Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
comparison amplicon_analysis_pipeline.py @ 48:04e71fda5b9c draft
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 06b2cc0d518a6a4d77b865b6567e0bc6a2fb26df-dirty
| author | pjbriggs |
|---|---|
| date | Tue, 17 Dec 2019 09:24:17 +0000 |
| parents | 1bc0077b2c91 |
| children | cf5597dc7d2a |
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| 47:1bc0077b2c91 | 48:04e71fda5b9c |
|---|---|
| 275 <body> | 275 <body> |
| 276 <h1>Amplicon analysis pipeline: Per-base Quality Boxplots (FastQC)</h1> | 276 <h1>Amplicon analysis pipeline: Per-base Quality Boxplots (FastQC)</h1> |
| 277 """) | 277 """) |
| 278 # Look for raw and trimmed FastQC output for each sample | 278 # Look for raw and trimmed FastQC output for each sample |
| 279 for sample_name in sample_names: | 279 for sample_name in sample_names: |
| 280 # Replace underscores with hyphens in sample names | |
| 281 sample_name = sample_name.replace('_','-') | |
| 282 # Write HTML file with links to the FastQC boxplots | |
| 280 fastqc_dir = os.path.join(sample_name,"FastQC") | 283 fastqc_dir = os.path.join(sample_name,"FastQC") |
| 281 quality_boxplots.write("<h2>%s</h2>" % sample_name) | 284 quality_boxplots.write("<h2>%s</h2>" % sample_name) |
| 282 for d in ("Raw","cutdapt_sickle/Q%s" % phred_score): | 285 for d in ("Raw","cutdapt_sickle/Q%s" % phred_score): |
| 283 quality_boxplots.write("<h3>%s</h3>" % d) | 286 quality_boxplots.write("<h3>%s</h3>" % d) |
| 284 fastqc_html_files = glob.glob( | 287 fastqc_html_files = glob.glob( |
| 298 except ValueError: | 301 except ValueError: |
| 299 pass | 302 pass |
| 300 if boxplot is None: | 303 if boxplot is None: |
| 301 boxplot = "Missing plot" | 304 boxplot = "Missing plot" |
| 302 quality_boxplots.write("<h4>%s</h4><p>%s</p>" % | 305 quality_boxplots.write("<h4>%s</h4><p>%s</p>" % |
| 303 | |
| 304 (os.path.basename(f), | 306 (os.path.basename(f), |
| 305 boxplot)) | 307 boxplot)) |
| 306 quality_boxplots.write("""</body> | 308 quality_boxplots.write("""</body> |
| 307 </html> | 309 </html> |
| 308 """) | 310 """) |