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1 import argparse
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2
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3 #docs.python.org/dev/library/argparse.html
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4 parser = argparse.ArgumentParser()
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5 parser.add_argument("--input", help="Input fasta")
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6 parser.add_argument("--output", help="Output fasta")
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7 parser.add_argument("--start", help="How many nucleotides to trim from the start", type=int)
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8 parser.add_argument("--end", help="How many nucleotides to trim from the end", type=int)
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9
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10 args = parser.parse_args()
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11 start = int(args.start)
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12 end = int(args.end)
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13
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14 print args.input
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15 print args.output
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16 print start
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17 print end
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18
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19 if end <= 0 and start <= 0:
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20 import shutil
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21 shutil.copy(args.input, args.output)
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22 import sys
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23 sys.exit()
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24
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3
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25 def trim(string, s, e):
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26 if e == 0:
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27 return string[s:]
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28 else:
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29 return string[s:-e]
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0
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30
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31 currentSeq = ""
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32 currentId = ""
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3
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33 with open(args.input, 'r') as i, open(args.output, 'w') as o:
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34 for line in i:
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35 print "ID:", currentId
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36 if line[0] == ">":
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37 currentSeq = trim(currentSeq, start, end)
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38 if len(currentId) > 0 and len(currentSeq) > 0:
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39 o.write(currentId)
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40 o.write(currentSeq + "\n")
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41 currentId = line
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42 currentSeq = ""
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43 else:
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44 currentSeq += line.rstrip()
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45 o.write(currentId)
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46 o.write(currentSeq + "\n")
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