Mercurial > repos > iuc > spades_metaviralspades
annotate write_tsv_script.py @ 6:e060c3987513 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 35f71aa486d8754ee6a8387659032fc7c93d1be3
author | iuc |
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date | Wed, 10 Aug 2022 13:15:57 +0000 |
parents | 86f66ab58e14 |
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f1532cb33c75
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
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1 #!/usr/bin/env python |
f1532cb33c75
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff
changeset
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2 |
f1532cb33c75
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
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changeset
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3 import re |
f1532cb33c75
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
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changeset
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4 import sys |
f1532cb33c75
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
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changeset
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5 |
5
86f66ab58e14
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents:
2
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6 search_str = r"^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*)(.*\$)?" |
2
f1532cb33c75
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
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7 |
f1532cb33c75
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff
changeset
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8 replace_str = r"\1_\2\t\3\t\4" |
f1532cb33c75
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff
changeset
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9 |
f1532cb33c75
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff
changeset
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10 cmd = re.compile(search_str) |
f1532cb33c75
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff
changeset
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11 |
f1532cb33c75
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff
changeset
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12 sys.stdout.write("#name\tlength\tcoverage\n") |
f1532cb33c75
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff
changeset
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13 |
f1532cb33c75
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
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changeset
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14 for i, line in enumerate(sys.stdin): |
f1532cb33c75
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff
changeset
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15 if cmd.match(line): |
f1532cb33c75
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff
changeset
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16 sys.stdout.write(cmd.sub(replace_str, line)) |