code/trackplot/trackplot_issue/OA-515-DC.bam
+2025-11-12 16:42:08.813 | INFO     | trackplot.plot:add_sites:279 - add sites: 89724829,89726948
+2025-11-12 16:42:08.813 | INFO     | trackplot.plot:plot:1094 - load annotation
+2025-11-12 16:42:08.827 | INFO     | trackplot.plot:plot:1108 - load data of 3 plots
+2025-11-12 16:42:08.886 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89715906-89717977:+ is not included
+2025-11-12 16:42:08.887 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89718055-89720312:+ is not included
+2025-11-12 16:42:08.887 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89720332-89723990:+ is not included
+2025-11-12 16:42:08.887 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724244-89724656:+ is not included
+2025-11-12 16:42:08.887 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724357-89724656:+ is not included
+2025-11-12 16:42:08.887 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724618-89735694:+ is not included
+2025-11-12 16:42:08.887 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724830-89735694:+ is not included
+2025-11-12 16:42:08.889 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89715906-89717977:+ is not included
+2025-11-12 16:42:08.890 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89715906-89717977:+ is not included
+2025-11-12 16:42:08.890 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89718055-89720312:+ is not included
+2025-11-12 16:42:08.890 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89718055-89723990:+ is not included
+2025-11-12 16:42:08.890 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89720332-89723990:+ is not included
+2025-11-12 16:42:08.890 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89718055-89720312:+ is not included
+2025-11-12 16:42:08.890 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724618-89735694:+ is not included
+2025-11-12 16:42:08.890 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89720332-89723990:+ is not included
+2025-11-12 16:42:08.890 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724618-89735696:+ is not included
+2025-11-12 16:42:08.890 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724618-89735696:+ is not included
+2025-11-12 16:42:08.890 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724830-89735694:+ is not included
+2025-11-12 16:42:08.890 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724618-89735694:+ is not included
+2025-11-12 16:42:08.890 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724830-89735694:+ is not included
+2025-11-12 16:42:08.891 | WARNING  | trackplot.file.Bam:check_junction_exists:35 - 1 bp mismatch between chr16:89724829-89726948:+ (from bam file) and chr16:89724830-89726948:+ (user input), please check the coordinates
+2025-11-12 16:42:08.891 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724830-89726948:+ is not included
+2025-11-12 16:42:08.902 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89715906-89717977:+ is not included
+2025-11-12 16:42:08.902 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89718055-89720312:+ is not included
+2025-11-12 16:42:08.902 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89720332-89723990:+ is not included
+2025-11-12 16:42:08.902 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724618-89735694:+ is not included
+2025-11-12 16:42:08.902 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724618-89735696:+ is not included
+2025-11-12 16:42:08.902 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89715906-89717977:+ is not included
+2025-11-12 16:42:08.902 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724830-89735694:+ is not included
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89718055-89723990:+ is not included
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89718055-89723990:+ is not included
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89718055-89720312:+ is not included
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724244-89724656:+ is not included
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89720332-89723990:+ is not included
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724357-89724656:+ is not included
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724618-89735696:+ is not included
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89715906-89717977:+ is not included
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89718055-89720312:+ is not included
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724618-89735694:+ is not included
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89720332-89723990:+ is not included
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724830-89735694:+ is not included
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724244-89724656:+ is not included
+2025-11-12 16:42:08.903 | WARNING  | trackplot.file.Bam:check_junction_exists:35 - 1 bp mismatch between chr16:89724829-89726948:+ (from bam file) and chr16:89724830-89726948:+ (user input), please check the coordinates
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724357-89724656:+ is not included
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724830-89726948:+ is not included
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724618-89735694:+ is not included
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89629652-90230653:+ is not included
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724830-89735696:+ is not included
+2025-11-12 16:42:08.903 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724830-89735694:+ is not included
+2025-11-12 16:42:08.904 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89325196-89907278:+ is not included
+2025-11-12 16:42:08.904 | WARNING  | trackplot.file.Bam:check_junction_exists:35 - 1 bp mismatch between chr16:89724829-89726948:+ (from bam file) and chr16:89724830-89726948:+ (user input), please check the coordinates
+2025-11-12 16:42:08.904 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724830-89726948:+ is not included
+2025-11-12 16:42:08.914 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89715906-89717977:+ is not included
+2025-11-12 16:42:08.914 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89718055-89720312:+ is not included
+2025-11-12 16:42:08.914 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89720332-89723990:+ is not included
+2025-11-12 16:42:08.915 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724244-89724656:+ is not included
+2025-11-12 16:42:08.915 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724357-89724656:+ is not included
+2025-11-12 16:42:08.915 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724618-89735694:+ is not included
+2025-11-12 16:42:08.915 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724830-89735694:+ is not included
+2025-11-12 16:42:08.915 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89325196-89907278:+ is not included
+2025-11-12 16:42:08.915 | WARNING  | trackplot.file.Bam:check_junction_exists:35 - 1 bp mismatch between chr16:89724829-89726948:+ (from bam file) and chr16:89724830-89726948:+ (user input), please check the coordinates
+2025-11-12 16:42:08.915 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724830-89726948:+ is not included
+2025-11-12 16:42:08.915 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89718055-89723990:+ is not included
+2025-11-12 16:42:08.915 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724618-89735696:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89715906-89717977:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89718055-89723990:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89715906-89717977:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89718055-89720312:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89718055-89720312:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89720332-89723990:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89720332-89723990:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724618-89735696:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724618-89735694:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724618-89735694:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724618-89735696:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724830-89735694:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724830-89735694:+ is not included
+2025-11-12 16:42:08.919 | WARNING  | trackplot.file.Bam:check_junction_exists:35 - 1 bp mismatch between chr16:89724829-89726948:+ (from bam file) and chr16:89724830-89726948:+ (user input), please check the coordinates
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89718055-89723990:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724830-89726948:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724244-89724656:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89629652-90230653:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724357-89724656:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724830-89735696:+ is not included
+2025-11-12 16:42:08.919 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89720429-89723990:+ is not included
+2025-11-12 16:42:08.943 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89715906-89717977:+ is not included
+2025-11-12 16:42:08.943 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89718055-89720312:+ is not included
+2025-11-12 16:42:08.943 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89720332-89723990:+ is not included
+2025-11-12 16:42:08.943 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724244-89724656:+ is not included
+2025-11-12 16:42:08.943 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724357-89724656:+ is not included
+2025-11-12 16:42:08.943 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724618-89735694:+ is not included
+2025-11-12 16:42:08.944 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724830-89735694:+ is not included
+2025-11-12 16:42:08.944 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89325196-89907278:+ is not included
+2025-11-12 16:42:08.944 | WARNING  | trackplot.file.Bam:check_junction_exists:35 - 1 bp mismatch between chr16:89724829-89726948:+ (from bam file) and chr16:89724830-89726948:+ (user input), please check the coordinates
+2025-11-12 16:42:08.944 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724830-89726948:+ is not included
+2025-11-12 16:42:08.944 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89718055-89723990:+ is not included
+2025-11-12 16:42:08.944 | DEBUG    | trackplot.file.Bam:load:317 - chr16:89724618-89735696:+ is not included
+2025-11-12 16:42:08.968 | DEBUG    | trackplot.plot:plot:1160 - plots n_rows=7; n_cols = 1
+2025-11-12 16:42:08.968 | INFO     | trackplot.plot:plot:1161 - init graph_coords
+2025-11-12 16:42:08.997 | INFO     | trackplot.plot:plot:1203 - --same-y is enabled
+2025-11-12 16:42:09.040 | INFO     | trackplot.plot:plot:1272 - Set for C_C by global: max_y=125.33333333333333; min_y=0.0
+2025-11-12 16:42:09.040 | INFO     | trackplot.plot:plot:1291 - plotting density at idx: 0 with height_ratio: 1
+2025-11-12 16:42:09.184 | INFO     | trackplot.plot:plot:1272 - Set for C_T by global: max_y=125.33333333333333; min_y=0.0
+2025-11-12 16:42:09.184 | INFO     | trackplot.plot:plot:1291 - plotting density at idx: 1 with height_ratio: 1
+2025-11-12 16:42:09.329 | INFO     | trackplot.plot:plot:1272 - Set for T_T by global: max_y=125.33333333333333; min_y=0.0
+2025-11-12 16:42:09.329 | INFO     | trackplot.plot:plot:1291 - plotting density at idx: 2 with height_ratio: 1
+2025-11-12 16:42:09.464 | INFO     | trackplot.plot:plot:1409 - plotting x-axis ticks at idx: 3 with height_ratio: 1
+2025-11-12 16:42:09.557 | INFO     | trackplot.plot:plot:1419 - plotting annotation at idx: 4 with height_ratio: 1
+2025-11-12 16:42:09.673 | INFO     | trackplot.plot:plot:1439 - saving fig into test.v053.included_junctions.png
+2025-11-12 16:42:10.413 | INFO     | trackplot.plot:plot:1453 - Plot done

trackplot-0.5.4/trackplot.egg-info/top_level.txt

@@ -1,2 +0,0 @@
-trackplot
-ui