Mercurial > repos > tomnl > create_msp

annotate msp_split.py @ 17:e1990c07bb5a draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
author tomnl
date Thu, 14 Jun 2018 09:25:22 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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17
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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1 from __future__ import print_function
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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2 import argparse
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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3 import textwrap
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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4 import os
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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5 import re
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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6 import csv
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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7 import math
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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8
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9 def msp_split(i, o, n):
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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10 spec_total = lcount('NAME', i)
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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11 spec_lim = math.ceil(spec_total/float(n))
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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12 spec_c = 0
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13 filelist = []
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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14 header = ''
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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15 print('spec_lim', spec_lim)
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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16 with open(i, 'r') as msp_in:
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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17 for i in range(1, n+1):
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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18 with open(os.path.join(o, 'file{}.msp'.format(str(i).zfill(len(str(n))))), 'w+') as msp_out:
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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19 while spec_c <= spec_lim:
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20 if header:
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21 msp_out.write(header)
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22 header = ''
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23 line = msp_in.readline()
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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25 if not line:
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26 break # end of file
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27
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28 if re.match('^NAME:.*$', line, re.IGNORECASE):
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29 header = line
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30 spec_c += 1
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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31 else:
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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32 msp_out.write(line)
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33 spec_c = 1
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34
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35 return filelist
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37 def lcount(keyword, fname):
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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38 with open(fname, 'r') as fin:
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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39 return sum([1 for line in fin if keyword in line])
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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40
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41 def main():
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42
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43 p = argparse.ArgumentParser(prog='PROG',
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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44 formatter_class=argparse.RawDescriptionHelpFormatter,
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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45 description='''split msp files''',
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46 )
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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47
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48 p.add_argument('-i', dest='i', help='msp file', required=True)
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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49 p.add_argument('-o', dest='o', help='out dir', required=True)
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50 p.add_argument('-n', dest='n',)
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51
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52
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53 args = p.parse_args()
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54
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55 if not os.path.exists(args.o):
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56 os.makedirs(args.o)
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57 print('in file', args.i)
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58 print('out dir', args.o)
e1990c07bb5a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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59 print('nm files', args.n)
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61 msp_split(args.i, args.o, int(args.n))
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62
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63
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64 if __name__ == '__main__':
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65 main()
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66