Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
diff amplicon_analysis_pipeline.py @ 4:86a12d75ebe4 draft default tip
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8
| author | pjbriggs |
|---|---|
| date | Fri, 20 Dec 2019 06:59:49 -0500 |
| parents | 3ab198df8f3f |
| children |
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--- a/amplicon_analysis_pipeline.py Thu Oct 18 09:18:04 2018 -0400 +++ b/amplicon_analysis_pipeline.py Fri Dec 20 06:59:49 2019 -0500 @@ -117,9 +117,9 @@ p.add_argument("-L",dest="minimum_length") p.add_argument("-l",dest="sliding_window_length") p.add_argument("-P",dest="pipeline", - choices=["vsearch","uparse","qiime"], - type=str.lower, - default="vsearch") + choices=["Vsearch","DADA2"], + type=str, + default="Vsearch") p.add_argument("-S",dest="use_silva",action="store_true") p.add_argument("-H",dest="use_homd",action="store_true") p.add_argument("-r",dest="reference_data_path") @@ -155,12 +155,15 @@ sample_names.append(sample_name) # Reference database - if args.use_silva: + if args.pipeline == "Vsearch": + if args.use_silva: + ref_database = "silva" + elif args.use_homd: + ref_database = "homd" + else: + ref_database = "gg" + elif args.pipeline == "DADA2": ref_database = "silva" - elif args.use_homd: - ref_database = "homd" - else: - ref_database = "gg" # Construct the pipeline command print "Amplicon analysis: constructing pipeline command" @@ -180,10 +183,11 @@ if args.reference_data_path: pipeline.add_args("-r",args.reference_data_path) pipeline.add_args("-P",args.pipeline) - if ref_database == "silva": - pipeline.add_args("-S") - elif ref_database == "homd": - pipeline.add_args("-H") + if args.pipeline == "Vsearch": + if ref_database == "silva": + pipeline.add_args("-S") + elif ref_database == "homd": + pipeline.add_args("-H") # Echo the pipeline command to stdout print "Running %s" % pipeline @@ -277,6 +281,9 @@ """) # Look for raw and trimmed FastQC output for each sample for sample_name in sample_names: + # Replace underscores with hyphens in sample names + sample_name = sample_name.replace('_','-') + # Write HTML file with links to the FastQC boxplots fastqc_dir = os.path.join(sample_name,"FastQC") quality_boxplots.write("<h2>%s</h2>" % sample_name) for d in ("Raw","cutdapt_sickle/Q%s" % phred_score): @@ -306,13 +313,41 @@ </html> """) + # Handle DADA2 error rate plot PDFs + if args.pipeline == "DADA2": + print("Amplicon analysis: collecting error rate plots") + error_rate_plots_dir = os.path.abspath( + os.path.join("DADA2_OTU_tables", + "Error_rate_plots")) + error_rate_plot_pdfs = [os.path.basename(pdf) + for pdf in + sorted(glob.glob( + os.path.join(error_rate_plots_dir,"*.pdf")))] + error_rate_plots_html = os.path.join(error_rate_plots_dir, + "error_rate_plots.html") + with open(error_rate_plots_html,"w") as error_rate_plots_out: + error_rate_plots_out.write("""<html> +<head> +<title>Amplicon analysis pipeline: DADA2 Error Rate Plots</title> +<head> +<body> +<h1>Amplicon analysis pipeline: DADA2 Error Rate Plots</h1> +""") + error_rate_plots_out.write("<ul>\n") + for pdf in error_rate_plot_pdfs: + error_rate_plots_out.write("<li>%s</li>\n" % ahref(pdf)) + error_rate_plots_out.write("<ul>\n") + error_rate_plots_out.write("""</body> +</html> +""") + # Handle additional output when categories file was supplied if args.categories_file is not None: # Alpha diversity boxplots print "Amplicon analysis: indexing alpha diversity boxplots" boxplots_dir = os.path.abspath( os.path.join("RESULTS", - "%s_%s" % (args.pipeline.title(), + "%s_%s" % (args.pipeline, ref_database), "Alpha_diversity", "Alpha_diversity_boxplot",