Reduce dependencies (#45)

Dockerfile

@@ -16,11 +16,11 @@ RUN tar -xf ont-vbz-hdf-plugin-1.0.1-Linux-x86_64.tar.gz
 RUN conda env create -f environment.yml
 
 # Activate the environment
-RUN echo "conda activate lrst_py39" >> ~/.bashrc
+RUN echo "conda activate longreadsum" >> ~/.bashrc
 SHELL ["/bin/bash", "--login", "-c"]
 
 # Ensure the correct environment is being used
-RUN export PATH="/opt/conda/envs/lrst_py39/bin/python"
+RUN export PATH="/opt/conda/envs/longreadsum/bin/python"
 RUN which python
 
 # Build LongReadSum
@@ -30,4 +30,4 @@ RUN make
 ENV HDF5_PLUGIN_PATH="/longreadsum/lib/"
 
 # The code to run when container is started:
-ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "lrst_py39", "python", "/app/longreadsum"]
+ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "longreadsum", "python", "/app/longreadsum"]

environment.yml

@@ -1,4 +1,4 @@
-name: lrst_py39
+name: longreadsum
 channels:
   - bioconda
   - anaconda
@@ -9,12 +9,8 @@ dependencies:
   - hdf5
   - htslib
   - swig
-  - matplotlib
-  - plotly=4.14
+  - plotly
   - pytest
-  - pip
-  - pip:
-    - kaleido
 
 # conda env create --file=environment.yml
-# conda activate lrst_py39
+# conda activate longreadsum

src/cli.py

@@ -85,9 +85,6 @@ def get_common_param(margs):
         try:
             if not os.path.isdir(output_dir):
                 os.makedirs(output_dir)
-            if not os.path.isdir(output_dir + '/' + getDefaultImageFolder()):
-                os.makedirs(output_dir + '/' +
-                            getDefaultImageFolder())
 
         except OSError as e:
             this_error_str += "Cannot create folder for " + \
@@ -164,12 +161,11 @@ def fq_module(margs):
         if exit_code == 0:
             logging.info("QC generated.")
             logging.info("Generating HTML report...")
-            plot_filepaths = create_base_quality_plots(fq_output, param_dict, "FASTQ: Basic statistics")
-            for static in [True, False]:
-                fq_html_gen = generate_html.ST_HTML_Generator(
-                    [["basic_st", "read_length_st", "read_length_hist", "base_st", "basic_info", "base_quality",
-                      "read_avg_base_quality"], "FASTQ QC", param_dict], plot_filepaths, static=static)
-                fq_html_gen.generate_st_html()
+            plot_filepaths = plot(fq_output, param_dict, 'FASTQ')
+            fq_html_gen = generate_html.ST_HTML_Generator(
+                [["basic_st", "read_length_bar", "read_length_hist", "base_counts", "base_quality",
+                  "read_avg_base_quality"], "FASTQ QC", param_dict], plot_filepaths, static=False)
+            fq_html_gen.generate_st_html()
 
             logging.info("Completed.")
         else:
@@ -208,15 +204,11 @@ def fa_module(margs):
         if exit_code == 0:
             logging.info("QC generated.")
             logging.info("Generating HTML report...")
-            from src import fasta_plot
-            plot_filepaths = fasta_plot.plot(fa_output, param_dict)
-
-            # TODO: Unused 'static' variable results in redundant function call
-            for static in [True, False]:
-                fa_html_gen = generate_html.ST_HTML_Generator(
-                    [["basic_st", "read_length_st", "read_length_hist", "base_st", "basic_info"], "FASTA QC",
-                     param_dict], plot_filepaths, static=True)
-                fa_html_gen.generate_st_html()
+            plot_filepaths = plot(fa_output, param_dict, 'FASTA')
+            fa_html_gen = generate_html.ST_HTML_Generator(
+                [["basic_st", "read_length_bar", "read_length_hist", "base_counts"], "FASTA QC",
+                 param_dict], plot_filepaths, static=True)
+            fa_html_gen.generate_st_html()
 
         else:
             logging.error("QC did not generate.")
@@ -252,14 +244,13 @@ def bam_module(margs):
         if exit_code == 0:
             logging.info("QC generated.")
             logging.info("Generating HTML report...")
-            from src import bam_plot
-            plot_filepaths = bam_plot.plot(bam_output, param_dict)
+            plot_filepaths = plot(bam_output, param_dict, 'BAM')
 
-            for static in [True, False]:
-                bam_html_gen = generate_html.ST_HTML_Generator(
-                    [["basic_st", "map_st", "err_st", "read_length_st", "read_length_hist", "base_st", "basic_info",
-                      "base_quality"], "BAM QC", param_dict], plot_filepaths, static=static)
-                bam_html_gen.generate_st_html()
+            # TODO: Add read average base quality plot (not currently generated by bam_plot.plot)
+            bam_html_gen = generate_html.ST_HTML_Generator(
+                [["basic_st", "read_alignments_bar", "base_alignments_bar", "read_length_bar", "read_length_hist", "base_counts", "basic_info",
+                  "base_quality"], "BAM QC", param_dict], plot_filepaths, static=False)
+            bam_html_gen.generate_st_html()
 
         else:
             logging.error("QC did not generate.")
@@ -301,18 +292,17 @@ def seqtxt_module(margs):
         if exit_code == 0:
             logging.info("QC generated.")
             logging.info("Generating HTML report...")
-            from src import seqtxt_plot
-            plot_filepaths = seqtxt_plot.plot(seqtxt_output, param_dict)
-            for static in [True, False]:
-                if margs.seq == 0:
-                    f5_html_gen = generate_html.ST_HTML_Generator(
-                        [["basic_st", "read_length_st", "read_length_hist", "base_st", "basic_info"],
-                         "sequencing_summary.txt QC", param_dict], plot_filepaths, static=static)
-                else:
-                    f5_html_gen = generate_html.ST_HTML_Generator(
-                        [["basic_st", "read_length_st", "read_length_hist", "basic_info"], "sequencing_summary.txt QC",
-                         param_dict], plot_filepaths, static=static)
-                f5_html_gen.generate_st_html()
+            plot_filepaths = plot(seqtxt_output, param_dict, 'SeqTxt')
+
+            if margs.seq == 0:
+                seqtxt_html_gen = generate_html.ST_HTML_Generator(
+                    [["basic_st", "read_length_bar", "read_length_hist", "base_counts", "base_quality", "basic_info"],
+                     "sequencing_summary.txt QC", param_dict], plot_filepaths, static=False)
+            else:
+                seqtxt_html_gen = generate_html.ST_HTML_Generator(
+                    [["basic_st", "read_length_bar", "read_length_hist", "basic_info"], "sequencing_summary.txt QC",
+                     param_dict], plot_filepaths, static=False)
+            seqtxt_html_gen.generate_st_html()
         else:
             logging.error("QC did not generate.")
 
@@ -348,12 +338,12 @@ def fast5_module(margs):
         if exit_code == 0:
             logging.info("QC generated.")
             logging.info("Generating HTML report...")
-            plot_filepaths = create_base_quality_plots(fast5_output, param_dict, "FAST5: Basic statistics")
-            for static in [True, False]:
-                fast5_html_obj = generate_html.ST_HTML_Generator(
-                    [["basic_st", "read_length_st", "read_length_hist", "base_st", "basic_info", "base_quality",
-                      "read_avg_base_quality"], "FAST5 QC", param_dict], plot_filepaths, static=static)
-                fast5_html_obj.generate_st_html()
+            plot_filepaths = plot(fast5_output, param_dict, 'FAST5')
+            fast5_html_obj = generate_html.ST_HTML_Generator(
+                [["basic_st", "read_length_bar", "read_length_hist", "base_counts", "basic_info", "base_quality",
+                  "read_avg_base_quality"], "FAST5 QC", param_dict], plot_filepaths, static=False)
+            fast5_html_obj.generate_st_html()
+
         else:
             logging.error("QC did not generate.")
 
@@ -390,13 +380,12 @@ def fast5_signal_module(margs):
         if exit_code == 0:
             logging.info("QC generated.")
             logging.info("Generating HTML report...")
-            from src import fast5_signal_plot
-            dynamic_plots, plot_filepaths = fast5_signal_plot.plot(fast5_output, param_dict)
-
-            # Generate a dynamic HTML file
+            plot_filepaths = plot(fast5_output, param_dict, 'FAST5s')
             fast5_html_obj = generate_html.ST_HTML_Generator(
-                [[], "FAST5 signal QC", param_dict], plot_filepaths, static=False)
-            fast5_html_obj.generate_st_html(signal_plots=dynamic_plots)
+                [["basic_st", "read_length_bar", "read_length_hist", "base_counts", "basic_info", "base_quality",
+                  "read_avg_base_quality", "ont_signal"], "FAST5 QC", param_dict], plot_filepaths, static=False)
+            fast5_html_obj.generate_st_html(signal_plots=True)
+
         else:
             logging.error("QC did not generate.")