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annotate write_tsv_script.py @ 24:d5887ace0dd4 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f53f7f297e551bf58e753752edd0dae5205bbc77
author iuc
date Mon, 15 Apr 2024 19:38:22 +0000
parents 78ced22d09a2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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d2d1df21dfb9 "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
d2d1df21dfb9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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d2d1df21dfb9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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3 import re
d2d1df21dfb9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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4 import sys
d2d1df21dfb9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
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78ced22d09a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
iuc
parents: 16
diff changeset
6 search_str = r"^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*)(.*\$)?"
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d2d1df21dfb9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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d2d1df21dfb9 "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"
d2d1df21dfb9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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d2d1df21dfb9 "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)
d2d1df21dfb9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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d2d1df21dfb9 "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")
d2d1df21dfb9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
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d2d1df21dfb9 "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):
d2d1df21dfb9 "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):
d2d1df21dfb9 "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))