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1 #!/usr/bin/env python
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2
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3 """
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4 Extract importent information from the standard output file and put it in some standard format, like BED and tabular.
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5 """
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6
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7 import sys
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8
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9 bed = open(sys.argv[2], 'w+')
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10 tabular = open(sys.argv[3], 'w+')
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11
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12 for line in open(sys.argv[1]):
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13 # ORGANISM: gi|21226102|ref|NC_003901.1| Methanosarcina mazei Go1 chromosome, complete genome
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14 if line.startswith('ORGANISM:'):
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15 organism = line.lstrip('ORGANISM:').strip()
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16 # CRISPR 1 Range: 679197 - 682529
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17 if line.startswith('CRISPR '):
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18 start,end = line.split('Range:')[1].strip().split('-')
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19 start = start.strip()
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20 end = end.strip()
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21 bed.write('%s\t%s\t%s\n' % (organism, start, end))
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22 if line.rstrip().endswith(']'):
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23 cols = line.split()
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24 tabular.write("%s\t%s\t%s\t%s\t%s\t%s\n" % (organism, cols[0], cols[1], cols[2], cols[4].rstrip(','), cols[5]))
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