Mercurial > repos > iuc > vardict_java
annotate split.py @ 3:e0734e88a104 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
author | iuc |
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date | Thu, 27 Jan 2022 15:19:23 +0000 |
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3
e0734e88a104
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
iuc
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1 import sys |
e0734e88a104
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
iuc
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2 |
e0734e88a104
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
iuc
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3 |
e0734e88a104
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
iuc
parents:
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4 fai = sys.argv[1] |
e0734e88a104
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
iuc
parents:
diff
changeset
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5 chunk_size = int(sys.argv[2]) |
e0734e88a104
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
iuc
parents:
diff
changeset
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6 overlap = int(sys.argv[3]) # Base pairs |
e0734e88a104
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
iuc
parents:
diff
changeset
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7 with open(fai, 'r') as infile: |
e0734e88a104
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
iuc
parents:
diff
changeset
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8 for line in infile: |
e0734e88a104
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
iuc
parents:
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changeset
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9 name = line.split('\t')[0] |
e0734e88a104
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
iuc
parents:
diff
changeset
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10 stop = int(line.split('\t')[1]) |
e0734e88a104
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
iuc
parents:
diff
changeset
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11 start = 1 |
e0734e88a104
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
iuc
parents:
diff
changeset
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12 while start < stop: |
e0734e88a104
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
iuc
parents:
diff
changeset
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13 start = max(1, start - overlap) |
e0734e88a104
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
iuc
parents:
diff
changeset
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14 print('\t'.join([name, str(start), |
e0734e88a104
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
iuc
parents:
diff
changeset
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15 str(min(start + chunk_size, stop))])) |
e0734e88a104
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
iuc
parents:
diff
changeset
|
16 start += chunk_size |