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1 #!/usr/bin/env python
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2 ### this version does not use st input!!!!
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3 # how to use:
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4 # renameSequences.py fasta.file true index.out prefix_length # for paired sequences
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5 # renameSequences.py fasta.file false index.out prefix_length # not paired sequences
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6
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7 import sys
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8 paired = sys.argv[2] == "true"
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9 index = open(sys.argv[3], 'w')
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10
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11 if len(sys.argv) == 4:
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12 prefix = 0
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13 else:
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14 prefix = int(sys.argv[4])
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15
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16 if paired:
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17 P = 2
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18 suffix = "f\n"
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19 else:
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20 P = 1
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21 suffix = "\n"
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22 i = j = 0
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23 reader = open(sys.argv[1], mode='r')
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24 for oneline in reader:
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25 if oneline == "":
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26 continue
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27 if oneline[0] == ">":
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28 i += 1
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29 j += 1
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30 prefix_string = oneline[1:(1 + prefix)].strip()
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31 if j == 1:
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32 header = ">" + prefix_string + str(i) + suffix
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33 index.write(oneline[1:].strip() + "\t" + prefix_string + str(i) +
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34 suffix)
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35 if j == 2:
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36 i -= 1
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37 header = ">" + prefix_string + str(i) + "r\n"
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38 index.write(oneline[1:].strip() + "\t" + prefix_string + str(i) +
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39 "r\n")
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40 sys.stdout.write(header)
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41 if j == P:
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42 j = 0
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43 else:
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44 sys.stdout.write(oneline)
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45 index.close()
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