trackplot 0.5.7__tar.gz → 0.5.9__tar.gz

{trackplot-0.5.7/trackplot.egg-info → trackplot-0.5.9}/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.4
 Name: trackplot
-Version: 0.5.7
+Version: 0.5.9
 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
-Requires-Python: >=3.11
+Requires-Python: <3.14,>=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: adjusttext>=1.3.0

{trackplot-0.5.7 → trackplot-0.5.9}/pyproject.toml

@@ -1,13 +1,13 @@
 [project]
 name = "trackplot"
-version = "0.5.7"
+version = "0.5.9"
 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" }
 ]
 license = "BSD-3-Clause"
 readme = "README.md"
-requires-python = ">=3.11"
+requires-python = ">=3.11, <3.14"
 dependencies = [
     "adjusttext>=1.3.0",
     "cairocffi>=1.7.1",

{trackplot-0.5.7 → trackplot-0.5.9}/trackplot/anno/AxLabel.py

@@ -1,12 +1,9 @@
 #!/usr/bin/env python3
 # -*- coding:utf-8 -*-
-u"""
-
-"""
+""" """
 
 
 class AxLabel(object):
-
     __slots__ = ["Ax", "Label"]
 
     def __init__(self, ax, label):
@@ -20,5 +17,5 @@ class AxLabel(object):
         return self.__hash__() == other.__hash__()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     pass

{trackplot-0.5.7 → trackplot-0.5.9}/trackplot/anno/theme.py

@@ -1,15 +1,16 @@
 #!/usr/bin/env python3
 # -*- coding:utf-8 -*-
-u"""
+"""
 This file contains the configuration of different themes
 """
+
 from matplotlib import axes
 
 
 class Theme(object):
     @classmethod
     def blank(cls, ax: axes.Axes):
-        u"""
+        """
 
         :param ax:
         :return:
@@ -23,15 +24,15 @@ class Theme(object):
 
     @classmethod
     def ticks(cls, ax: axes.Axes):
-        ax.spines['top'].set_visible(False)
-        ax.spines['right'].set_visible(False)
+        ax.spines["top"].set_visible(False)
+        ax.spines["right"].set_visible(False)
         ax.tick_params(bottom=True, top=False, left=True, right=False)
 
     @classmethod
     def ticks_blank(cls, ax: axes.Axes):
-        ax.spines['top'].set_visible(False)
-        ax.spines['right'].set_visible(False)
-        ax.spines['bottom'].set_visible(False)
+        ax.spines["top"].set_visible(False)
+        ax.spines["right"].set_visible(False)
+        ax.spines["bottom"].set_visible(False)
         ax.set_xticklabels([])
         ax.tick_params(bottom=False, top=False, left=True, right=False)
 

{trackplot-0.5.7 → trackplot-0.5.9}/trackplot/base/CoordinateMap.py

@@ -2,10 +2,11 @@
 # -*- coding: utf-8 -*-
 # @Time    : 2019/1/11 2:55 PM
 
-u"""
+"""
 Convert aa position into genomic coordinate, Ran zhou.
 
 """
+
 from itertools import islice
 from typing import Optional
 
@@ -13,38 +14,41 @@ import numpy as np
 
 
 class Coordinate(object):
-    u"""
+    """
     A Coordinate object for genomic regions.
     """
 
     __slots__ = ["strand", "se"]
 
     def __init__(self, coordinate_list: list, strand: str = "*"):
-        u"""
+        """
         Set genomic coordinates
         :param coordinate_list: a nested tuple of list
         :param strand: a strands of given coordinate object
         """
         self.strand = strand
         self.se = self.__fmt_exons__(coordinate_list)
-        assert len(self.location_list) == len(set(self.location_list)), \
+        assert len(self.location_list) == len(set(self.location_list)), (
             f"Overlapped regions were found in {self.se}"
+        )
 
     @staticmethod
     def __fmt_exons__(coordinate_list: list) -> list:
-        u"""
+        """
         Format and sort exon list
         :param coordinate_list: a nested tuple of list. like [('5','6'),('1','4')]
         :return: a nested tuple of list. like [(1,4), (5,6)]
         """
         # sorting coordinate based on first of location.
-        formatted_coordinate_list = list(map(lambda x: tuple(map(int, x)), coordinate_list))
+        formatted_coordinate_list = list(
+            map(lambda x: tuple(map(int, x)), coordinate_list)
+        )
         formatted_coordinate_list.sort(key=lambda x: x[0])
         return formatted_coordinate_list
 
     @staticmethod
     def __get_s_or_e__(coordinate_list: list, index: int) -> list:
-        u"""
+        """
         Get start or end site for each given coordinates
         :param coordinate_list: a nested tuple of list, like [(1,3),(5,6)]
         :param index: the index of tuple, 0 for the left site and 1 for the right end site.
@@ -62,7 +66,7 @@ class Coordinate(object):
 
     @property
     def introns(self):
-        u"""
+        """
         Set intronic regions for each coordinate object
         :return: a nested tuple of list which contained intronic coordinates.
         """
@@ -71,19 +75,16 @@ class Coordinate(object):
         else:
             introns_list = []
             for left_exon, right_exon in self.__slide_window__(self.se, num_of_chunk=2):
-                introns_list.append(tuple(
-                    [left_exon[1] + 1,
-                     right_exon[0] - 1]
-                ))
+                introns_list.append(tuple([left_exon[1] + 1, right_exon[0] - 1]))
             return introns_list
 
     @staticmethod
     def __slide_window__(nested_list: list, num_of_chunk: int):
-        u"""
+        """
         A sliding window to slice the given list
         :param nested_list: a nested tuple of list, like [(1,3),(5,6)]
         :param num_of_chunk:  num of element for each chunk.
-        :return: 
+        :return:
         """
         nested_list = iter(nested_list)
         chunked_list = list(islice(nested_list, num_of_chunk))
@@ -95,7 +96,7 @@ class Coordinate(object):
 
     @classmethod
     def __flatten__(cls, nested_list: list):
-        u"""
+        """
         Flatten the nested list
         :param nested_list: a nested tuple of list, like [(1,3),(5,6)]
         :return:
@@ -109,33 +110,33 @@ class Coordinate(object):
 
     @property
     def location_list(self) -> np.ndarray:
-        u"""
+        """
         Get a list which contained all position.
         For example, an exon list `[(10, 15), (20,25)]` as input,
         [10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25] will return
         :return: a list which contained all position
         """
         # Add 1 offset because of 0-based coordinate
-        position_list = list(self.__flatten__(list(map(
-            lambda x: range(x[0], x[1] + 1), self.se
-        ))))
+        position_list = list(
+            self.__flatten__(list(map(lambda x: range(x[0], x[1] + 1), self.se)))
+        )
 
-        if self.strand == '-':
+        if self.strand == "-":
             return np.array(position_list[::-1])
 
         return np.array(position_list)
 
     @property
     def pep_index(self) -> np.ndarray:
-        u"""
+        """
         Relative position of pep coordinates
-        :return: 
+        :return:
         """
         return np.array(list(map(lambda x: int(x / 3), range(len(self.location_list)))))
 
     @property
     def cds_index(self) -> np.ndarray:
-        u"""
+        """
         Relative position of cds coordinates
         :return:
         """
@@ -143,7 +144,7 @@ class Coordinate(object):
 
     @staticmethod
     def __group_consecutive_value__(location_list: np.ndarray, strand: str) -> list:
-        u"""
+        """
         group the consecutive value into a list
 
         :param location_list: a list of location site
@@ -153,46 +154,39 @@ class Coordinate(object):
         offset = -1 if strand == "-" else 1
         group_ids = np.concatenate(([0], (np.diff(location_list) != offset).cumsum()))
 
-        grouped_truncated_location_array = \
-            np.split(
-                location_list,
-                np.unique(group_ids, return_counts=True)[1].cumsum().tolist()
-            )
+        grouped_truncated_location_array = np.split(
+            location_list, np.unique(group_ids, return_counts=True)[1].cumsum().tolist()
+        )
 
         return grouped_truncated_location_array
 
     @classmethod
     def init_from_location_list(cls, truncated_location_array: np.ndarray, strand: str):
-        u"""
+        """
         init class based on the list of location
         :param truncated_location_array: truncated location array
         :param strand: the strand of the current list
         :return:
         """
         __coordinate_list = []
-        for sub_array in cls.__group_consecutive_value__(truncated_location_array, strand):
+        for sub_array in cls.__group_consecutive_value__(
+            truncated_location_array, strand
+        ):
             if len(sub_array) == 0:
                 continue
 
-            __coordinate_list.append(
-                tuple(
-                    [
-                        min(sub_array),
-                        max(sub_array)
-                    ]
-                )
-            )
+            __coordinate_list.append(tuple([min(sub_array), max(sub_array)]))
         return cls(__coordinate_list, strand)
 
 
 class CoordinateMapper(Coordinate):
-    u"""
+    """
     Convert positions between CDS and protein coordinates.
     TODO: Add cds to pep coordinate?
     """
 
     def __init__(self, coordinates_list, strand: str):
-        u"""
+        """
         Set genomic coordinates to be used for mapping
         :param coordinates_list: a nested tuple of list
         :param strand: a strands of given coordinate object
@@ -200,7 +194,7 @@ class CoordinateMapper(Coordinate):
         super().__init__(coordinate_list=coordinates_list, strand=strand)
 
     def pep_to_cds(self, pep_start: int, pep_end: Optional[int] = None):
-        u"""
+        """
         Convert pep position into genomic position
         :param pep_start: the start position of pep
         :param pep_end: the end position of pep, if None, the start site is equal to end site
@@ -216,9 +210,9 @@ class CoordinateMapper(Coordinate):
         cds_left_index, cds_right_index = start_ind[0], end_ind[-1] + 1
 
         return self.init_from_location_list(
-            self.location_list[cds_left_index:cds_right_index],
-            self.strand)
+            self.location_list[cds_left_index:cds_right_index], self.strand
+        )
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     pass

{trackplot-0.5.7 → trackplot-0.5.9}/trackplot/base/GenomicLoci.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 # -*- coding:utf-8 -*-
-u"""
+"""
 Created by ygidtu@gmail.com at 2019.01.04
 
 This script contains all the basic data types used by this suite of scripts
@@ -13,23 +13,16 @@ Changelog:
 
 
 class GenomicLoci(object):
-    u"""
+    """
     Created by ygidtu at 2018.12.19
 
     A base class to handle the position relationships
     """
 
-    __slots__ = [
-        "chromosome",
-        "start",
-        "end",
-        "strand",
-        "gtf_line",
-        "name"
-    ]
+    __slots__ = ["chromosome", "start", "end", "strand", "gtf_line", "name"]
 
     def __init__(self, chromosome, start, end, strand, name="", gtf_line=None):
-        u"""
+        """
         init this class
         :param chromosome: str
         :param start: int
@@ -47,7 +40,9 @@ class GenomicLoci(object):
         self.name = name
 
         if self.end < self.start:
-            raise ValueError(f"End site should bigger than start site, not {self.start} -> {self.end}")
+            raise ValueError(
+                f"End site should bigger than start site, not {self.start} -> {self.end}"
+            )
         if strand == ".":
             strand = "*"
         if strand not in ("+", "-", "*"):
@@ -56,7 +51,7 @@ class GenomicLoci(object):
         self.strand = strand
 
     def __str__(self):
-        u"""
+        """
         convert this to string
         :return:
         """
@@ -65,11 +60,11 @@ class GenomicLoci(object):
         return f"{self.chromosome}:{self.start}-{self.end}:{self.strand}"
 
     def __iter__(self):
-        for i in range(self.start, self.end+1):
+        for i in range(self.start, self.end + 1):
             yield i
 
     def __gt__(self, other):
-        u"""
+        """
         if other downstream of other
 
         Note:
@@ -88,7 +83,7 @@ class GenomicLoci(object):
         return self.end < other.end
 
     def __lt__(self, other):
-        u"""
+        """
         if other is upstream of other
 
         Note:
@@ -107,7 +102,7 @@ class GenomicLoci(object):
         return self.end > other.end
 
     def __eq__(self, other):
-        u"""
+        """
         if two objects are the same
         :param other:
         :return:
@@ -115,7 +110,7 @@ class GenomicLoci(object):
         return hash(self) == hash(other)
 
     def __add__(self, other):
-        u"""
+        """
         merge two sites into one
         :param other:
         :return:
@@ -124,11 +119,11 @@ class GenomicLoci(object):
             chromosome=self.chromosome,
             start=min(self.start, other.start),
             end=max(self.end, other.end),
-            strand=self.strand
+            strand=self.strand,
         )
 
     def __hash__(self):
-        u"""
+        """
         generate hash
         :return:
         """
@@ -138,16 +133,20 @@ class GenomicLoci(object):
         return self.end - self.start + 1
 
     def is_overlap(self, other):
-        u"""
+        """
         whether two loci have any overlaps
         :param other: another GenomicLoci and it's children class
         :return: Boolean
         """
-        return self.chromosome == other.chromosome and self.start <= other.end and self.end >= other.start
+        return (
+            self.chromosome == other.chromosome
+            and self.start <= other.end
+            and self.end >= other.start
+        )
 
     @classmethod
     def create_loci(cls, string):
-        u"""
+        """
         Create loci from String
         :param string: chr1:1-100:+
         :return:

{trackplot-0.5.7 → trackplot-0.5.9}/trackplot/base/Junction.py

@@ -1,12 +1,12 @@
 #!/usr/bin/env python3
 # -*- coding:utf-8 -*-
-u"""
+"""
 Created by ygidtu@gmail.com at 2019.12.06
 """
 
 
 class Junction(object):
-    u"""
+    """
     Created by ygidtu at 2018.12.19
 
     This is used to collect information of single junction
@@ -16,7 +16,7 @@ class Junction(object):
     __slots__ = ["chromosome", "start", "end", "strand"]
 
     def __init__(self, chromosome, start, end, strand: str = "+"):
-        u"""
+        """
         init this class
         :param chromosome: the chromosome name of the given junction
         :param start: the start site of the given junction
@@ -33,14 +33,14 @@ class Junction(object):
 
     @property
     def length(self):
-        u"""
+        """
         :return: int, the length of this junction
         """
         return self.end - self.start
 
     @classmethod
     def create_junction(cls, string):
-        u"""
+        """
         create Junction from chr1:1-100:+
         :param string: str, chr1:1-100:+ format or chr1:1-100 also work
         :return:
@@ -57,21 +57,21 @@ class Junction(object):
         return cls(chromosome=chromosome, start=start, end=end, strand=strand)
 
     def __hash__(self):
-        u"""
+        """
         generate hash
         :return:
         """
         return hash((self.chromosome, self.start, self.end, self.strand))
 
     def __str__(self):
-        u"""
+        """
         convert junctions to string
         :return:
         """
         return f"{self.chromosome}:{self.start}-{self.end}:{self.strand}"
 
     def __gt__(self, other):
-        u"""
+        """
         greater than
         compare two junction by length
         :param other:
@@ -80,7 +80,7 @@ class Junction(object):
         return self.length > other.length
 
     def __lt__(self, other):
-        u"""
+        """
         less than
         compare two junction by length
         :param other:a
@@ -89,7 +89,7 @@ class Junction(object):
         return self.length < other.length
 
     def __eq__(self, other):
-        u"""
+        """
         same length
         :param other:
         :return:
@@ -97,7 +97,7 @@ class Junction(object):
         return self.length == other.length
 
     def is_overlap(self, other):
-        u"""
+        """
         whether any overlap with another Junction or GenomicLoci
         :param other:
         :return:
@@ -109,7 +109,7 @@ class Junction(object):
         return self.start < other.end and self.end > other.start
 
     def is_upstream(self, other):
-        u"""
+        """
         whether this junction is upstream of other
         :param other:
         :return:
@@ -122,7 +122,7 @@ class Junction(object):
         return self.end < self.start
 
     def is_downstream(self, other):
-        u"""
+        """
         whether this junction is downstream of other
         :param other:
         :return:
@@ -135,8 +135,8 @@ class Junction(object):
         return self.start > other.end
 
     def str(self, with_strand: bool = True) -> str:
-        u"""convert junctions to string, with or without strand
-        
+        """convert junctions to string, with or without strand
+
         Keyword arguments:
         :param with_strand: as name says
         Return: chr:strat-end:strand or chr:start-end
@@ -144,11 +144,11 @@ class Junction(object):
         if with_strand:
             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 """
+        """判断两个位点是否一致"""
         return self.str(with_strand) == other.str(with_strand)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     pass