Mercurial > repos > ggricourt > data_manager_bigg

annotate data_manager/metanetx_chem_prop_fetcher.py @ 14:8e8a9e51f1d7 draft

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"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 7db54c0555a12ecb8b3f756032228c54fe028e0a-dirty"
author ggricourt
date Wed, 09 Mar 2022 15:18:07 +0000
parents c1d4f14dc768
children
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ggricourt
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1 import argparse
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2 import json
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3 import os
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4 import shutil
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5 import sys
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6 import tempfile
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7 # import pandas as pd
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8 try:
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9 # For Python 3.0 and later
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10 from urllib.request import Request, urlopen
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11 except ImportError:
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12 # Fall back to Python 2 imports
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13 from urllib2 import Request, urlopen
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16 METANETX_URL = "https://www.metanetx.org/ftp/"
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18
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19 def url_download(url, path):
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20 try:
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21 with urlopen(Request(url)) as fod:
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22 with open(path, "wb") as dst:
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23 while True:
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24 chunk = fod.read(2**10)
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25 if chunk:
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26 dst.write(chunk)
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27 else:
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28 break
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29 except Exception as e:
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30 sys.exit(str(e))
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31
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32
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33 def clean_metanetx_file(path):
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34 ftmp = tempfile.NamedTemporaryFile()
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35 isHeaderFound = False
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36 with open(path) as fid, open(ftmp.name, 'w') as fod:
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37 for line in fid:
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38 if line.startswith("#"):
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39 last_line = line
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40 else:
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41 if not isHeaderFound:
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42 last_line = last_line.replace("#", "")
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43 fod.write(last_line)
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44 isHeaderFound = True
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45 fod.write(line)
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46 shutil.copyfile(ftmp.name, path)
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47
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48
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49 # def records_chem_prop_pandas(path):
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50 # df = pd.read_csv(path, sep="\t")
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51 # df["name"] = df.apply(lambda x: "%s: %s (%s)" % (x["ID"], x["name"], x["formula"]), axis=1)
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52 # df.drop(columns=["reference", "formula", "charge", "mass", "InChIKey", "SMILES"], inplace=True)
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53 # df.rename(columns={"ID": "value", "InChI": "inchi"})
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54 # return df.to_dict('records')
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55
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56
13
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57 def records_chem_prop(path):
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58 records = []
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59 with open(path) as fid:
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60 for ix, line in enumerate(fid):
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61 if ix == 0:
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62 continue
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63 line = line.split("\t")
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64 if line[7] != '':
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65 records.append({
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66 "value": line[0],
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67 "name": "%s: %s (%s)" % (line[0], line[1], line[3]),
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68 "inchi": line[7],
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69 })
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70 return records
13
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71
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72
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73 if __name__ == "__main__":
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74 parser = argparse.ArgumentParser()
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75 pinput = parser.add_mutually_exclusive_group(required=True)
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76 pinput.add_argument("--version", help="Version to download")
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77 parser.add_argument("--out-file", help="JSON output file")
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78 args = parser.parse_args()
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79
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80 # Init.
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81 data_manager_json = {"data_tables": {}}
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82 with open(args.out_file) as fh:
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83 params = json.load(fh)
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84
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85 workdir = params["output_data"][0]["extra_files_path"]
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86 os.makedirs(workdir)
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87
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88 # Load models and models metadata.
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89 ftmp = tempfile.NamedTemporaryFile()
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90 url = '/'.join([METANETX_URL, args.version, 'chem_prop.tsv'])
c1d4f14dc768 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 7db54c0555a12ecb8b3f756032228c54fe028e0a-dirty"
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91 url_download(url, ftmp.name)
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92
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93 # Clean header
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94 clean_metanetx_file(ftmp.name)
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95
c1d4f14dc768 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 7db54c0555a12ecb8b3f756032228c54fe028e0a-dirty"
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96 # Select records.
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97 records = records_chem_prop(ftmp.name)
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98
c1d4f14dc768 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 7db54c0555a12ecb8b3f756032228c54fe028e0a-dirty"
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99 # Write data.
c1d4f14dc768 "planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 7db54c0555a12ecb8b3f756032228c54fe028e0a-dirty"
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100 data_manager_json["data_tables"]["metanetx_chem_prop"] = records
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101 with open(args.out_file, "w") as fh:
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102 json.dump(data_manager_json, fh, sort_keys=True)