Mercurial > repos > mvdbeek > dapars

annotate filter_utr.py @ 18:e041f9f3271f draft

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planemo upload for repository https://github.com/mvdbeek/dapars commit b1b007c561ea6c9db145c88b6b128d66ecd05e24-dirty
author mvdbeek
date Fri, 30 Oct 2015 10:46:41 -0400
parents bb84ee2f2137
children
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bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
parents:
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1 #!/usr/bin/env python
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
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2 # Filter out UTRs and, if a gene has multiple UTRs, return a single UTR with minimum start and maximum end coordinate
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
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3 # usage: python filter_utr.py input.gtf output.gtf
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4
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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5 import sys
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
mvdbeek
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6 from collections import OrderedDict
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7
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8 def get_gtf_fields():
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9 return [ "chr", "source", "feature", "start", "end", "score", "strand", "frame", "group" ]
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10
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11 def get_feature_dict(line, gtf_fields, utr_dict, feature="UTR"):
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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12 """
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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13 Return a dictionary with lines of a GTF if the line describes a UTR.
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14 Key is the first attribute of the group.
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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15 """
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16 if line.split("\t")[2] == feature:
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17 fields = line.strip().split("\t")
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18 fields[3] = int(fields[3])
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19 fields[4] = int(fields[4])
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20 gene_id = fields[-1].split("\"")[1]
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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21 if not gene_id in utr_dict:
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22 utr_dict[gene_id] = [OrderedDict(zip(gtf_fields, fields))]
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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23 else:
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24 utr_dict[gene_id].append(OrderedDict(zip(gtf_fields, fields)))
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25
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26 def remove_five_prime_utrs(utr_dict, start_codon_dict):
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27 for gene, features in start_codon_dict.iteritems():
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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28 is_reverse = features[0]["strand"] == "-"
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29 if is_reverse:
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30 stop_codon_end = min([feature["start"] for feature in features])
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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31 else:
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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32 stop_codon_end = max([feature["end"] for feature in features])# get last start codon
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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33 to_remove = []
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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34 if gene in utr_dict:
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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35 for utr in utr_dict[gene]:
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36 start = utr["start"]
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37 end = utr["end"]
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38 if is_reverse:
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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39 if end >= stop_codon_end:
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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40 to_remove.append(utr)
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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41 else:
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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42 if start <= stop_codon_end:
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43 to_remove.append(utr)
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44 [utr_dict[gene].remove(utr) for utr in to_remove ]
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45
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46
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47 def get_longest_utr(utr_dict):
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48 """
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49 Start of the composite utr is the most 5p start, end is the most 3p end.
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50 """
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51 gtf = []
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52 for gene_id, values in utr_dict.iteritems():
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53 if not values:
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54 continue
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55 if len(values) == 1:
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56 values[0]["start"] = str(values[0]["start"])
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57 values[0]["end"] = str(values[0]["end"])
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58 gtf.append( "\t".join( values[0].values() ) )
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59 else:
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60 start = min( [fields["start"] for fields in values] )
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61 end = max( [fields["end"] for fields in values] )
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62 values[0]["start"] = str(start)
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63 values[0]["end"] = str(end)
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64 gtf.append( "\t".join( values[0].values() ) )
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65 return gtf
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66
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67 def main():
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68 utr_dict = OrderedDict()
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69 start_codon_dict = {}
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70 header = []
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71 gtf_fields = get_gtf_fields()
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72 with open(sys.argv[1]) as input:
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73 for line in input:
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74 if line.startswith("#"):
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75 header.append( line.strip() )
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76 else:
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77 get_feature_dict(line, gtf_fields, utr_dict, feature="UTR")
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78 get_feature_dict(line, gtf_fields, start_codon_dict, feature="CDS")
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79 remove_five_prime_utrs(utr_dict, start_codon_dict)
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80 gtf = header + get_longest_utr(utr_dict)
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81 if len(sys.argv) == 3:
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82 with open(sys.argv[2], "w") as output:
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83 [output.write(line + "\n") for line in gtf]
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84 else:
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85 for line in gtf:
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86 print(line)
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87
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88 if __name__ == "__main__":
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89 main()
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90
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91
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92
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