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1 #!/usr/bin/env python3
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2 import argparse
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3 import tempfile
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4 import shutil
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5 import sys
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6
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7 def parse_args():
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8 '''Argument parsin'''
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9 description = """
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10 parsing cap3 assembly aln output
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11 """
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12
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13 parser = argparse.ArgumentParser(
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14 description=description,
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15 formatter_class=argparse.RawTextHelpFormatter)
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16 parser.add_argument(
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17 '-g',
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18 '--gff_file',
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19 default=None,
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20 required=True,
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21 help="input gff3 file for appending coverage information",
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22 type=str,
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23 action='store')
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24 parser.add_argument(
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25 '-p',
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26 '--profile',
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27 default=None,
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28 required=True,
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29 help="output file for coverage profile",
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30 type=str,
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31 action="store")
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32 return parser.parse_args()
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33
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34 def read_coverage(profile):
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35 with open(profile) as p:
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36 d = {}
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37 for name, prof in zip(p, p):
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38 d[name[1:].strip()] = [int(i) for i in prof.split()]
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39 print(d, file=sys.stderr)
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40 return d
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41
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42
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43 def main():
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44 args = parse_args()
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45 coverage_hash = read_coverage(args.profile)
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46 gff_tmp = tempfile.NamedTemporaryFile()
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47 with open(args.gff_file) as f, open(gff_tmp.name, 'w') as out:
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48 for line in f:
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49 if line[0] == "#":
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50 out.write(line)
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51 else:
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52 line_parts = line.split()
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53 start = int(line_parts[3])
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54 end = int(line_parts[4])
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55 coverage = round( sum(coverage_hash[line_parts[0]][(
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56 start - 1):end]) / (end - start + 1), 3)
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57 new_line = "{};Coverage={}\n".format(line.strip(), coverage)
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58 out.write(new_line)
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59
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60 shutil.copyfile(gff_tmp.name, args.gff_file)
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61
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62
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63 if __name__ == "__main__":
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64
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65 main()
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