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annotate karyotype-from-fasta.py @ 7:ecaa0210e62b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
author iuc
date Mon, 25 May 2020 14:50:52 +0000
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children b7c1698df177
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ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
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1 #!/usr/bin/env python
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
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2 import sys
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
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3 from Bio import SeqIO
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
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4
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
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ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
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6 # Process fasta data, extracting only headers
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
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7 for idx, seq in enumerate(SeqIO.parse(sys.argv[1], "fasta")):
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
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8 sys.stdout.write(
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
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9 "chr - {seq_id} {seq_id} 0 {length} chr{idx}color\n".format(
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
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10 seq_id=seq.id, idx=idx, length=len(seq)
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
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11 )
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
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12 )