toulligqc 2.6__tar.gz → 2.7__tar.gz

{toulligqc-2.6 → toulligqc-2.7}/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.1
 Name: toulligqc
-Version: 2.6
+Version: 2.7
 Summary: A post sequencing QC tool for Oxford Nanopore sequencers
-Home-page: https://github.com/GenomicParisCentre/toulligQC
+Home-page: https://github.com/GenomiqueENS/toulligQC
 Author: Genomic Paris Centre team
-Author-email: toulligqc@biologie.ens.fr
+Author-email: toulligqc@bio.ens.psl.eu
 License: GPL V3
 Keywords: Nanopore MinION QC report
 Platform: ALL
@@ -15,7 +15,7 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: License :: OSI Approved :: CEA CNRS Inria Logiciel Libre License, version 2.1 (CeCILL-2.1)
-Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.11.0
 License-File: LICENSE-CeCILL.txt
 License-File: LICENSE.txt

{toulligqc-2.6 → toulligqc-2.7}/README.md

@@ -24,6 +24,7 @@ Support is availlable on [GitHub issue page](https://github.com/GenomicParisCent
   * 1.3 [Docker](#docker)
      *  [Docker image recovery](#docker-image-recovery)
      *  [Launching Docker image with docker run](#launching-Docker-image-with-docker-run)
+  * 1.4 [nf-core module](#nfcore-module)
 
 * 2.[Usage](#usage)
   * 2.1 [Command line](#command-line)
@@ -93,14 +94,25 @@ $ docker run -ti \
              -v /path/to/basecaller/sequencing/summary/file:/path/to/basecaller/sequencing/summary/file \
              -v /path/to/basecaller/sequencing/telemetry/file:/path/to/basecaller/telemetry/summary/file \
              -v /path/to/result/directory:/path/to/result/directory \
-             toulligqc:latest
+             genomicpariscentre/toulligqc:latest
 ```
+
+<a name="nfcore-module"></a>
+### 1.4 Using nf-core module
+ToulligQC is also available on nf-core as a module written in nextflow. To install nf-core on your system, please visit their website (<https://nf-co.re/docs/usage/introduction>).
+
+The following command line will install the latest version of the ToulligQC module:
+
+```bash
+$ nf-core modules install toulligqc
+```
+
 <a name="usage"></a>
 ## 2. Usage
 <a name="command-line"></a>
 
 ToulligQC is adapted to RNA-Seq along with DNA-Seq and it is compatible with 1D² runs.
-This QC tool supports only Guppy basecalling ouput files.
+This QC tool supports only Guppy and Dorado basecalling ouput files.
 It also needs a single FAST5 file (to catch the flowcell ID and the run date) if a telemetry file is not provided.
 Flow cells and kits version are retrieved using the telemetry file.
 ToulligQC can take barcoding samples by adding the barcode list as a command line option.
@@ -111,7 +123,7 @@ To do so, ToulligQC deals with different file formats: gz, tar.gz, bz2, tar.bz2
 This tool will produce a set of graphs, statistic file in plain text format and a HTML report.
 
 
-To run ToulligQC you need the Guppy basecaller output files : ```sequencing_summary.txt``` and ```sequencing_telemetry.js```. or ```FASTQ``` or ```BAM```
+To run ToulligQC you need the Guppy/ Dorado basecaller output files : ```sequencing_summary.txt``` and ```sequencing_telemetry.js```. or ```FASTQ``` or ```BAM```
 This can be compressed with gzip or bzip2. 
 You can use your initial Fast5 ONT file too.
 ToulligQC can perform analyses on your data if the directory is organised as the following:
@@ -132,7 +144,7 @@ RUN_ID
     └── sequencing_1dsq_summary.txt
  ```
 
-For a barcoded run you can add the barcoding files generated by Guppy ```barcoding_summary_pass.txt``` and ```barcoding_summary_fail.txt``` to ToulligQC or a single file ```sequencing_summary_all.txt``` containing sequencing_summary and barcoding_summary information combined.
+For a barcoded run you can add the barcoding files generated by Guppy/ Dorado ```barcoding_summary_pass.txt``` and ```barcoding_summary_fail.txt``` to ToulligQC or a single file ```sequencing_summary_all.txt``` containing sequencing_summary and barcoding_summary information combined.
 
 For the barcode list to use in the command line options, ToulligQC handle the following naming schemes: BCXX, RBXX, NBXX and barcodeXX where XX is the number of the barcode.
 The barcode naming schemes are case insensitive.
@@ -156,14 +168,16 @@ This is a directory for 1D² analysis with barcoding files:
 
 General Options:
 ```
-usage: ToulligQC V2.2.1 -a SEQUENCING_SUMMARY_SOURCE [-t TELEMETRY_SOURCE]
-                        [--fastq -q FASTQ] [--bam -u BAM]
-                        [-f FAST5_SOURCE] [-n REPORT_NAME]
-                        [--output-directory OUTPUT] [-o HTML_REPORT_PATH]
-                        [--data-report-path DATA_REPORT_PATH]
-                        [--images-directory IMAGES_DIRECTORY]
-                        [-d SEQUENCING_SUMMARY_1DSQR_SOURCE] [-b]
-                        [-l BARCODES] [--quiet] [--force] [-h] [--version]
+usage: ToulligQC V2.6 [-a SEQUENCING_SUMMARY_SOURCE] [-t TELEMETRY_SOURCE]
+                      [-f FAST5_SOURCE] [-p POD5_SOURCE] [-q FASTQ] [-u BAM]
+                      [--thread THREAD] [--batch-size BATCH_SIZE] [--qscore-threshold THRESHOLD]
+                      [-n REPORT_NAME] [--output-directory OUTPUT] [-o HTML_REPORT_PATH]
+                      [--data-report-path DATA_REPORT_PATH] 
+                      [--images-directory IMAGES_DIRECTORY]
+                      [-d SEQUENCING_SUMMARY_1DSQR_SOURCE]
+                      [-s SAMPLESHEET]
+                      [-b] [-l BARCODES]
+                      [--quiet] [--force] [-h] [--version]
 
 required arguments:
   -a SEQUENCING_SUMMARY_SOURCE, --sequencing-summary-source SEQUENCING_SUMMARY_SOURCE
@@ -175,6 +189,9 @@ required arguments:
   -f FAST5_SOURCE, --fast5-source FAST5_SOURCE
                         Fast5 file source (necessary if no telemetry file),
                         can also be in a tar.gz/tar.bz2 archive or a directory
+  -p POD5_SOURCE, --pod5-source POD5_SOURCE
+                        pod5 file source (necessary if no telemetry file), 
+                        can also be in a tar.gz/tar.bz2 archive or a directory
   -q FASTQ, --fastq FASTQ
                         FASTQ file (necessary if no sequencing summary file),
                         can also be in a .gz archive
@@ -183,6 +200,8 @@ required arguments:
                         can also be a SAM format
 
 optional arguments:
+  -s SAMPLESHEET, --samplesheet SAMPLESHEET
+                        Samplesheet (.csv file) to fill out sample names in MinKNOW.
   -n REPORT_NAME, --report-name REPORT_NAME
                         Report name
   --output-directory OUTPUT
@@ -197,8 +216,9 @@ optional arguments:
                         Basecaller 1dsq summary source
   -b, --barcoding       Option for barcode usage
   -l BARCODES, --barcodes BARCODES
-                        Coma separated barcode list (e.g.
-                        BC05,RB09,NB01,barcode10)
+                        Comma-separated barcode list (e.g.,
+                        BC05,RB09,NB01,barcode10) or a range separated with ':' (e.g.,
+                        barcode01:barcode19)
   --thread THREAD       Number of threads for parsing FASTQ or BAM files (default: 2).
   --batch-size BATCH_SIZE Batch size for each threads (default: 500).
   --qscore-threshold THRESHOLD Q-score threshold to distinguish between passing filter and
@@ -213,7 +233,41 @@ optional arguments:
  * #### Examples
 
 
-Example with optional arguments:
+* Sequencing summary alone \
+Note that the fowcell ID and run date will be missing from report, found in telemetry file or single fast5 file
+
+```bash
+$ toulligqc --report-name summary_only \
+            --sequencing-summary-source /path/to/basecaller/output/sequencing_summary.txt \
+            --html-report-path /path/to/output/report.html
+```
+* Sequencing summary + telemetry file
+
+```bash
+$ toulligqc --report-name summary_plus_telemetry \
+            --telemetry-source /path/to/basecaller/output/sequencing_telemetry.js \
+            --sequencing-summary-source /path/to/basecaller/output/sequencing_summary.txt \
+            --html-report-path /path/to/output/report.html
+```
+
+* Telemetry file + fast5 files
+
+```bash
+$ toulligqc --report-name telemetry_plus_fast5 \
+            --telemetry-source /path/to/basecaller/output/sequencing_telemetry.js \
+            --fast5-source /path/to/basecaller/output/fast5_files.fast5.gz \ 
+            --html-report-path /path/to/output/report.html
+```
+
+* Fastq/ bam files only
+
+```bash
+$ toulligqc --report-name FAF0256 \
+            --fastq /path/to/basecaller/output/fastq_files.fq.gz \ # (replace with --bam)
+            --html-report-path /path/to/output/report.html
+```
+
+* Optional arguments for 1D² analysis
 
 ```bash
 $ toulligqc --report-name FAF0256 \
@@ -223,7 +277,7 @@ $ toulligqc --report-name FAF0256 \
             --html-report-path /path/to/output/report.html
 ```
 
-Example with optional arguments to deal with barcoded samples:
+* Optional arguments to deal with barcoded samples
 
 ```bash
 $ toulligqc --report-name FAF0256 \
@@ -271,7 +325,7 @@ $ toulligqc \
     --sequencing-summary-source sequencing_summary.txt \
     --sequencing-summary-source barcoding_summary_pass.txt \
     --sequencing-summary-source barcoding_summary_fail.txt \
-    --barcodes                  BC01,BC02,BC03,BC04,BC05,BC07 \
+    --barcodes                  BC01:BC07 \
     --output-directory          output
 ```
 

{toulligqc-2.6 → toulligqc-2.7}/setup.py

@@ -14,11 +14,11 @@ setup(
     long_description='See project website for more information.',
 
     # The project's main homepage.
-    url='https://github.com/GenomicParisCentre/toulligQC',
+    url='https://github.com/GenomiqueENS/toulligQC',
 
     # Author details
     author='Genomic Paris Centre team',
-    author_email='toulligqc@biologie.ens.fr',
+    author_email='toulligqc@bio.ens.psl.eu',
 
     license='GPL V3',
     platforms='ALL',
@@ -34,7 +34,7 @@ setup(
         'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
         'License :: OSI Approved :: CEA CNRS Inria Logiciel Libre License, version 2.1 (CeCILL-2.1)',
 
-        'Programming Language :: Python :: 3.11'
+        'Programming Language :: Python :: 3.12'
     ],
 
     keywords='Nanopore MinION QC report',
@@ -46,10 +46,10 @@ setup(
     include_package_data=True,
 
     python_requires='>=3.11.0',
-    install_requires=['matplotlib>=3.6.3',   'plotly>=5.15.0', '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',
-                      'pod5>=0.3.6'],
+    install_requires=['matplotlib>=3.6.3',   'plotly==5.15.0', 'h5py>=3.10.0',
+                      'pandas>=2.1.4',       'numpy>=1.26.4',  'scipy>=1.11.4',
+                      'scikit-learn>=1.4.1', 'tqdm>=4.66.2',   'pysam>=0.22.0',
+                      'pod5>=0.3.10', 'ezcharts==0.7.6'],
 
     entry_points={
         'console_scripts': [

{toulligqc-2.6 → toulligqc-2.7}/toulligqc/bam_extractor.py

@@ -64,8 +64,9 @@ class uBAM_Extractor:
         
         # Add missing categories
         if 'barcode_arrangement' in self.dataframe.columns:
-           self.dataframe['barcode_arrangement'].cat.add_categories([0, 'other barcodes', 'passes_filtering'],
-                                                                       inplace=True)
+            self.dataframe['barcode_arrangement'] = self.dataframe['barcode_arrangement'].cat.add_categories([0,
+                                                                                        'other barcodes',
+                                                                                        'passes_filtering'])
         
         # Replace all NaN values by 0 to avoid data manipulation errors when columns are not the same length
         self.dataframe = self.dataframe.fillna(0)
@@ -124,21 +125,29 @@ class uBAM_Extractor:
         add_image_to_result(self.quiet, images, time.time(), pgg.phred_score_over_time(self.dataframe_dict, result_dict, self.images_directory))
         add_image_to_result(self.quiet, images, time.time(), pgg.speed_over_time(self.dataframe_dict, self.images_directory))
         if self.is_barcode:
+            if "barcode_alias" in self.config_dictionary:
+                barcode_alias = self.config_dictionary['barcode_alias']
+            else:
+                barcode_alias = None 
             add_image_to_result(self.quiet, images, time.time(), pgg.barcode_percentage_pie_chart_pass(self.dataframe_dict,
                                                                                                        self.barcode_selection,
-                                                                                                       self.images_directory))
+                                                                                                       self.images_directory,
+                                                                                                       barcode_alias))
 
             read_fail = self.dataframe_dict["read.fail.barcoded"]
             if not (len(read_fail) == 1 and read_fail["other barcodes"] == 0):
                 add_image_to_result(self.quiet, images, time.time(), pgg.barcode_percentage_pie_chart_fail(self.dataframe_dict,
                                                                                                       self.barcode_selection,
-                                                                                                      self.images_directory))
+                                                                                                      self.images_directory,
+                                                                                                      barcode_alias))
 
             add_image_to_result(self.quiet, images, time.time(), pgg.barcode_length_boxplot(self.dataframe_dict,
-                                                                                            self.images_directory))
+                                                                                            self.images_directory,
+                                                                                            barcode_alias))
 
             add_image_to_result(self.quiet, images, time.time(), pgg.barcoded_phred_score_frequency(self.dataframe_dict,
-                                                                                                    self.images_directory))
+                                                                                                    self.images_directory,
+                                                                                                    barcode_alias))
         return images
 
 
@@ -271,8 +280,10 @@ class uBAM_Extractor:
         """
         #def process_bam_chunk(bam_chunk):
         rec_data = []
+        record_count = 0
         for rec in uBAM_chunk:
-            rec_dict = self._process_record(rec)
+            record_count += 1
+            rec_dict = self._process_record(rec, record_count)
             rec_data.append(rec_dict)
         return rec_data
 
@@ -290,41 +301,45 @@ class uBAM_Extractor:
 
 
     def _get_header(self):
-        samfile = pysam.AlignmentFile(self.ubam[0], "rb", check_sq=False)
-        header = samfile.header.to_dict()
-        run_id, model_version_id =  extract_headerTag(header,'RG','ID').split('_', 1)
+        sam_file = pysam.AlignmentFile(self.ubam[0], "rb", check_sq=False)
+        header = sam_file.header.to_dict()
+        run_id, model_version_id = extract_headerTag(header, 'RG','ID',
+                                                     'Unknown_Unknown').split('_', 1)
         self.header = {
-        "run_id" : run_id,
-        "run_date" : extract_headerTag(header, 'RG', 'DT'),
-        "sample_id" : extract_headerTag(header,'RG','SM'),
-        "basecaller" : extract_headerTag(header,'PG','PN'),
-        "basecaller_version" : extract_headerTag(header,'PG','VN'),
-        "model_version_id" : model_version_id,
-        "flow_cell_id" : extract_headerTag(header,'RG','PU')
+            "run_id": run_id,
+            "run_date": extract_headerTag(header, 'RG', 'DT', 'Unknown'),
+            "sample_id": extract_headerTag(header, 'RG', 'SM', 'Unknown'),
+            "basecaller": extract_headerTag(header, 'PG', 'PN', 'Unknown'),
+            "basecaller_version": extract_headerTag(header, 'PG', 'VN', 'Unknown'),
+            "model_version_id": model_version_id,
+            "flow_cell_id": extract_headerTag(header, 'RG', 'PU', 'Unknown')
         }
 
-    
-    
-    def _process_record(self, rec):
+
+    def _process_record(self, rec, record_count):
         """
         extract QC info from BAM record
         return : dict of QC info
         """
-        tags = rec.split("\t")
-        tag_dict = defaultdict(lambda:'unclassified')
-        tag_dict.update({key : value for key,_, value in [item.split(':',2) for item in tags[11:]]})
-        start_time = timeISO_to_float(tag_dict['st'], '%Y-%m-%dT%H:%M:%S.%f%z')
-        qual = avg_qual(tags[10]) 
+        fields = rec.split("\t")
+
+        # Parse optional fields
+        attributes = {}
+        for t in fields[11:]:
+            k, t, v = t.split(':', 2)
+            attributes[k] = v
+
+        iso_start_time = attributes.get('st', None)
+        qual = avg_qual(fields[10])
         passes_filtering = True if qual > self.threshold_Qscore else False
         data = [
-            len(tags[9]),
-            qual,
-            passes_filtering,
-            start_time,
-            tag_dict['ch'],
-            tag_dict['du']
+            len(fields[9]), # read length
+            qual, # AVG Qscore
+            passes_filtering, # Passing filter
+            float(record_count) if iso_start_time is None else timeISO_to_float(iso_start_time, '%Y-%m-%dT%H:%M:%S.%f%z'), # start time
+            attributes.get('ch', '1'),  # Channel
+            attributes.get('du', '1')  # Duration
         ]
         if self.is_barcode:
-            bc = tag_dict['BC'].split('_')[-1]
-            data.append(bc)
-        return data
+            data.append(attributes.get('BC', 'unclassified'))
+        return data

{toulligqc-2.6 → toulligqc-2.7}/toulligqc/extractor_common.py

@@ -164,16 +164,24 @@ def extract_barcode_info(extractor, result_dict, barcode_selection, dataframe_di
     if "unclassified" not in barcode_selection:
         barcode_selection.append("unclassified")
 
+
+    # If the barcode_arrangement column contains a barcode kit id
+    mask = df['barcode_arrangement'].str.startswith(('SQK', 'VQK'))
+
+    if mask.any():
+        df['barcode_arrangement'] = df['barcode_arrangement'].astype(str)
+        df.loc[mask, 'barcode_arrangement'] = df.loc[mask, 'barcode_arrangement'].str.extract(r'[SV]QK-.+_(.+)$')[0]
+
     # Create keys barcode.arrangement, and read.pass/fail.barcode in dataframe_dict with all values of
     # column barcode_arrangement when reads are passed/failed
-    dataframe_dict["barcode.arrangement"] = df["barcode_arrangement"]
+    dataframe_dict["barcode.arrangement"] = df['barcode_arrangement']
+
 
     # Print warning message if a barcode is unknown
-    barcodes_found = set(dataframe_dict["barcode.arrangement"].unique())
+    barcodes_found = set(df["barcode_arrangement"].unique())
     for element in barcode_selection:
         if element not in barcodes_found and element != 'other barcodes':
-            sys.stderr.write("Warning: The barcode {} doesn't exist in input data\n".format(element))
-
+            sys.stderr.write("\033[93mWarning:\033[0m The barcode {} doesn't exist in input data\n".format(element))
 
     # Get barcodes frequency by Bases
     df_base_pass_barcode = series_cols_boolean_elements(df, ["barcode_arrangement",  "sequence_length"],
@@ -218,6 +226,7 @@ def extract_barcode_info(extractor, result_dict, barcode_selection, dataframe_di
                      (read_fail_barcoded_count / total_reads) * 100)
 
     # Replaces all rows with unused barcodes (ie not in barcode_selection) in column barcode_arrangement with the 'other' value
+
     df.loc[~df['barcode_arrangement'].isin(
         barcode_selection), 'barcode_arrangement'] = 'other barcodes'
 

{toulligqc-2.6 → toulligqc-2.7}/toulligqc/fastq_bam_common.py

@@ -2,8 +2,23 @@ import multiprocessing as mp
 from tqdm import tqdm
 from concurrent.futures import ProcessPoolExecutor, as_completed
 
-def extract_headerTag(header, tagGroup, tag):
-        return header[tagGroup][0][tag]
+def extract_headerTag(header, tagGroup, tag, defaultValue = None):
+
+    if tagGroup not in header:
+        if defaultValue is not None:
+            return defaultValue
+        else:
+            raise KeyError(tagGroup)
+
+    first_entry = header[tagGroup][0]
+
+    if tag not in first_entry:
+        if defaultValue is not None:
+            return defaultValue
+        else:
+            raise KeyError(tag)
+
+    return first_entry[tag]
 
 
 def batch_iterator(iterator, batch_size):

{toulligqc-2.6 → toulligqc-2.7}/toulligqc/fastq_extractor.py

@@ -64,8 +64,9 @@ class fastqExtractor:
 
         # Add missing categories
         if 'barcode_arrangement' in self.dataframe_1d.columns:
-           self.dataframe_1d['barcode_arrangement'].cat.add_categories([0, 'other barcodes', 'passes_filtering'],
-                                                                       inplace=True)
+            self.dataframe_1d['barcode_arrangement'] = self.dataframe_1d['barcode_arrangement'].cat.add_categories([0, 
+                                                                                                    'other barcodes',
+                                                                                                    'passes_filtering'])
         self.dataframe_1d = self.dataframe_1d.fillna(0)
         self.barcode_selection = self.config_dictionary['barcode_selection']
         
@@ -326,9 +327,10 @@ 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-2.6 → toulligqc-2.7}/toulligqc/html_report_generator.py

@@ -72,7 +72,7 @@ def html_report(config_dictionary, result_dict, graphs):
     report = """<!doctype html>
 <html>
   <head>
-    <title>Report run MinION : {report_name} </title>
+    <title>ToulligQC: {report_name} </title>
     <meta charset='UTF-8'>
     <script>{plotlyjs}</script>
 
@@ -91,7 +91,7 @@ def html_report(config_dictionary, result_dict, graphs):
       <div id="header_filename">
         Sample ID: {sample_id} <br>
         Run date: {run_date} <br>
-        Report date : {report_date} <br>
+        Report date: {report_date} <br>
       </div>
     </div>
 

{toulligqc-2.6 → toulligqc-2.7}/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
 
@@ -476,7 +483,7 @@ def _over_time_graph(data_series,
 
 
 def _barcode_boxplot_graph(graph_name, df, barcode_selection, pass_color, fail_color, yaxis_title, legend_title,
-                           result_directory):
+                           result_directory, barcode_alias=None):
     # Sort reads by read type and drop read type column
     pass_df = df.loc[df['passes_filtering'] == bool(True)].drop(columns='passes_filtering')
     fail_df = df.loc[df['passes_filtering'] == bool(False)].drop(columns='passes_filtering')
@@ -504,7 +511,7 @@ def _barcode_boxplot_graph(graph_name, df, barcode_selection, pass_color, fail_c
                 lowerfence=[d['lowerfence']],
                 upperfence=[d['upperfence']],
                 name=read_type + " reads",
-                x0=barcode,
+                x0=barcode_alias.get(barcode, barcode) if barcode_alias else barcode,
                 marker_color=color,
                 offsetgroup=read_type.lower(),
                 showlegend=first
@@ -539,10 +546,12 @@ def _barcode_boxplot_graph(graph_name, df, barcode_selection, pass_color, fail_c
     return graph_name, output_file, table_html, div
 
 
-def _pie_chart_graph(graph_name, count_sorted, color_palette, one_d_square, result_directory):
+def _pie_chart_graph(graph_name, count_sorted, color_palette, one_d_square, result_directory, barcode_alias=None):
     read_count_sorted = count_sorted[0]
     base_count_sorted = count_sorted[1]
     labels = read_count_sorted.index.values.tolist()
+    if barcode_alias:
+        labels = [barcode_alias.get(label, label) for label in labels]
 
     fig = go.Figure()
 
@@ -622,9 +631,9 @@ 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 +647,9 @@ 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"
@@ -664,6 +673,9 @@ def _pie_chart_graph(graph_name, count_sorted, color_palette, one_d_square, resu
     barcode_table = pd.DataFrame({"Barcode arrangement (%)": read_count_sorted / sum(read_count_sorted) * 100,
                                   count_col_name: read_count_sorted,
                                  "Base count": base_count_sorted})
+    if barcode_alias:
+        barcode_table = barcode_table.rename(index=barcode_alias)
+
     barcode_table.sort_index(inplace=True)
     pd.options.display.float_format = percent_format_str.format
     barcode_table[count_col_name] = barcode_table[count_col_name].astype(int).apply(lambda x: _format_int(x))

{toulligqc-2.6 → toulligqc-2.7}/toulligqc/plotly_graph_generator.py

@@ -598,7 +598,7 @@ def plot_performance(df, result_directory):
 #
 
 
-def barcode_percentage_pie_chart_pass(dataframe_dict, barcode_selection, result_directory):
+def barcode_percentage_pie_chart_pass(dataframe_dict, barcode_selection, result_directory, barcode_alias):
     """
     Plots a pie chart of 1D read pass percentage per barcode of a run.
     """
@@ -612,10 +612,11 @@ def barcode_percentage_pie_chart_pass(dataframe_dict, barcode_selection, result_
                             count_sorted=[read_count_sorted, base_count_sorted],
                             color_palette=toulligqc_colors['pie_chart_palette'],
                             one_d_square=False,
-                            result_directory=result_directory)
+                            result_directory=result_directory,
+                            barcode_alias=barcode_alias)
 
 
-def barcode_percentage_pie_chart_fail(dataframe_dict, barcode_selection, result_directory):
+def barcode_percentage_pie_chart_fail(dataframe_dict, barcode_selection, result_directory, barcode_alias):
     """
     Plots a pie chart of 1D read fail percentage per barcode of a run.
     Needs the samplesheet file describing the barcodes to run
@@ -630,10 +631,11 @@ def barcode_percentage_pie_chart_fail(dataframe_dict, barcode_selection, result_
                             count_sorted=[read_count_sorted, base_count_sorted],
                             color_palette=toulligqc_colors['pie_chart_palette'],
                             one_d_square=False,
-                            result_directory=result_directory)
+                            result_directory=result_directory,
+                            barcode_alias=barcode_alias)
 
 
-def barcode_length_boxplot(datafame_dict, result_directory):
+def barcode_length_boxplot(datafame_dict, result_directory, barcode_alias):
     """
     Boxplots all the 1D pass and fail read length for each barcode indicated in the sample sheet
     """
@@ -649,10 +651,11 @@ def barcode_length_boxplot(datafame_dict, result_directory):
                                   fail_color=toulligqc_colors['fail'],
                                   yaxis_title="Sequence length (bp)",
                                   legend_title="Read type",
-                                  result_directory=result_directory)
+                                  result_directory=result_directory,
+                                  barcode_alias=barcode_alias)
 
 
-def barcoded_phred_score_frequency(dataframe_dict, result_directory):
+def barcoded_phred_score_frequency(dataframe_dict, result_directory, barcode_alias):
     """
     Plot boxplot of the 1D pass and fail read qscore for each barcode indicated in the sample sheet
     """
@@ -668,7 +671,8 @@ def barcoded_phred_score_frequency(dataframe_dict, result_directory):
                                   fail_color=toulligqc_colors['fail'],
                                   yaxis_title="PHRED score",
                                   legend_title="Read type",
-                                  result_directory=result_directory)
+                                  result_directory=result_directory,
+                                  barcode_alias=barcode_alias)
 
 
 def sequence_length_over_time(dataframe_dict, result_directory):

{toulligqc-2.6 → toulligqc-2.7}/toulligqc/pod5_extractor.py

@@ -183,7 +183,7 @@ class Pod5Extractor:
         if self.pod5_file_extension == 'tar' or \
                 self.pod5_file_extension == 'tar.gz' or \
                 self.pod5_file_extension == 'tar.bz2':
-            self.fast5_file = self._pod5_tar_extraction(self.file_to_process, self.pod5_file_extension,
+            self.pod5_file = self._pod5_tar_extraction(self.file_to_process, self.pod5_file_extension,
                                                          self.temporary_directory)
         elif self.pod5_file_extension == 'pod5' or self.pod5_file_extension == '.pod5':
             self.pod5_file = self.file_to_process

{toulligqc-2.6 → toulligqc-2.7}/toulligqc/sequencing_summary_extractor.py

@@ -63,6 +63,7 @@ class SequencingSummaryExtractor:
         self.sequencing_summary_source = config_dictionary['sequencing_summary_source']
         self.images_directory = config_dictionary['images_directory']
         self.sequencing_summary_files = self.sequencing_summary_source.split('\t')
+        self.barcode_colname = 'barcode_arrangement'
         self.threshold_Qscore = int(config_dictionary['threshold'])
         if 'quiet' not in config_dictionary or config_dictionary['quiet'].lower() != 'true':
             self.quiet = False
@@ -74,6 +75,8 @@ class SequencingSummaryExtractor:
             for f in self.sequencing_summary_files:
                 if self._is_barcode_file(f) or self._is_sequencing_summary_with_barcodes(f):
                     self.is_barcode = True
+                    self._get_barcode_colname(f)
+                    break
 
     def check_conf(self):
         """
@@ -107,17 +110,20 @@ class SequencingSummaryExtractor:
         start_time = time.time()
 
         self.dataframe_1d = self._load_sequencing_summary_data()
+
         if self.dataframe_1d.empty:
             raise pd.errors.EmptyDataError("Dataframe is empty")
 
         # Rename 'sequence_length_template' and 'mean_qscore_template'
         self.dataframe_1d.rename(columns={'sequence_length_template': 'sequence_length',
                                           'mean_qscore_template': 'mean_qscore'}, inplace=True)
+        
+        # Rename 'barcode_arrangement'
+        if self.is_barcode and self.barcode_colname == "barcode":
+            self.dataframe_1d.rename(columns={'barcode': 'barcode_arrangement'}, inplace=True)
 
         # Add missing categories
         if 'barcode_arrangement' in self.dataframe_1d.columns:
-            #self.dataframe_1d['barcode_arrangement'].cat.add_categories([0, 'other barcodes', 'passes_filtering'],
-            #                                                            inplace=True)
             self.dataframe_1d['barcode_arrangement'] = self.dataframe_1d['barcode_arrangement'].cat.add_categories(
                                                                         [0, 'other barcodes', 'passes_filtering'])
         if 'passes_filtering' not in self.dataframe_1d.columns:
@@ -283,21 +289,30 @@ class SequencingSummaryExtractor:
         add_image_to_result(self.quiet, images, time.time(), pgg.speed_over_time(self.dataframe_dict, self.images_directory))
 
         if self.is_barcode:
+            if "barcode_alias" in self.config_dictionary:
+                barcode_alias = self.config_dictionary['barcode_alias']
+            else:
+                barcode_alias = None 
+
             add_image_to_result(self.quiet, images, time.time(), pgg.barcode_percentage_pie_chart_pass(self.dataframe_dict,
                                                                                                        self.barcode_selection,
-                                                                                                       self.images_directory))
+                                                                                                       self.images_directory,
+                                                                                                       barcode_alias))
 
             read_fail = self.dataframe_dict["read.fail.barcoded"]
             if not (len(read_fail) == 1 and read_fail["other barcodes"] == 0):
                 add_image_to_result(self.quiet, images, time.time(), pgg.barcode_percentage_pie_chart_fail(self.dataframe_dict,
                                                                                                       self.barcode_selection,
-                                                                                                      self.images_directory))
+                                                                                                      self.images_directory,
+                                                                                                      barcode_alias))
 
             add_image_to_result(self.quiet, images, time.time(), pgg.barcode_length_boxplot(self.dataframe_dict,
-                                                                                            self.images_directory))
+                                                                                            self.images_directory,
+                                                                                            barcode_alias))
 
             add_image_to_result(self.quiet, images, time.time(), pgg.barcoded_phred_score_frequency(self.dataframe_dict,
-                                                                                                    self.images_directory))
+                                                                                                    self.images_directory,
+                                                                                                    barcode_alias))
         return images
 
 
@@ -327,12 +342,13 @@ class SequencingSummaryExtractor:
             'duration': np.float32}
 
         # If barcoding files are provided, merging of dataframes must be done on read_id column
-        barcoding_summary_columns = ['read_id', 'barcode_arrangement']
+        if self.is_barcode:
+            barcoding_summary_columns = ['read_id', self.barcode_colname]
 
-        barcoding_summary_datatypes = {
-            'read_id': object,
-            'barcode_arrangement': 'category'
-        }
+            barcoding_summary_datatypes = {
+                'read_id': object,
+                self.barcode_colname: 'category'
+            }
 
         try:
             # If 1 file and it's a sequencing_summary.txt
@@ -341,9 +357,10 @@ class SequencingSummaryExtractor:
 
             # If 1 file and it's a sequencing_summary.txt with barcode info, load column barcode_arrangement
             elif len(files) == 1 and self._is_sequencing_summary_with_barcodes(files[0]):
-                sequencing_summary_columns.append('barcode_arrangement')
+                if self.is_barcode:
+                    sequencing_summary_columns.append(self.barcode_colname)
                 sequencing_summary_datatypes.update(
-                    {'barcode_arrangement': 'category'})
+                    {self.barcode_colname: 'category'})
 
                 return pd_read_sequencing_summary(files[0], cols=sequencing_summary_columns, data_type=sequencing_summary_datatypes)
 
@@ -357,14 +374,14 @@ class SequencingSummaryExtractor:
                         barcode_dataframe = dataframe
                     # if a barcoding file has already been read, append the 2 dataframes
                     else:
-                        barcode_dataframe = barcode_dataframe.append(
-                            dataframe, ignore_index=True)
+                        barcode_dataframe = pd.concat([barcode_dataframe, dataframe], ignore_index=True)
 
-                # check for presence of sequencing_summary file with barcode info, if true load column barcode_arrangement and ignore barcoding files.
+                # check for presence of sequencing_summary file with barcode info, if true load barcode column and ignore barcoding files.
                 elif self._is_sequencing_summary_with_barcodes(f):
-                    sequencing_summary_columns.append('barcode_arrangement')
+                    if self.is_barcode:
+                        sequencing_summary_columns.append(self.barcode_colname)
                     sequencing_summary_datatypes.update(
-                        {'barcode_arrangement': 'category'})
+                        {self.barcode_colname: 'category'})
                     sys.stderr.write('Warning: The sequencing summary file {} contains barcode information.'
                                      ' The barcoding summary files will be skipped.\n'.format(f))
                     return pd_read_sequencing_summary(f, cols=sequencing_summary_columns,
@@ -382,8 +399,7 @@ class SequencingSummaryExtractor:
                         if summary_dataframe is None:
                             summary_dataframe = dataframe
                         else:
-                            summary_dataframe = summary_dataframe.append(
-                                dataframe, ignore_index=True)
+                            summary_dataframe = pd.concat([summary_dataframe,dataframe], ignore_index=True)
 
             if barcode_dataframe is None:
                 # If no barcodes in files, no merged dataframes on column 'read_id'
@@ -392,20 +408,20 @@ class SequencingSummaryExtractor:
                 dataframes_merged = pd.merge(
                     summary_dataframe, barcode_dataframe, on='read_id', how='left')
 
-                missing_barcodes_count = dataframes_merged['barcode_arrangement'].isna().sum()
+                missing_barcodes_count = dataframes_merged[self.barcode_colname].isna().sum()
                 if missing_barcodes_count > 0:
                     sys.stderr.write('Warning: {} barcodes values are missing in sequencing summary file(s).'
                                      ' They will be marked as "unclassified".\n'.format(missing_barcodes_count))
 
                 # Replace missing barcodes values by 'unclassified'
-                dataframes_merged['barcode_arrangement'] = dataframes_merged['barcode_arrangement'].fillna(
+                dataframes_merged[self.barcode_colname] = dataframes_merged[self.barcode_colname].fillna(
                     'unclassified')
 
                 # Delete column read_id after merging
                 del dataframes_merged['read_id']
 
                 # Set 'barcode_arrangement' column type as category
-                dataframes_merged['barcode_arrangement'] = dataframes_merged['barcode_arrangement'].astype('category')
+                dataframes_merged[self.barcode_colname] = dataframes_merged[self.barcode_colname].astype('category')
 
                 return dataframes_merged
 
@@ -420,7 +436,7 @@ class SequencingSummaryExtractor:
         :return: True if the filename is a barcoding summary file
         """
         header = read_first_line_file(filename)
-        return header.startswith('read_id') and 'barcode_arrangement' in header
+        return header.startswith('read_id') and any(col in header for col in ['barcode_arrangement', 'barcode'])
 
     @staticmethod
     def _is_sequencing_summary_file(filename):
@@ -430,7 +446,7 @@ class SequencingSummaryExtractor:
         :return: True if the file is indeed a sequencing summary file
         """
         header = read_first_line_file(filename)
-        return header.startswith('filename') and not 'barcode_arrangement' in header
+        return header.startswith('filename') and not any(col in header for col in ['barcode_arrangement', 'barcode'])
 
     @staticmethod
     def _is_sequencing_summary_with_barcodes(filename):
@@ -441,7 +457,18 @@ class SequencingSummaryExtractor:
         :return: True if the filename is a sequencing summary file with barcodes
         """
         header = read_first_line_file(filename)
-        return header.startswith('filename') and 'barcode_arrangement' in header
+        return header.startswith('filename') and any(col in header for col in ['barcode_arrangement', 'barcode'])
+    
+    def _get_barcode_colname(self, filename):
+        """
+        Check if the barcode colname in sequencing summary is "barcode_arrangement" or "barcode"
+        :param filename: path of the file to test
+        """
+        header = read_first_line_file(filename)
+        if 'barcode_arrangement' in header:
+            self.barcode_colname = 'barcode_arrangement'
+        else :
+            self.barcode_colname = 'barcode'
 
 
 

{toulligqc-2.6 → toulligqc-2.7}/toulligqc/sequencing_summary_onedsquare_extractor.py

@@ -115,7 +115,7 @@ class OneDSquareSequencingSummaryExtractor(SSE):
 
         # Copy dataframe to avoid changing original df when dropping columns
         dataframe_1d_copy = self.dataframe_1d.copy(deep=True)
-        dataframe_1d_copy.drop(columns=["sequence_length", "mean_qscore", "passes_filtering"], inplace=True)
+        dataframe_1d_copy = dataframe_1d_copy.drop(columns=["sequence_length", "mean_qscore", "passes_filtering"])
 
         # Load dataframe_1dsqr df from 1D² files
         self.dataframe_1dsqr = self._load_sequencing_summary_1dsqr_data()
@@ -123,7 +123,7 @@ class OneDSquareSequencingSummaryExtractor(SSE):
         # Create duration column in dataframe_1dsqr
         self.dataframe_1dsqr['duration'] = self.dataframe_1dsqr['trimmed_duration1'] + self.dataframe_1dsqr[
             'trimmed_duration2']  # duration of the 2 strands sequenced
-        self.dataframe_1dsqr.drop(columns=['trimmed_duration1', 'trimmed_duration2'], inplace=True)
+        self.dataframe_1dsqr = self.dataframe_1dsqr.drop(columns=['trimmed_duration1', 'trimmed_duration2'])
 
         # dataframe_dicts
         self.dataframe_dict_1dsqr = {}
@@ -398,8 +398,7 @@ class OneDSquareSequencingSummaryExtractor(SSE):
                         barcode_dataframe = dataframe
                     # if a barcoding file has already been read, append the 2 dataframes
                     else:
-                        barcode_dataframe = barcode_dataframe.append(
-                            dataframe, ignore_index=True)
+                        barcode_dataframe = pd.concat([barcode_dataframe, dataframe], ignore_index=True)
 
                 # check for presence of sequencing_summary file, if True add column read_id for merging with barcode dataframe
                 else:
@@ -416,15 +415,13 @@ class OneDSquareSequencingSummaryExtractor(SSE):
                         if summary_dataframe is None:
                             summary_dataframe = dataframe
                         else:
-                            summary_dataframe = summary_dataframe.append(
-                                dataframe, ignore_index=True)
+                            summary_dataframe = pd.concat([summary_dataframe, dataframe], ignore_index=True)
 
             if barcode_dataframe is None:
                 # If no barcodes in files, no merged dataframes on column 'read_id'
                 return summary_dataframe.drop(columns=['read_id1'])
             else:
-                summary_dataframe.rename(columns={"read_id1": "read_id"},
-                                         inplace=True)
+                summary_dataframe = summary_dataframe.rename(columns={"read_id1": "read_id"})
                 dataframes_merged = pd.merge(summary_dataframe,
                                              barcode_dataframe,
                                              on='read_id',
@@ -436,10 +433,9 @@ class OneDSquareSequencingSummaryExtractor(SSE):
                     sys.stderr.write('Warning: {} barcodes values are missing in sequencing summary file(s).'
                                      ' They will be marked as "unclassified".\n'.format(missing_barcodes_count))
                 # Add missing categories
-                dataframes_merged['barcode_arrangement'].cat.add_categories([0, 'other barcodes', 'passes_filtering'],
-                                                                            inplace=True)
+                dataframes_merged['barcode_arrangement'] = dataframes_merged['barcode_arrangement'].cat.add_categories([0, 'other barcodes', 'passes_filtering'])
                 if 'unclassified' not in dataframes_merged['barcode_arrangement'].cat.categories:
-                    dataframes_merged['barcode_arrangement'].cat.add_categories(['unclassified'], inplace=True)
+                    dataframes_merged['barcode_arrangement'] = dataframes_merged['barcode_arrangement'].cat.add_categories(['unclassified'])
 
                 # Replace missing barcodes values by 'unclassified'
                 dataframes_merged['barcode_arrangement'] = dataframes_merged['barcode_arrangement'].fillna(

{toulligqc-2.6 → toulligqc-2.7}/toulligqc/toulligqc.py

@@ -32,9 +32,6 @@
 # 4. In the case of barcoded sequencing, it searches all barcodes from the command line argument --barcodes
 # 5. It uses all the information collected to generate a qc in the form of a htl-report and a report.data file
 
-import matplotlib
-
-matplotlib.use('Agg')
 import shutil
 import sys
 import re
@@ -42,6 +39,7 @@ import argparse
 import os
 import time
 import datetime
+import pandas as pd
 
 import warnings
 from toulligqc import toulligqc_info_extractor
@@ -97,6 +95,9 @@ def _parse_args(config_dictionary):
                                'can also be in SAM format')
     
     # Add all optional arguments
+    optional.add_argument('-s', '--samplesheet', action='store', dest="samplesheet", 
+                          help='a samplesheet (.csv file) to fill out sample names in MinKNOW')
+
     optional.add_argument("--thread", action='store', dest="thread", help="Number of threads", type=int, default=2)
     optional.add_argument("--batch-size", action='store', dest="batch_size", help="Batch size", type=int, default=500)
     optional.add_argument("--qscore-threshold", action='store', dest="threshold", help="Qscore threshold", type=int, default=9)
@@ -113,7 +114,7 @@ def _parse_args(config_dictionary):
     optional.add_argument("-b", "--barcoding", action='store_true', dest='is_barcode', help="Option for barcode usage",
                           default=False)
     optional.add_argument('-l', '--barcodes', action='store', default='', dest='barcodes',
-                          help='Coma separated barcode list (e.g. BC05,RB09,NB01,barcode10)')
+                          help='Comma-separated barcode list (e.g., BC05,RB09,NB01,barcode10) or a range separated with ":" (e.g., barcode01:barcode19)')
     optional.add_argument("--quiet", action='store_true', dest='is_quiet', help="Quiet mode",
                           default=False)
     optional.add_argument("--report-only", action='store_true', dest='report_only',
@@ -132,8 +133,8 @@ def _parse_args(config_dictionary):
     is_barcode = args.is_barcode
     barcodes = args.barcodes
 
-    # If a barcode list is provided, automatically add --barcoding argument
-    if len(barcodes) > 0:
+    # If a barcode list or samplesheet are is provided, automatically add --barcoding argument
+    if len(barcodes) > 0 or args.samplesheet:
         is_barcode = True
 
     # If no report_name specified, create default one : ToulligQC-report-YYYYMMDD_HHMMSS
@@ -150,6 +151,7 @@ def _parse_args(config_dictionary):
         ('sequencing_summary_source', _join_parameter_arguments(args.sequencing_summary_source)),
         ('sequencing_summary_1dsqr_source', _join_parameter_arguments(args.sequencing_summary_1dsqr_source)),
         ('sequencing_telemetry_source', args.telemetry_source),
+        ('samplesheet', args.samplesheet),
         ('fastq', _join_parameter_arguments(args.fastq)),
         ('bam', _join_parameter_arguments(args.bam)), 
         ('thread', args.thread),
@@ -235,7 +237,6 @@ def _check_conf(config_dictionary):
     _check_if_file_exists(config_dictionary['html_report_path'], force)
     _check_if_file_exists(config_dictionary['data_report_path'], force)
 
-    print(config_dictionary['html_report_path'])
 
 
 def _check_if_dir_exists(dir, force):
@@ -323,6 +324,20 @@ def _create_extractor_list(config_dictionary):
     return result
 
 
+def parse_samplesheet(sample_sheet):
+    columns = ['flow_cell_id', 'experiment_id',
+                                      'flow_cell_product_code',
+                                      'kit',
+                                      'barcode',
+                                      'alias']
+    try:
+        samplesheet = pd.read_csv(sample_sheet, usecols=columns)
+    except IOError:
+            raise FileNotFoundError("Error while reading samplesheet file")
+    
+    return samplesheet
+
+
 def main():
     """
     Main function creating graphs and statistics
@@ -360,12 +375,22 @@ def main():
                     if pattern:
                         barcode = 'barcode{}'.format(pattern.group(2))
                         barcode_set.add(barcode)
+                    else: 
+                        sys.stderr.write("\033[93mWarning:\033[0m Barcode '{}' is non-standard custom arrangement.\n".format(b))
+                        barcode_set.add(b)
 
             barcode_selection = sorted(barcode_set)
 
             if len(barcode_selection) == 0:
                 sys.exit("ERROR: No known barcode found in provided list of barcodes")
             config_dictionary['barcode_selection'] = barcode_selection
+
+        elif 'samplesheet' in config_dictionary:
+            samplesheet = parse_samplesheet(config_dictionary['samplesheet'])
+            config_dictionary['barcode_selection'] = list(samplesheet['barcode'])
+            config_dictionary['barcode_alias'] = pd.Series(samplesheet.alias.values, 
+                                                           index=samplesheet.barcode).to_dict()
+
     else:
         config_dictionary['barcode_selection'] = ''
 
@@ -420,4 +445,4 @@ def main():
 
 
 if __name__ == "__main__":
-    main()
+    main()

toulligqc-2.7/toulligqc/version.py

@@ -0,0 +1 @@
+__version__ = '2.7'

{toulligqc-2.6 → toulligqc-2.7}/toulligqc.egg-info/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.1
 Name: toulligqc
-Version: 2.6
+Version: 2.7
 Summary: A post sequencing QC tool for Oxford Nanopore sequencers
-Home-page: https://github.com/GenomicParisCentre/toulligQC
+Home-page: https://github.com/GenomiqueENS/toulligQC
 Author: Genomic Paris Centre team
-Author-email: toulligqc@biologie.ens.fr
+Author-email: toulligqc@bio.ens.psl.eu
 License: GPL V3
 Keywords: Nanopore MinION QC report
 Platform: ALL
@@ -15,7 +15,7 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: License :: OSI Approved :: CEA CNRS Inria Logiciel Libre License, version 2.1 (CeCILL-2.1)
-Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.11.0
 License-File: LICENSE-CeCILL.txt
 License-File: LICENSE.txt

toulligqc-2.7/toulligqc.egg-info/requires.txt

@@ -0,0 +1,11 @@
+ezcharts==0.7.6
+h5py>=3.10.0
+matplotlib>=3.6.3
+numpy>=1.26.4
+pandas>=2.1.4
+plotly==5.15.0
+pod5>=0.3.10
+pysam>=0.22.0
+scikit-learn>=1.4.1
+scipy>=1.11.4
+tqdm>=4.66.2

toulligqc-2.6/toulligqc/version.py

@@ -1 +0,0 @@
-__version__ = '2.6'

toulligqc-2.6/toulligqc.egg-info/requires.txt

@@ -1,10 +0,0 @@
-h5py>=3.7.0
-matplotlib>=3.6.3
-numpy>=1.24.2
-pandas>=1.5.3
-plotly>=5.15.0
-pod5>=0.3.6
-pysam>=0.21.0
-scikit-learn>=1.2.1
-scipy>=1.10.1
-tqdm>=4.64.1