Mercurial > repos > rdvelazquez > mmvc

annotate extract_mmvc_consensus @ 3:4ca91bf87f1f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'35710f754cc8be97c423c95eb91197df01d0520d\n'-dirty
author rdvelazquez
date Wed, 20 Mar 2019 15:58:26 -0400
parents c5c1faa433e4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
diff changeset
1 #!/usr/bin/env python3
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
diff changeset
2
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
diff changeset
3 import json
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
diff changeset
4 import sys
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
diff changeset
5
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
diff changeset
6 # first argument is script name; second should be mmvcOutput path; third should be name for fasta header; the fourth argument should be the path to save the fasta at
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
diff changeset
7 mmvcOutput = sys.argv[1]
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
diff changeset
8 fastaHeaderName = sys.argv[2]
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
diff changeset
9 fastaFilePath = sys.argv[3]
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
diff changeset
10
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
diff changeset
11 with open(mmvcOutput) as f:
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
diff changeset
12 data = json.load(f)
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
diff changeset
13 consensus = data["consensus"]
3
4ca91bf87f1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'35710f754cc8be97c423c95eb91197df01d0520d\n'-dirty
rdvelazquez
parents: 0
diff changeset
14 consensusFasta = ">" + fastaHeaderName + "\n" + consensus + "\n"
0
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
diff changeset
15 f = open(fastaFilePath, "w")
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
diff changeset
16 f.write(consensusFasta)