Mercurial > repos > fubar > jbrowse2

annotate autogenJB2.py @ 19:bde6b1d09f7d draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
author fubar
date Tue, 30 Jan 2024 06:05:03 +0000
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19
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1 import argparse
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2 import os
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3
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4 from jbrowse2 import jbrowseConnector as jbC
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5
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6
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7
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8
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9 if __name__ == "__main__":
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10 parser = argparse.ArgumentParser(description="", epilog="")
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11 parser.add_argument("--yaml", help="Track Configuration")
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12 parser.add_argument("--outdir", help="Output directory", default="out")
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13 parser.add_argument("--version", "-V", action="version", version="%(prog)s 0.0.1")
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14 args = parser.parse_args()
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15 if os.path.exists(args.outdir):
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16 root = args.outdir
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17 dirList = os.scandir(root)
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18 subdirs = [f.path for f in dirList if f.is_dir()]
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19 genome_paths = [f.path for f in dirList if f.name.startswith('genome') and f.is_file()]
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20 if len(genome_paths) > 0:
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21 genome_fnames = [os.path.basename(x).split('_')[2:] for x in genome_paths] # expect genome_1_genomename.fasta etc
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22 jc = jbC(
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23 outdir=args.outdir,
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24 genomes=[
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25 {
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26 "path": x,
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27 "meta": {"name" : genome_fnames[i], },
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28 }
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29 for i,x in enumerate(genome_paths)
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30 ],
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31 )
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32 jc.process_genomes()
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33 # .add_default_view() replace from https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py
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34 default_session_data = {
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35 "visibility": {
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36 "default_on": [],
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37 "default_off": [],
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38 },
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39 "style": {},
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40 "style_labels": {},
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41 }
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42
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43 track_paths = [x for x in genome_paths if not x.startswith('genome') and x.is_file()]
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44 for i, track in enumerate(track_paths):
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45 track_conf = {}
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46 track_conf['format']= os.path.basename(track).split('_')[0]
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47 track_conf["name"] = os.path.basename(track).split('_')[2:] # expect genome_1_genomename.fasta etc
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48 fext = os.path.splitext(os.path.basename(track)).replace('.','')
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49 track_conf["label"] = "%s_%i" % (os.path.basename(track), i)
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50 track_conf["trackfiles"] = []
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51 keys = jc.process_annotations(track_conf)
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52
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53 if keys:
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54 for key in keys:
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55 default_session_data["visibility"][
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56 track.attrib.get("visibility", "default_off")
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57 ].append(key)
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58 if track_conf.get("style", None):
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59 default_session_data["style"][key] = track_conf[
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60 "style"
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61 ] # TODO do we need this anymore?
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62 if track_conf.get("style_lables", None):
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63 default_session_data["style_labels"][key] = track_conf.get(
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64 "style_labels", None
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65 )
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66 # default_session_data["defaultLocation"] = root.find(
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67 # "metadata/general/defaultLocation"
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68 # ).text
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69 # default_session_data["session_name"] = root.find(
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70 # "metadata/general/session_name"
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71 # ).text
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72 # general_data = {
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73 # "analytics": root.find("metadata/general/analytics").text,
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74 # "primary_color": root.find("metadata/general/primary_color").text,
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75 # "secondary_color": root.find("metadata/general/secondary_color").text,
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76 # "tertiary_color": root.find("metadata/general/tertiary_color").text,
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77 # "quaternary_color": root.find("metadata/general/quaternary_color").text,
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78 # "font_size": root.find("metadata/general/font_size").text,
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79 # }
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80 # jc.add_general_configuration(general_data)
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81 trackconf = jc.config_json.get("tracks", None)
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82 if trackconf:
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83 jc.config_json["tracks"].update(jc.tracksToAdd)
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84 else:
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85 jc.config_json["tracks"] = jc.tracksToAdd
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
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86 jc.write_config()
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
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87 jc.add_default_session(default_session_data)
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
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88 # jc.text_index() not sure what broke here.