Mercurial > repos > iuc > spades_rnaviralspades

annotate write_tsv_script.py @ 8:de1260f8a300 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 066e075c1599b29e92708194db2b2ccc30b7677c
author iuc
date Mon, 12 Feb 2024 21:45:41 +0000
parents b3490b036c5a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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249f6a28c751 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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1 #!/usr/bin/env python
249f6a28c751 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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249f6a28c751 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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3 import re
249f6a28c751 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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4 import sys
249f6a28c751 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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b3490b036c5a 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*)(.*\$)?"
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249f6a28c751 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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249f6a28c751 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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8 replace_str = r"\1_\2\t\3\t\4"
249f6a28c751 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
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249f6a28c751 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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10 cmd = re.compile(search_str)
249f6a28c751 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
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249f6a28c751 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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12 sys.stdout.write("#name\tlength\tcoverage\n")
249f6a28c751 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
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249f6a28c751 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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14 for i, line in enumerate(sys.stdin):
249f6a28c751 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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15 if cmd.match(line):
249f6a28c751 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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16 sys.stdout.write(cmd.sub(replace_str, line))