Mercurial > repos > iuc > jbrowse
comparison jbrowse.py @ 28:d0743cb18ed8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3b3c0f1ea1756b0b250b5eb91661f33f11cc9c6d
| author | iuc |
|---|---|
| date | Fri, 22 Feb 2019 03:20:59 -0500 |
| parents | 61ce21e36cb5 |
| children | 2bb2e07a7a21 |
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| 27:61ce21e36cb5 | 28:d0743cb18ed8 |
|---|---|
| 612 | 612 |
| 613 def _sort_gff(self, data, dest): | 613 def _sort_gff(self, data, dest): |
| 614 | 614 |
| 615 if not os.path.exists(dest): | 615 if not os.path.exists(dest): |
| 616 # Only index if not already done | 616 # Only index if not already done |
| 617 cmd = "grep ^\"#\" '%s' > '%s'" % (data, dest) | 617 cmd = "gff3sort.pl --precise '%s' | grep -v \"^$\" > '%s'" % (data, dest) |
| 618 self.subprocess_popen(cmd) | |
| 619 | |
| 620 cmd = "grep -v ^\"#\" '%s' | grep -v \"^$\" | grep \"\t\" | sort -k1,1 -k4,4n >> '%s'" % (data, dest) | |
| 621 self.subprocess_popen(cmd) | 618 self.subprocess_popen(cmd) |
| 622 | 619 |
| 623 cmd = ['bgzip', '-f', dest] | 620 cmd = ['bgzip', '-f', dest] |
| 624 self.subprocess_popen(' '.join(cmd)) | 621 self.subprocess_popen(' '.join(cmd)) |
| 625 cmd = ['tabix', '-f', '-p', 'gff', dest + '.gz'] | 622 cmd = ['tabix', '-f', '-p', 'gff', dest + '.gz'] |