Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

annotate relabel_fasta.py @ 26:f0917c340f13 draft

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730-dirty
author pjbriggs
date Thu, 30 Aug 2018 08:41:11 -0400
parents fe354f5dd0ee
children
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24
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1 #!/usr/bin/env python
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2
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3 DESCRIPTION = \
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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4 """Replace FASTA labels with new labels <PREFIX>1, <PREFIX>2,
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5 <PREFIX>3 ... (<PREFIX> is provided by the user via the command
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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6 line).
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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7
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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8 Can be used to label OTUs as OTU_1, OTU_2 etc.
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9
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10 This reimplements the functionality of the fasta_number.py utility
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11 from https://drive5.com/python/fasta_number_py.html
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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12 """
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13
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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14 import argparse
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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15
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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16 def relabel_fasta(fp,prefix,include_size=False):
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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17 """
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18 Relabel sequence records in a FASTA file
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19
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20 Arguments:
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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21 fp (File): file-like object opened for reading
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22 input FASTA data from
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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23 prefix (str): prefix to use in new labels
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24 include_size (bool): if True then copy
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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25 'size=...' records into new labels (default
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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26 is not to copy the size)
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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27
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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28 Yields: updated lines from the input FASTA.
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29 """
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30 # Iterate over lines in file
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31 nlabel = 0
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32 for line in fp:
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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33 # Strip trailing newlines
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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34 line = line.rstrip('\n')
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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35 if not line:
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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36 # Skip blank lines
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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37 continue
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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38 elif line.startswith('>'):
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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39 # Deal with start of a sequence record
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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40 nlabel += 1
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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41 label = line[1:].strip()
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42 if include_size:
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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43 # Extract size from the label
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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44 try:
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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45 size = filter(
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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46 lambda x: x.startswith("size="),
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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47 label.split(';'))[0]
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48 except Exception as ex:
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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49 raise Exception("Couldn't locate 'size' in "
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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50 "label: %s" % label)
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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51 yield ">%s%d;%s" % (args.prefix,
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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52 nlabel,
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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53 size)
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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54 else:
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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55 yield ">%s%d" % (args.prefix,
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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56 nlabel)
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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57 else:
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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58 # Echo the line to output
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59 yield line
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60
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61 if __name__ == "__main__":
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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62 # Set up command line parser
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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63 p = argparse.ArgumentParser(description=DESCRIPTION)
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64 p.add_argument("--needsize",
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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65 action="store_true",
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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66 help="include the size as part of the "
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67 "output label ('size=...' must be present "
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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68 "in the input FASTA labels). Output labels "
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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69 "will be '<PREFIX><NUMBER>;size=<SIZE>'")
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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70 p.add_argument("--nosize",
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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71 action="store_true",
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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72 help="don't include the size as part of "
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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73 "the output label (this is the default)")
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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74 p.add_argument("fasta",
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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75 metavar="FASTA",
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76 help="input FASTA file")
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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77 p.add_argument("prefix",
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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78 metavar="PREFIX",
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79 help="prefix to use for labels in output")
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80 # Process command line
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81 args = p.parse_args()
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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82 # Relabel FASTA
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83 with open(args.fasta,'rU') as fasta:
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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84 for line in relabel_fasta(fasta,
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85 args.prefix,
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86 include_size=args.needsize):
fe354f5dd0ee planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
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87 print line
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88