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3
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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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4
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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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3
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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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5
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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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4
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19 if end <= 0 and start <= 0:
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3
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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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4
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24
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25
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3
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26
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27 currentSeq = ""
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28 currentId = ""
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29
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4
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30 if end is 0:
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31 with open(args.input, 'r') as i:
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32 with open(args.output, 'w') as o:
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33 for line in i.readlines():
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34 if line[0] is ">":
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35 currentSeq = currentSeq[start:]
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36 if currentSeq is not "" and currentId is not "":
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37 o.write(currentId)
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38 o.write(currentSeq + "\n")
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39 currentId = line
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40 currentSeq = ""
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41 else:
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42 currentSeq += line.rstrip()
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43 o.write(currentId)
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44 o.write(currentSeq[start:] + "\n")
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45 else:
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46 with open(args.input, 'r') as i:
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47 with open(args.output, 'w') as o:
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48 for line in i.readlines():
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49 if line[0] is ">":
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50 currentSeq = currentSeq[start:-end]
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51 if currentSeq is not "" and currentId is not "":
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52 o.write(currentId)
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53 o.write(currentSeq + "\n")
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54 currentId = line
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55 currentSeq = ""
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56 else:
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57 currentSeq += line.rstrip()
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58 o.write(currentId)
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59 o.write(currentSeq[start:-end] + "\n")
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