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annotate mature_mir_gff_translation.py @ 2:fe1ed513da99 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 9c4974c701cff559853ebd0d899c87023f65d840
author artbio
date Tue, 18 Jul 2017 06:49:21 -0400
parents 10f0e4c00b13
children ee99c6374a3b
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10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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1 #!/usr/bin/env python
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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2
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3 import sys
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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4 import argparse
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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5
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6
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7 def Parser():
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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8 the_parser = argparse.ArgumentParser()
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9 the_parser.add_argument(
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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10 '--input', action="store", type=str, help="input miRBase GFF3 file")
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11 the_parser.add_argument(
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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12 '--output', action="store", type=str, help="output GFF3 file with converted mature mir coordinates")
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13 args = the_parser.parse_args()
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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14 return args
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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16 GFF3_header= '''##gff-version 3
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17 ##generated by mature_mir_gff_translation.py
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18 #
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19 # Chromosomal coordinates of microRNAs ** relative to the hairpin precursors **
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20 # microRNAs: miRBase current_version
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21 # genome-build-id: check http://mirbase.org/
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22 #
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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23 # Hairpin precursor sequences have type "miRNA_primary_transcript".
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24 # Note, these sequences do not represent the full primary transcript,
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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25 # rather a predicted stem-loop portion that includes the precursor
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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26 # miRNA. Mature sequences have type "miRNA".
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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27 #
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28 '''
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29
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30 def load_gff_in_dict(gff_input_file):
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31 '''
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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32 Reads the gff3 file and return a dictionary of dictionaries
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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33 with keys equal to standard gff3 fields (9)
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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34 Note that the key of the primary dictionary is the ID
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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35 '''
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36 gff_dict = {}
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37 for line in open(gff_input_file, "r"):
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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38 if line[0]=="#":
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39 continue
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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40 gff_fields=line[:-1].split("\t")
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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41 ID=gff_fields[8].split("ID=")[1].split(";")[0]
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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42 gff_dict[ID] = {}
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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43 gff_dict[ID]["seqid"]=gff_fields[0]
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44 gff_dict[ID]["source"]=gff_fields[1]
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45 gff_dict[ID]["type"]=gff_fields[2]
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46 gff_dict[ID]["start"]=gff_fields[3]
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47 gff_dict[ID]["end"]=gff_fields[4]
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48 gff_dict[ID]["score"]=gff_fields[5]
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49 gff_dict[ID]["strand"]=gff_fields[6]
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50 gff_dict[ID]["phase"]=gff_fields[7]
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51 gff_dict[ID]["attributes"]=gff_fields[8]
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52 if "Derives_from" in gff_dict[ID]["attributes"]:
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53 parent_primary_transcript=gff_dict[ID]["attributes"].split("Derives_from=")[1]
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54 parent_primary_transcript=gff_dict[parent_primary_transcript]["attributes"].split("Name=")[1]
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55 gff_dict[ID]["attributes"]="%s;Parent_mir_Name=%s" % (gff_dict[ID]["attributes"], parent_primary_transcript)
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56 return gff_dict
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57
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58
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59 def genome_to_mir_gff(gff_dict, output):
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60 '''
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61 Converts seqid field from chromosome to item Name
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62 Then converts coordinates relative to "miRNA_primary_transcript"
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63 Note that GFF files are 1-based coordinates
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64 '''
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65 for key in gff_dict:
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66 name=gff_dict[key]["attributes"].split("Name=")[1].split(";")[0]
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67 gff_dict[key]["seqid"]=name
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68 if "Derives_from=" in gff_dict[key]["attributes"]:
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69 parent_ID=gff_dict[key]["attributes"].split("Derives_from=")[1].split(";")[0]
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70 gff_dict[key]["start"]=str(int(gff_dict[key]["start"]) - int(gff_dict[parent_ID]["start"]) + 1)
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71 gff_dict[key]["end"]=str(int(gff_dict[key]["end"]) - int(gff_dict[parent_ID]["start"]) + 1)
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72 hairpins={}
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73 matures={}
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74 for key in gff_dict: ## treats miRNA_primary_transcript coordinates in a second loop to avoid errors in conversion
10f0e4c00b13 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3a6181bd181729f642b75c4e689f063fc2821cf1
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75 if gff_dict[key]["type"]=="miRNA_primary_transcript":
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76 gff_dict[key]["end"]=str(int(gff_dict[key]["end"]) - int(gff_dict[key]["start"]) + 1)
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77 gff_dict[key]["start"]="1"
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78 # now, do a dict[ID]=Name but only for miRNA_primary_transcript
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79 hairpins[key]=gff_dict[key]["attributes"].split("Name=")[1].split(";")[0]
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80 else:
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81 matures[key]=gff_dict[key]["attributes"].split("Name=")[1].split(";")[0]
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82 with open(output, "w") as output:
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83 output.write(GFF3_header)
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84 for ID in sorted(hairpins, key=hairpins.get):
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85 output.write("\t".join([gff_dict[ID]["seqid"], gff_dict[ID]["source"],
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86 gff_dict[ID]["type"], gff_dict[ID]["start"], gff_dict[ID]["end"],
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87 gff_dict[ID]["score"], gff_dict[ID]["strand"], gff_dict[ID]["phase"],
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88 gff_dict[ID]["attributes"]]))
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89 output.write("\n")
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90 for id in sorted(matures, key=matures.get, reverse=True):
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91 if ID in gff_dict[id]["attributes"]:
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92 output.write("\t".join([gff_dict[id]["seqid"], gff_dict[id]["source"],
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93 gff_dict[id]["type"], gff_dict[id]["start"], gff_dict[id]["end"],
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94 gff_dict[id]["score"], gff_dict[id]["strand"],
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95 gff_dict[id]["phase"], gff_dict[id]["attributes"]]))
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96 output.write("\n")
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97
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98
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99 def main(infile, outfile):
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100 gff_dict = load_gff_in_dict(infile)
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101 genome_to_mir_gff(gff_dict, outfile)
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102
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103
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104 if __name__ == "__main__":
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105 args = Parser()
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106 main(args.input, args.output)