Mercurial > repos > artbio > yac_clipper
comparison yac.py @ 4:f7947c5a18b8 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 48768de9d682fb80c4981cd52ef724fdf8f6961e
| author | artbio |
|---|---|
| date | Mon, 08 Apr 2019 07:26:41 -0400 |
| parents | 94d67b195acd |
| children | acbf910cd2ae |
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| 3:94d67b195acd | 4:f7947c5a18b8 |
|---|---|
| 109 if i % 2: | 109 if i % 2: |
| 110 qscore = line.rstrip() | 110 qscore = line.rstrip() |
| 111 else: | 111 else: |
| 112 read = line.rstrip() | 112 read = line.rstrip() |
| 113 continue | 113 continue |
| 114 trimmed_read, trimmed_qscore = self.scanadapt( | 114 try: |
| 115 self.adaptmotifs, read, qscore) | 115 trimmed_read, trimmed_qscore = self.scanadapt( |
| 116 self.adaptmotifs, read, qscore) | |
| 117 except ValueError: | |
| 118 continue | |
| 116 if self.minsize <= len(trimmed_read) <= self.maxsize: | 119 if self.minsize <= len(trimmed_read) <= self.maxsize: |
| 117 if (self.Nmode == "reject") and ("N" in trimmed_read): | 120 if (self.Nmode == "reject") and ("N" in trimmed_read): |
| 118 continue | 121 continue |
| 119 id += 1 | 122 id += 1 |
| 120 self.write_output(id, trimmed_read, trimmed_qscore, output) | 123 self.write_output(id, trimmed_read, trimmed_qscore, output) |