Mercurial > repos > chrisw > monorail_test
comparison Snakefile @ 15:3fa68a0d59c5 draft
Uploaded
| author | chrisw |
|---|---|
| date | Wed, 13 Feb 2019 17:03:56 -0500 |
| parents | f2258de365ee |
| children | d2770bc432e1 |
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| 14:f2258de365ee | 15:3fa68a0d59c5 |
|---|---|
| 55 # e.g. SRR1557855,SRP045778,ce10 | 55 # e.g. SRR1557855,SRP045778,ce10 |
| 56 #create links which will be used in the align step | 56 #create links which will be used in the align step |
| 57 i = 1 | 57 i = 1 |
| 58 for f in fastqs: | 58 for f in fastqs: |
| 59 newf = '%s/%s_%s_%s_%s_%d.fastq' % (config['temp'], run_acc, study_acc, genome, method, i) | 59 newf = '%s/%s_%s_%s_%s_%d.fastq' % (config['temp'], run_acc, study_acc, genome, method, i) |
| 60 run_command(['zcat',f,'>',newf]) | 60 if 'compressed' in config: |
| 61 run_command(['zcat',f,'>',newf]) | |
| 62 else: | |
| 63 os.symlink(os.path.abspath(f), newf) | |
| 61 #create fastq 0 | 64 #create fastq 0 |
| 62 if i == 1: | 65 if i == 1: |
| 63 try: | 66 os.symlink(os.path.abspath(newf), '%s/%s_%s_%s_%s_%d.fastq' % (config['temp'], run_acc, study_acc, genome, method, 0)) |
| 64 os.symlink(os.path.abspath(newf), '%s/%s_%s_%s_%s_%d.fastq' % (config['temp'], run_acc, study_acc, genome, method, 0)) | |
| 65 except FileExistsError as fee: | |
| 66 pass | |
| 67 i += 1 | 67 i += 1 |
| 68 #create fastq 2 if not paired | 68 #create fastq 2 if not paired |
| 69 if i == 2: | 69 if i == 2: |
| 70 open('%s/%s_%s_%s_%s_%d.fastq' % (config['temp'], run_acc, study_acc, genome, method, 2), "w").close() | 70 open('%s/%s_%s_%s_%s_%d.fastq' % (config['temp'], run_acc, study_acc, genome, method, 2), "w").close() |
| 71 #create expected file structure for annotated exon bed file & reference index | 71 #create expected file structure for annotated exon bed file & reference index |
