Mercurial > repos > rdvelazquez > mmvc

annotate extract_mmvc_consensus @ 1:853065b53ee6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'-dirty
author rdvelazquez
date Fri, 15 Mar 2019 13:34:54 -0400
parents c5c1faa433e4
children 4ca91bf87f1f
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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:
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c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
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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:
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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:
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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:
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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:
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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:
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10
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
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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:
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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:
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13 consensus = data["consensus"]
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
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14 consensusFasta = ">" + fastaHeaderName + "\n" + consensus
c5c1faa433e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
rdvelazquez
parents:
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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:
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16 f.write(consensusFasta)