Mercurial > repos > iuc > control_freec
annotate ratio2circos.py @ 0:e46944a59b31 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
author | iuc |
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date | Thu, 13 Aug 2020 09:50:35 -0400 |
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children | 2c6349fb175c |
rev | line source |
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0
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
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1 import argparse |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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2 import math |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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3 import os |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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4 |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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5 parser = argparse.ArgumentParser() |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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6 parser.add_argument('-i', '--input', required=True, default='./output/sample.bam_ratio.BedGraph', type=str) |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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7 parser.add_argument('-o', '--output', required=True, default='./output/sample.bam_ratio_log2_circos.txt', type=str) |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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8 parser.add_argument('-p', '--ploidy', required=True, default=2, type=int) |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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9 args = parser.parse_args() |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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10 |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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11 path = os.path.dirname(args.input) |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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12 output = os.path.join(path, args.output) |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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13 |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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14 with open(args.input) as file: |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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15 for line in file.readlines(): |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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16 ls = line.split() |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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17 if ls[0] != "track" and float(ls[3]) > 0: |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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18 log2_ratio = math.log2(float(ls[3]) / args.ploidy) |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
changeset
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19 with open(output, "a") as out: |
e46944a59b31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
iuc
parents:
diff
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20 out.write("{}\t{}\t{}\t{}\n".format(ls[0], ls[1], ls[2], log2_ratio)) |