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Merge pull request #231 from abyzovlab/master
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update code for py12
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@arpanda
arpanda authored Jul 23, 2024
2 parents 1c5e46b + 0f1ac88 commit 9a34b60
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Showing 3 changed files with 45 additions and 19 deletions.
32 changes: 17 additions & 15 deletions cnvpytor/genome.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,15 +5,16 @@ class Genome: detect reference / parity / naming functions / reference genome da
"""
from __future__ import absolute_import, print_function, division
from .utils import *
from .utils import get_install_path
from collections import OrderedDict
import logging
import pkg_resources
import os

_logger = logging.getLogger("cnvpytor.genome")


class Genome:
pytor_datapath = get_install_path().joinpath("data")
reference_genomes = {
"hg19": {
"name": "GRCh37",
Expand All @@ -28,8 +29,8 @@ class Genome:
("chr19", (59128983, "A")), ("chr20", (63025520, "A")), ("chr21", (48129895, "A")),
("chr22", (51304566, "A")), ("chrX", (155270560, "S")), ("chrY", (59373566, "S")),
("chrM", (16571, "M"))]),
"gc_file": pkg_resources.resource_filename('cnvpytor', 'data') + "/gc_hg19.pytor",
"mask_file": pkg_resources.resource_filename('cnvpytor', 'data') + "/mask_hg19.pytor",
"gc_file": pytor_datapath.joinpath("gc_hg19.pytor"),
"mask_file": pytor_datapath.joinpath("mask_hg19.pytor"),
"ensembl_api_region": "https://grch37.rest.ensembl.org/overlap/region/human/{region}?content-type=application/json;feature=gene;"
},
"hg38": {
Expand All @@ -45,8 +46,8 @@ class Genome:
("chr19", (58617616, "A")), ("chr20", (64444167, "A")), ("chr21", (46709983, "A")),
("chr22", (50818468, "A")), ("chrX", (156040895, "S")), ("chrY", (57227415, "S")),
("chrM", (16569, "M"))]),
"gc_file": pkg_resources.resource_filename('cnvpytor', 'data') + "/gc_hg38.pytor",
"mask_file": pkg_resources.resource_filename('cnvpytor', 'data') + "/mask_hg38.pytor",
"gc_file": pytor_datapath.joinpath("gc_hg38.pytor"),
"mask_file": pytor_datapath.joinpath("mask_hg38.pytor"),
"ensembl_api_region": "https://rest.ensembl.org/overlap/region/human/{region}?content-type=application/json;feature=gene;"
},
"chm13": {
Expand All @@ -63,7 +64,7 @@ class Genome:
("chr22", (51324926, "A")), ("chrX", (154259566, "S")), ("chrY", (62460029, "S")),
("chrMT", (16569, "M"))
]),
"gc_file": pkg_resources.resource_filename('cnvpytor', 'data') + "/gc_chm13v2.0.pytor",
"gc_file": pytor_datapath.joinpath("gc_chm13v2.0.pytor"),
},
"chm13v1.1": {
"name": "CHM13 v1.1 + hg38 chrY",
Expand All @@ -79,18 +80,19 @@ class Genome:
("chr22", (51324926, "A")), ("chrX", (154259566, "S")), ("chrY", (57227415, "S")),
("chrMT", (16569, "M"))
]),
"gc_file": pkg_resources.resource_filename('cnvpytor', 'data') + "/gc_chm13v1.1.pytor",
"gc_file": pytor_datapath.joinpath("gc_chm13v1.1.pytor"),
},
"kn99": {
"name": "Cryptococcus neoformans var. grubii KN99 GCA_002216725.1",
"species": "cryptococcus neoformans",
"chromosomes": OrderedDict([
("CP022321.1", (2291500,"A")), ("CP022322.1", (1621676,"A")), ("CP022323.1", (1574972,"A")), ("CP022324.1", (1084805,"A")),
("CP022325.1", (1814975,"A")), ("CP022326.1", (1422463,"A")), ("CP022327.1", (1399209,"A")), ("CP022328.1", (1398693,"A")),
("CP022329.1", (1186813,"A")), ("CP022330.1", (1059962,"A")), ("CP022331.1", (1562107,"A")), ("CP022332.1", (774060,"A")),
("CP022333.1", (756017,"A")), ("CP022334.1", (942472,"A")), ("CP022335.1", (24923,"M"))
("CP022321.1", (2291500, "A")), ("CP022322.1", (1621676, "A")), ("CP022323.1", (1574972, "A")),
("CP022324.1", (1084805, "A")), ("CP022325.1", (1814975, "A")), ("CP022326.1", (1422463, "A")),
("CP022327.1", (1399209, "A")), ("CP022328.1", (1398693, "A")), ("CP022329.1", (1186813, "A")),
("CP022330.1", (1059962, "A")), ("CP022331.1", (1562107, "A")), ("CP022332.1", (774060, "A")),
("CP022333.1", (756017, "A")), ("CP022334.1", (942472, "A")), ("CP022335.1", (24923, "M"))
]),
"gc_file": pkg_resources.resource_filename('cnvpytor', 'data') + "/gc_kn99.pytor",
"gc_file": pytor_datapath.joinpath("gc_kn99.pytor"),
}
}

Expand Down Expand Up @@ -170,7 +172,7 @@ def check_resources(cls):
@classmethod
def download_resources(cls):
"""
Download missing resource files files from github.
Download missing resource files from gitHub.
Returns
-------
Expand All @@ -188,7 +190,7 @@ def download_resources(cls):
_logger.info("Downloading GC resource file: %s", fn)
try:
download(url, res)
_logger.info("File downlaoded.")
_logger.info("File downloaded.")
except Exception as e:
_logger.error("Problem with downloading/saving resource files.")
_logger.error("Exception details: " + str(e))
Expand All @@ -204,7 +206,7 @@ def download_resources(cls):
_logger.info("Downloading MASK resource file: %s", fn)
try:
download(url, res)
_logger.info("File downlaoded.")
_logger.info("File downloaded.")
except Exception as e:
_logger.error("Problem with downloading/saving resource files.")
_logger.error("Exception details: " + str(e))
Expand Down
7 changes: 3 additions & 4 deletions cnvpytor/report.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,12 +6,11 @@

from fpdf import FPDF, XPos, YPos
import logging
import pkg_resources
from .utils import get_install_path

_logger = logging.getLogger("cnvpytor.report")



class Report(FPDF):
def __init__(self):
FPDF.__init__(self)
Expand Down Expand Up @@ -47,8 +46,8 @@ def header(self):
self.cell(self.epw-105, 6, "SINGLE SAMPLE REPORT", new_x=XPos.LEFT, new_y=YPos.NEXT)
self.cell(self.epw-105, 6, "SAMPLE: {:}".format(self.sample), new_x=XPos.LEFT, new_y=YPos.NEXT)
self.cell(self.epw-105, 6, "DATE: {:}".format(self.date), new_x=XPos.LEFT, new_y=YPos.NEXT)

self.image(pkg_resources.resource_filename('cnvpytor', 'imgs')+"/cnvpytor_640.png",x=11,y=2,w=80)
logo_path = get_install_path().joinpath("imgs/cnvpytor_640.png")
self.image(logo_path, x=11, y=2, w=80)

# Line break
self.ln(5)
Expand Down
25 changes: 25 additions & 0 deletions cnvpytor/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
import logging
import readline
import requests
from pathlib import Path

_logger = logging.getLogger("cnvpytor.utils")

Expand Down Expand Up @@ -1238,3 +1239,27 @@ def calculate_likelihood(io, bin_size, chrom, snp_use_mask=True, snp_use_id=Fals
likelihood[i] /= s

return likelihood


def get_install_path():
"""
Retrieve the installation path of the 'cnvpytor' package.
This function attempts to locate the installation path of the 'cnvpytor' package.
It first uses the `importlib.resources` module, available in Python 3.9 and later.
If `importlib.resources` is not available or an error occurs, the function falls
back to using the `pkg_resources` module, which is compatible with older Python versions.
Returns:
PosixPath: The installation path of the 'cnvpytor' package.
"""
try:
from importlib import resources
# Use importlib.resources for Python 3.9+
data_path = resources.files('cnvpytor')
except Exception as e:
# Fallback to pkg_resources for older Python versions
import pkg_resources
data_path = Path(pkg_resources.resource_filename('cnvpytor', ""))

return data_path

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