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1 #!/usr/bin/env python
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2
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3 """
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4 Replace FASTA labels with new labels <PREFIX>1, <PREFIX>2,
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5 <PREFIX>3 etc (where <PREFIX> is a user-provided argument).
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6
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7 Can be used to label OTUs as OTU_1, OTU_2 etc.
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8
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9 This is a reimplementation of the fasta_number.py script from
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10 https://drive5.com/python/fasta_number_py.html
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11 """
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12
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13 import argparse
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14
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15 def relabel_fasta(fp,prefix,include_size=False):
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16 """
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17 """
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18 # Iterate over lines in file
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19 nlabel = 0
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20 for line in fp:
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21 # Strip trailing newlines
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22 line = line.rstrip('\n')
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23 if not line:
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24 # Skip blank lines
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25 continue
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26 elif line.startswith('>'):
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27 #
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28 nlabel += 1
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29 label = line[1:].strip()
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30 if args.needsize:
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31 # Extract size from the label
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32 try:
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33 size = filter(
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34 lambda x: x.startswith("size="),
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35 label.split(';'))[0]
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36 except Exception as ex:
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37 raise Exception("Couldn't locate 'size' in "
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38 "label: %s" % label)
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39 yield ">%s%d;%s" % (args.prefix,
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40 nlabel,
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41 size)
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42 else:
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43 yield ">%s%d" % (args.prefix,
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44 nlabel)
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45 else:
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46 # Echo the line to output
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47 yield line
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48
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49 if __name__ == "__main__":
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50
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51 # Set up command line parser
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52 p = argparse.ArgumentParser()
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53 p.add_argument("--needsize",action="store_true")
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54 p.add_argument("--nosize",action="store_true")
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55 p.add_argument("fasta")
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56 p.add_argument("prefix")
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57
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58 # Process command line
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59 args = p.parse_args()
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60
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61 # Relabel FASTA
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62 with open(args.fasta,'rU') as fasta:
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63 for line in relabel_fasta(fasta,
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64 args.prefix,
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65 include_size=args.needsize):
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66 print line
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67
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68
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