trackplot 0.5.0__tar.gz → 0.5.2__tar.gz

{trackplot-0.5.0 → trackplot-0.5.2}/PKG-INFO

@@ -1,24 +1,23 @@
 Metadata-Version: 2.1
 Name: trackplot
-Version: 0.5.0
+Version: 0.5.2
 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/
 License: BSD-3
 Author: ygidtu
 Author-email: ygidtu@gmail.com
-Requires-Python: >=3.8,<3.12
+Requires-Python: >=3.10,<3.13
 Classifier: License :: Other/Proprietary License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Requires-Dist: adjusttext (>=0.7.3,<0.8.0)
 Requires-Dist: cairocffi (>=1.4.0,<2.0.0)
 Requires-Dist: click (>=8.1.3,<9.0.0)
 Requires-Dist: click-option-group (>=0.5.5,<0.6.0)
 Requires-Dist: filetype (>=1.2.0,<2.0.0)
 Requires-Dist: flask (>=2.3.2,<3.0.0)
-Requires-Dist: hicmatrix (>=15,<16)
+Requires-Dist: hicmatrix (>=17,<18)
 Requires-Dist: loguru (>=0.6.0,<0.7.0)
 Requires-Dist: matplotlib (>=3.6.3,<4.0.0)
 Requires-Dist: numpy (>=1.24.1,<2.0.0)

{trackplot-0.5.0 → trackplot-0.5.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "trackplot"
-version = "0.5.0"
+version = "0.5.2"
 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 <ygidtu@gmail.com>"]
 license = "BSD-3"
@@ -13,13 +13,13 @@ include = [
 ]
 
 [tool.poetry.dependencies]
-python = ">=3.8,<3.12"
+python = ">=3.10,<3.13"
 adjusttext = "^0.7.3"
 cairocffi = "^1.4.0"
 click = "^8.1.3"
 click-option-group = "^0.5.5"
 filetype = "^1.2.0"
-hicmatrix = "^15"
+hicmatrix = "^17"
 loguru = "^0.6.0"
 matplotlib = "^3.6.3"
 numpy = "^1.24.1"
@@ -34,7 +34,7 @@ flask = "^2.3.2"
 
 [[tool.poetry.source]]
 name = "mirrors"
-url = "https://pypi.tuna.tsinghua.edu.cn/simple/"
+url = "https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple/"
 priority = "primary"
 
 [[tool.poetry.source]]

{trackplot-0.5.0 → trackplot-0.5.2}/trackplot/cli.py

@@ -8,7 +8,7 @@ This script contains all the command line parameters
 import os
 import sys
 from multiprocessing import cpu_count
-from typing import Optional, Dict, Set, Tuple
+from typing import Optional
 
 import click
 from click_option_group import optgroup

{trackplot-0.5.0 → trackplot-0.5.2}/trackplot/file/Bam.py

@@ -161,8 +161,7 @@ class Bam(SingleCell):
         spanned_junctions = kwargs.get("junctions", {})
         included_junctions = kwargs.get("included_junctions", {})
         remove_duplicate_umi = kwargs.get("remove_duplicate_umi", False)
-        spanned_junctions_plus = dict()
-        spanned_junctions_minus = dict()
+        spanned_junctions_plus, spanned_junctions_minus = {}, {}
         plus, minus = np.zeros(len(region), dtype=np.int32), np.zeros(len(region), dtype=np.int32)
         site_plus, site_minus = np.zeros(len(region), dtype=np.int32), np.zeros(len(region), dtype=np.int32)
 

{trackplot-0.5.0 → trackplot-0.5.2}/trackplot/plot.py

@@ -30,7 +30,7 @@ logging.getLogger('matplotlib.font_manager').setLevel(logging.ERROR)
 faulthandler.enable()
 
 
-__version__ = "0.5.0"
+__version__ = "0.5.2"
 __author__ = "ygidtu & Ran Zhou"
 __email__ = "ygidtu@gmail.com"
 
@@ -1181,22 +1181,24 @@ class Plot(object):
 
         max_used_y_val, min_used_y_val, same_y_by_groups = {}, {}, {}
         
+                 
         default_y = {}
-        if kwargs.get("y_limit") and os.path.exists(kwargs.get("y_limit")):
-            default_y = {}
-            with open(kwargs.get("y_limit")) as r:
-                for line in r:
-                    if line.startswith("#"):
-                        continue
-                    line = line.split()
-                    
-                    if len(line) > 1:
-                        try:
-                            default_y[line[0]] = [float(x) for x in default_y[1:]]
-                        except Exception as err:
-                            logger.warning(f"The y limit of {line[0]} is invalid: {err}")
-                        
-            
+        if kwargs.get("y_limit"):
+            if not os.path.exists(kwargs.get("y_limit")):
+                logger.warning(f'{kwargs.get("y_limit")} not exists')
+            else:
+                logger.info("load y-limit settings from: " + kwargs.get("y_limit"))
+                with open(kwargs.get("y_limit")) as r:
+                    for line in r:
+                        if line.startswith("#"):
+                            continue
+                        line = line.split()
+                        if len(line) > 1:
+                            try:
+                                default_y[line[0]] = [float(x) for x in line[1:]]
+                            except Exception as err:
+                                logger.warning(f"The y limit of {line[0]} is invalid: {err}")
+      
         if kwargs.get("same_y") or kwargs.get("same_y_sc"):
             logger.info("--same-y is enabled")
             # read the y groups            
@@ -1246,6 +1248,7 @@ class Plot(object):
                                 max_used_y_val[key] = max_used_y_val[obj.path]
                                 min_used_y_val[key] = min_used_y_val[obj.path]
 
+
         curr_idx = 0
         for p in self.plots:
             if p.type == "igv":
@@ -1267,7 +1270,24 @@ class Plot(object):
             elif kwargs.get("same_y"):
                 max_y_val_, min_y_val_ = max(max_used_y_val.values()), min(min_used_y_val.values())
                 logger.info(f"Set for {p.obj[0].label} by global: max_y={max_y_val_}; min_y={min_y_val_}")
-
+            elif default_y:
+                if p.type in ["density", "site-plot", "line"]:
+                    for obj in p.obj:
+                        # set y limit
+                        if obj.label in default_y:
+                            max_y_val_ = default_y[obj.label][0]
+                            
+                            if len(default_y[obj.label]) > 1:
+                                min_y_val_ = default_y[obj.label][1]
+                            
+                            if same_y_by_groups and obj.label in same_y_by_groups:
+                                key = same_y_by_groups[obj.label]
+                                max_y_val_ = max_used_y_val[obj.path]
+                                min_y_val_ = min_used_y_val[obj.path]
+                            logger.info(f"Set for {p.obj[0].label} by limited: max_y={max_y_val_}; min_y={min_y_val_}")
+                            break
+                
+                
             logger.info(f"plotting {p.type} at idx: {curr_idx} with height_ratio: {height_ratio[curr_idx]}")
             if p.type == "density":
                 if isinstance(p.obj[0], Depth):

{trackplot-0.5.0 → trackplot-0.5.2}/trackplot/plot_func.py

@@ -436,7 +436,13 @@ def plot_annotation(
     for transcript in data:
         strand = transcript.strand
         # @2018.12.20 add transcript id, based on fixed coordinates
-        if transcript.transcript:
+        # @2025.02.04 add warnings for transcript name and id check
+        if transcript.transcript or transcript.transcript_id:
+            show_text = transcript.transcript
+            if not transcript.transcript:
+                logger.warning(f"there is not transcript_name, using transcript_id instead")
+                show_text = transcript.transcript_id
+            
             if show_gene and transcript.gene and transcript.gene_id != transcript.transcript_id:
                 if show_id:
                     ax.text(x=-.01 * max(graph_coords), y=y_loc + 0.25,
@@ -445,9 +451,11 @@ def plot_annotation(
                             s=transcript.transcript_id, fontsize=font_size, ha="right")
                 else:
                     ax.text(x=-.01 * max(graph_coords), y=y_loc,
-                            s=transcript.gene + " | " + transcript.transcript, fontsize=font_size, ha="right")
+                            s=transcript.gene + " | " + show_text, fontsize=font_size, ha="right")
             else:
-                ax.text(x=-1, y=y_loc - 0.1, s=transcript.transcript, fontsize=font_size, ha="right")
+                ax.text(x=-1, y=y_loc - 0.1, s=show_text, fontsize=font_size, ha="right")
+        else:
+            logger.warning(f"there is no transcript_name and transcript_id")
 
         # @2018.12.19
         # s and e is the start and end site of single exon

trackplot-0.5.2/ui/assets/Home-RdVPWns6.js

@@ -0,0 +1 @@
+import{d as _,o as m,c as u,a as c,t as f,b as e,w as t,E as g,e as n,u as i,f as h,_ as y}from"./index-Dd6Bavnk.js";import{E as k,a as w,b as E,m as v,v as b}from"./el-divider-eEJXnQD5.js";const x={name:"Home",data(){return{msg:"Welcome to trackplot App",example:"https://trackplot.readthedocs.io/en/latest/imgs/diagram.png"}}},C=_({...x,setup(B){return(r,a)=>{const s=k,l=w,o=h,p=g,d=E;return m(),u("div",null,[c("h1",null,f(r.msg),1),e(s),e(p,null,{default:t(()=>[e(o,{span:12,offset:3},{default:t(()=>[e(l,{type:"primary",href:"/#/plot"},{default:t(()=>a[0]||(a[0]=[n("Create your own plot")])),_:1})]),_:1}),e(o,{span:6},{default:t(()=>[e(l,{type:"primary",href:"https://github.com/ygidtu/trackplot/issues",icon:i(v)},{default:t(()=>a[1]||(a[1]=[n("Report bug at Github")])),_:1},8,["icon"]),e(s,{direction:"vertical"}),e(l,{type:"primary",icon:i(b),href:"https://trackplot.readthedocs.io/en/latest/web/"},{default:t(()=>a[2]||(a[2]=[n("Read the tutorial")])),_:1},8,["icon"])]),_:1}),e(o,{span:6})]),_:1}),e(s),e(p,null,{default:t(()=>[e(o,{span:20,offset:2},{default:t(()=>[e(d,{src:r.example,width:"100%"},null,8,["src"])]),_:1})]),_:1})])}}}),V=y(C,[["__scopeId","data-v-3d7de397"]]);export{V as default};