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fatmacankara commited on
Commit
771222f
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1 Parent(s): f9b9a8c

Update code/modbaseModelAdd.py

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  1. code/modbaseModelAdd.py +0 -149
code/modbaseModelAdd.py CHANGED
@@ -1,152 +1,3 @@
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- # import requests
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- # import numpy as np
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- # import pandas as pd
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- # from utils import *
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- # from pathlib import Path
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- # from bs4 import BeautifulSoup
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- # from add_sasa import *
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- # def addModbaseModels(dataframe, path_to_input_files, path_to_output_files):
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- # if len(dataframe) != 0:
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- # # GET MODBASE MODELS
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- # # Get IDs from data to retrieve only their models from MODBASE
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- # dataframe.reset_index(inplace=True, drop=True)
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- # existing_modbase_models = list(Path(path_to_output_files / 'modbase_structures').glob("*"))
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- # existing_modbase_models = [str(i) for i in existing_modbase_models]
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- # existing_modbase_models = [i.split('/')[-1].split('.')[0] for i in existing_modbase_models]
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-
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- # existing_modbase_models_ind = list(Path(path_to_output_files / 'modbase_structures_individual').glob("*"))
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- # existing_modbase_models_ind = [str(i) for i in existing_modbase_models_ind]
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- # existing_modbase_models_ind = [i.split('/')[-1].split('.')[0] for i in existing_modbase_models_ind]
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-
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- # modbase_reduced = pd.DataFrame(columns = ['uniprotID', 'target_begin', 'target_end', 'quality_score',
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- # 'model_id', 'coordinates','AAonPDB', 'coordVAR'])
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- # print('Retrieving ModBase models...\n')
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- # modbase = pd.DataFrame(
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- # columns=['uniprotID', 'target_begin', 'target_end', 'quality_score', 'model_id',
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- # 'coordinates', 'AAonPDB', 'coordVAR'])
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- # no_modbase = pd.DataFrame(
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- # columns=['uniprotID', 'target_begin', 'target_end', 'quality_score', 'model_id',
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- # 'coordinates', 'AAonPDB', 'coordVAR'])
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- # # Get model files associated with each UniProtID
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- # existing_free_sasa = list(Path(path_to_output_files / 'freesasa_files').glob("*"))
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- # existing_free_sasa = [str(i) for i in existing_free_sasa]
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- # existing_free_sasa = [i.split('/')[-1].split('.')[0] for i in existing_free_sasa]
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- # keep_cols = dataframe.columns
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- # for i in dataframe.index:
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- # coordDict = {}
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- # protein = dataframe.at[i, 'uniprotID']
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- # varPos = int(dataframe.at[i, 'pos'])
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- # wt = dataframe.at[i, 'wt']
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- # mut = dataframe.at[i, 'mut']
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- # datapoint = dataframe.at[i, 'datapoint']
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-
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- # if protein not in existing_modbase_models:
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- # print('Downloading Modbase models for ', protein)
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- # url = 'https://salilab.org/modbase/retrieve/modbase/?databaseID=' + protein
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- # req = requests.get(url)
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- # name = path_to_output_files / 'modbase_structures' / f'{protein}.txt'
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- # with open(name, 'wb') as f:
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- # f.write(req.content)
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- # else:
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- # print('Model exists for', protein)
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- # name = Path(path_to_output_files / 'modbase_structures' / f'{protein}.txt')
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-
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- # with open(name, encoding="utf8") as f:
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- # a = open(name, 'r').read()
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- # soup = BeautifulSoup(a, 'lxml')
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- # if soup.findAll('pdbfile') != []:
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- # for pdb in soup.findAll('pdbfile'):
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- # model_id = str(pdb.contents[1])[10:-11]
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- # if model_id not in existing_modbase_models_ind:
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- # with open(path_to_output_files / 'modbase_structures_individual' / f'{model_id}.txt', 'w', encoding="utf8") as individual:
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- # individual.write(str('UniProt ID: ' + protein))
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- # individual.write('\n')
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- # individual.write(str(pdb.contents[3])[10:-11].strip())
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- # run_freesasa(
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- # Path(path_to_output_files / 'modbase_structures_individual' / f'{model_id.lower()}.txt'),
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- # Path(path_to_output_files / 'freesasa_files' / f'{model_id.lower()}.txt'),
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- # include_hetatms=True,
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- # outdir=None, force_rerun=False, file_type='pdb')
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- # filename = Path(path_to_output_files / 'freesasa_files' / f'{model_id.lower()}.txt')
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- # st.write('filename', filename)
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- # st.write('varPos', varPos)
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- # st.write('wt', wt)
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- # st.write('protein', protein)
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- # st.write('path_to_output_files', path_to_output_files)
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- # dataframe.loc[i, 'sasa'] = sasa(protein, varPos, wt, 1, filename, path_to_output_files, file_type='pdb')
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- # st.write('sasa', dataframe.loc[i, 'sasa'] )
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- # st.write('model_id', model_id)
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- # with open(path_to_output_files / 'modbase_structures_individual'/ f'{model_id}.txt', encoding="utf8") as m:
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-
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- # lines = m.readlines()
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- # quality_score = -999
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- # for ind_line in lines:
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- # if ind_line[0:10] == 'UniProt ID':
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- # uniprot_id = ind_line.split(':')[1].strip()
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- # if ind_line[0:23] == 'REMARK 220 TARGET BEGIN':
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- # target_begin = ind_line[40:43].strip()
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- # if ind_line[0:21] == 'REMARK 220 TARGET END':
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- # target_end = ind_line[40:43].strip()
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- # coordDict, AAonPDB, coordVAR = {},np.NaN,np.NaN
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- # if (int(varPos) > int(target_begin)) & (int(varPos) < int(target_end)):
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- # coordDict = {}
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- # for ind_line in lines:
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- # if ind_line[0:27] == 'REMARK 220 MODPIPE MODEL ID':
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- # model_id = ind_line[40:].strip()
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- # if ind_line[0:15].strip() == 'REMARK 220 MPQS':
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- # quality_score = ind_line[40:].strip()
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- # if ind_line[0:4] == 'ATOM' and ind_line[13:15] == 'CA':
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- # position = int(ind_line[22:26].strip())
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- # chain = ind_line[20:22].strip()
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- # aminoacid = threeToOne(ind_line[17:20])
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- # coords = [ind_line[31:38].strip(), ind_line[39:46].strip(), ind_line[47:54].strip()]
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- # coordDict[position] = coords
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- # if position == int(varPos):
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- # AAonPDB = aminoacid
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- # coordVAR = str(coords)
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- # if ind_line[0:3] == 'TER':
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- # break
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- # try:
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- # k = pd.Series(
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- # [uniprot_id, target_begin, target_end,quality_score, model_id, coordDict, AAonPDB, coordVAR])
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- # new_row = {'uniprotID': uniprot_id, 'target_begin': target_begin,
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- # 'target_end': target_end, 'quality_score': quality_score,
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- # 'model_id': model_id, 'coordinates': coordDict,
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- # 'AAonPDB': AAonPDB, 'coordVAR': coordVAR}
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- # modbase_reduced = modbase_reduced.append(new_row, ignore_index=True)
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- # modbase_reduced = modbase_reduced[['uniprotID', 'quality_score', 'model_id', 'coordinates', 'AAonPDB', 'coordVAR']]
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- # modbase = dataframe.merge(modbase_reduced, on='uniprotID', how='left')
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- # modbase.quality_score = modbase.quality_score.astype(float)
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- # modbase = modbase.sort_values(by=['datapoint', 'quality_score'], ascending=False)
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- # modbase.reset_index(inplace=True, drop=True)
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- # modbase.fillna(np.NaN, inplace=True)
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- # modbase.replace({'\'?\', ': '',
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- # ', \'?\'': '',
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- # '(': '', ')': '',
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- # '[\'?\']': np.NaN,
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- # '[]': np.NaN,
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- # 'nan-nan': np.NaN,
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- # '': np.NaN}, inplace=True)
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- # except NameError:
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- # print('This file doesnt have Quality Score. Replacer: -999', model_id)
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- # else:
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- # new_row = {'uniprotID': uniprot_id, 'wt': wt,
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- # 'pos': varPos, 'mut': mut, 'datapoint': datapoint }
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- # no_modbase = no_modbase.append(new_row, ignore_index=True)
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-
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- # else:
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- # new_row = {'uniprotID': uniprot_id, 'wt': wt,
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- # 'pos': varPos, 'mut': mut, 'datapoint': datapoint }
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- # no_modbase = no_modbase.append(new_row, ignore_index=True)
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-
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-
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-
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- # no_modbase_no_Coord = modbase[pd.isna(modbase['coordVAR'])]
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- # no_modbase = pd.concat([no_modbase, no_modbase_no_Coord])
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- # modbase = modbase[~pd.isna(modbase['coordVAR'])]
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- # no_modbase = no_modbase[keep_cols]
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- # return modbase, no_modbase
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-
150
  import requests
151
  import numpy as np
152
  import pandas as pd
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
  import requests
2
  import numpy as np
3
  import pandas as pd