Mercurial > repos > estrain > microrunqc

annotate median_size.py @ 0:4e629e82c5b1 draft default tip

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planemo upload commit a820b38dea9a409c11e220ba904da232fdbc4c05
author estrain
date Fri, 13 Mar 2026 12:51:10 +0000
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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1 #!/usr/bin/env
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2
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3 ## Errol Strain (estrain@gmail.com)
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4 ## calculate median insert size from sam file
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5
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6 import numpy as np
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7
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8 def get_data(infile):
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9 lengths = []
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10 for line in infile:
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11 if line.startswith('@'):
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12 pass
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13 else:
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14 line = line.rsplit()
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15 length = int(line[8])
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16 if length > 0:
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17 lengths.append(length)
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18 else:
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19 pass
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20 return lengths
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21
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22 if __name__ == "__main__":
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23 import sys
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24 lengths = get_data(sys.stdin)
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25 md = int(np.median(lengths))
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26 print(md)