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annotate split_by_allele.py @ 1:4e03573653fe draft default tip

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planemo upload commit 008f4667b70be22e9ddf496738b3f74bb942ed28
author nml
date Tue, 19 Sep 2017 16:34:57 -0400
parents fc0f15ca12e0
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1 #!/usr/bin/env python
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2 import getopt
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3 import os
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4 import sys
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6 from Bio import SeqIO
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8 ERROR_MSG = "Error could not parse out allele name and number from '%s'"
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11 def split_allele_file(alleles, profiles):
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13 writers = {}
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15 handle = open(alleles, "rU")
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16 for record in SeqIO.parse(handle, "fasta"):
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18 seqid = record.id
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20 # split out the alelle name from the version number
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21 # attempting to split based on '-' first, if that fails, then '_'
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22 result = seqid.split('_')
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24 if len(result) != 2:
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25 result = seqid.split('-')
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26 if len(result) == 2:
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27 newid = '_'.join(result)
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28 record.id = newid
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29 else:
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30 print(ERROR_MSG % seqid)
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31 exit(0)
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32
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33 name, num = result
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35 # if writer exist, then write to that current fasta file
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36 if name in writers:
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37 SeqIO.write(record, writers[name], "fasta")
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38 else:
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39 # new allele found, create new writer and add the first record
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40 file_name = name + '.fasta'
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41 output_fh = open(file_name, "w")
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42 SeqIO.write(record, output_fh, "fasta")
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43 writers[name] = output_fh
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45 handle.close()
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46
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47 # create config file based on the alleles found
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48 with open('config.txt', 'w') as cfile:
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49 cfile.write("[loci]\n")
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50 for name, writer in writers.items():
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51 path = os.path.realpath(writer.name)
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52 cfile.write("%s\t%s\n" % (name, path))
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53 cfile.write("[profile]\n")
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54 cfile.write("profile\t%s\n" % profiles)
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56 return
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58
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59 alleles = None
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60 profiles = None
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62 """Input arguments"""
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63 options, remainder = getopt.getopt(sys.argv[1:], '', [
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64 'alleles=',
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65 'profiles='
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66 ])
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67
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68 for opt, arg in options:
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69 if opt in ('--alleles'):
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70 alleles = arg
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71 elif opt in ('--profiles'):
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72 profiles = arg
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73
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74 if alleles and profiles:
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75 split_allele_file(alleles, profiles)