toulligqc 2.5.4__tar.gz → 2.5.6__tar.gz

{toulligqc-2.5.4 → toulligqc-2.5.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: toulligqc
-Version: 2.5.4
+Version: 2.5.6
 Summary: A post sequencing QC tool for Oxford Nanopore sequencers
 Home-page: https://github.com/GenomicParisCentre/toulligQC
 Author: Genomic Paris Centre team

{toulligqc-2.5.4 → toulligqc-2.5.6}/setup.py

@@ -46,7 +46,7 @@ setup(
     include_package_data=True,
 
     python_requires='>=3.11.0',
-    install_requires=['matplotlib>=3.6.3',   'plotly>=5.15.0', 'h5py>=3.7.0',
+    install_requires=['matplotlib>=3.6.3',   'plotly==4.5.0', 'h5py>=3.7.0',
                       'pandas>=1.5.3',       'numpy>=1.24.2',  'scipy>=1.10.1',
                       'scikit-learn>=1.2.1', 'tqdm>=4.64.1',   'pysam>=0.21.0'],
 

{toulligqc-2.5.4 → toulligqc-2.5.6}/toulligqc/fastq_extractor.py

@@ -283,9 +283,10 @@ class fastqExtractor:
                 fastq_lines.append((len(read[1]), qscore, passes_filtering, start_time, ch))
         else:
             for read in read_batch:
-                qscore = avg_qual(read)
-                passes_filtering = True if qscore > self.threshold_Qscore else False
-                fastq_lines.append((len(read), qscore, passes_filtering))
+                if len(read)>0:
+                    qscore = avg_qual(read)
+                    passes_filtering = True if qscore > self.threshold_Qscore else False
+                    fastq_lines.append((len(read), qscore, passes_filtering))
         return fastq_lines
 
 

{toulligqc-2.5.4 → toulligqc-2.5.6}/toulligqc/plotly_graph_common.py

@@ -22,6 +22,7 @@
 
 from collections import defaultdict
 
+import pkgutil
 import numpy as np
 import pandas as pd
 import plotly.graph_objs as go
@@ -301,6 +302,10 @@ def _transparent_component(c, b, a):
         return '0' + r
     return r
 
+def _copy_latest_minjs(result_directory, js_file):
+    with open(result_directory + '/' + js_file , 'w+') as f:
+        plotly_min_js = pkgutil.get_data(__name__, "resources/plotly-latest.min.js").decode('utf8')
+        f.write(plotly_min_js) 
 
 def _create_and_save_div(fig, result_directory, main):
     div = py.plot(fig,
@@ -311,11 +316,13 @@ def _create_and_save_div(fig, result_directory, main):
 
     if result_directory is not None:
         output_file = result_directory + '/' + '_'.join(main.split())
+        js_file="plotly.min.js"
         py.plot(fig,
                 filename=output_file,
                 output_type="file",
-                include_plotlyjs="directory",
+                include_plotlyjs= js_file, 
                 auto_open=False)
+        _copy_latest_minjs(result_directory, js_file)
     else:
         output_file = None
 
@@ -622,9 +629,9 @@ def _pie_chart_graph(graph_name, count_sorted, color_palette, one_d_square, resu
                         method="update"
                     ),
                     dict(
-                        args=[{'visible': [False, False, False, True]},
+                        args=[{'visible': [False, False, True, False]},
                               {**_xaxis('Barcodes', dict(visible=True)),
-                               **_yaxis('Base count', dict(visible=True)),
+                               **_yaxis('Read count', dict(visible=True)),
                                'plot_bgcolor': plotly_background_color}],
                         label="Reads Histogram",
                         method="update"
@@ -638,9 +645,9 @@ def _pie_chart_graph(graph_name, count_sorted, color_palette, one_d_square, resu
                         method="update"
                     ),
                     dict(
-                        args=[{'visible': [False, False, True, False]},
+                        args=[{'visible': [False, False, False, True]},
                               {**_xaxis('Barcodes', dict(visible=True)),
-                               **_yaxis('Read count', dict(visible=True)),
+                               **_yaxis('Base count', dict(visible=True)),
                                'plot_bgcolor': plotly_background_color}],
                         label="Bases Histogram",
                         method="update"

toulligqc-2.5.6/toulligqc/version.py

@@ -0,0 +1 @@
+__version__ = '2.5.6'

{toulligqc-2.5.4 → toulligqc-2.5.6}/toulligqc.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: toulligqc
-Version: 2.5.4
+Version: 2.5.6
 Summary: A post sequencing QC tool for Oxford Nanopore sequencers
 Home-page: https://github.com/GenomicParisCentre/toulligQC
 Author: Genomic Paris Centre team

{toulligqc-2.5.4 → toulligqc-2.5.6}/toulligqc.egg-info/requires.txt

@@ -2,7 +2,7 @@ h5py>=3.7.0
 matplotlib>=3.6.3
 numpy>=1.24.2
 pandas>=1.5.3
-plotly>=5.15.0
+plotly==4.5.0
 pysam>=0.21.0
 scikit-learn>=1.2.1
 scipy>=1.10.1

toulligqc-2.5.4/toulligqc/version.py

@@ -1 +0,0 @@
-__version__ = '2.5.4'