Delete src/sabdab_downloader.py

src/sabdab_downloader.py

@@ -1,438 +0,0 @@
-description='''
-
-
-SAbDab Download Script                         \\\    //
-The OPIG Antibody Database                      \\\  //
-Authors: James Dunbar and Konrad Krawczyk 2013.   ||
-Contributors: Jinwoo Leem                         ||
-Supervisor: Charlotte Deane
-
-Contact: opig@stats.ox.ac.uk
-
-In collaboration with:
-UCB: Jiye Shi, Terry Baker.
-Roche: Angelika Fuchs, Guy Georges.
-
-
-o This is a script that allows a user to download data from SAbDab.
-o It requires a csv summary file downloaded from the website (opig.stats.ox.ac.uk/webapps/sabdab)
-
-o This file should contain AT LEAST:
-
-    1. A header line with tab-separated fields as "pdb    Hchain    Lchain    model"
-    2. The pdb identifier, heavy chain, light chain and model id on new lines e.g.
-
-    pdb    Hchain    Lchain    model
-    12e8   H         L         0
-    12e8   P         M         0
-    1ahw   B         A         0
-    1ahw   E         D         0
-    .      .         .         .
-    .      .         .         .
-    .      .         .         .
-
-o Other fields will be ignored but may be included in the file.
-
-o The user must provide a directory in which the data should be downloaded to.
-o The type of data that should be downloaded should be specified using the command-line options.
-
-o Example useage:
-    To run on a linux command line type:
-
-    python sabdab_downloader.py -s summary_file.csv -o path/to/output/ --original_pdb
-
-    This will create a directory in  "path/to/output/" name sabdab_dataset.
-    It will contain a directory for each unique pdb code in the summary_file.csv .
-    The structure for each of these pdbs will be downloaded there.
-'''
-
-epilogue="""
-Copyright (C) 2013 James Dunbar
-"""
-
-
-import argparse, sys, os, urllib.request
-
-def getpdb(pdb_entry, out_path):
-    """
-    Get the PDB file from sabdab.
-    Check that it has successfully downloaded.
-    """
-    out_file = os.path.join( out_path, "%s.pdb"%pdb_entry)
-    try:
-        urllib.request.urlretrieve("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/structure/%s.pdb"%(pdb_entry,pdb_entry), out_file)
-    except Exception as e:
-        print("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/structure/%s.pdb failed"%(pdb_entry,pdb_entry))
-        return False
-    if os.path.isfile(out_file):
-        Retrieved = open(out_file).read()
-        if not Retrieved.count("ATOM"):
-            print("Failed to retrieve PDB file from SAbDab")
-            os.remove(out_file)
-            return False
-        else:
-            return True
-    else:
-        return False
-
-def getchothpdb(pdb_entry, out_path):
-    """
-    Get the chothia PDB file from sabdab.
-    Check that it has successfully downloaded.
-    """
-    out_file = os.path.join( out_path, "%s.pdb"%pdb_entry)
-    try:
-        urllib.request.urlretrieve("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/structure/chothia/%s.pdb"%(pdb_entry,pdb_entry), out_file)
-    except Exception as e:
-        print("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/structure/chothia/%s.pdb failed"%(pdb_entry,pdb_entry))
-        return False
-    if os.path.isfile(out_file):
-        Retrieved = open(out_file).read()
-        if not Retrieved.count("ATOM"):
-            print("Failed to retrieve PDB file from SAbDab")
-            os.remove(out_file)
-            return False
-        else:
-            return True
-    else:
-        return False
-
-def getsequence(entry, fab_list, out_path):
-    """
-    Get the sequence files
-    Check that they successfully download
-    Put them into the directory
-    """
-
-    out_file = os.path.join( out_path, "%s_raw.pdb"%entry)
-    try:
-        urllib.request.urlretrieve("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/sequences/%s_raw.fa"%(entry,entry), out_file)
-    except Exception as e:
-        print("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/sequences/%s_raw.fa failed"%(entry,entry))
-        return False
-    if os.path.isfile(out_file):
-        Retrieved = open(out_file).read()
-        if not Retrieved.count(">%s"%entry):
-            print("Failed to retrieve sequence file from SAbDab.")
-            os.remove(out_file)
-            return False
-    else:
-        return False
-
-    for fab in fab_list:
-        Hchain = fab[1].upper()
-        if Hchain!="NA":
-            out_file = os.path.join( out_path, "%s_%s_VH.fa"%(entry,Hchain) )
-            try:
-                urllib.request.urlretrieve("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/sequences/%s_%s_VH.fa"%(entry,entry,Hchain), out_file)
-            except Exception as e:
-                Hchain = Hchain.lower()
-                out_file = os.path.join( out_path, "%s_%s_VH.fa"%(entry,Hchain) )
-                try:
-                    urllib.request.urlretrieve("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/sequences/%s_%s_VH.fa"%(entry,entry,Hchain), out_file)
-                except Exception as e:
-                    print("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/sequences/%s_%s_VH.fa failed"%(entry,entry,Hchain))
-                    return False
-            if os.path.isfile(out_file):
-                Retrieved = open(out_file).read()
-                if not Retrieved.count(">%s"%entry):
-                    print("Failed to retrieve sequence file from SAbDab.")
-                    os.remove(out_file)
-                    return False
-            else:
-                return False
-
-        Lchain = fab[2].upper()
-        if Lchain!="NA":
-            out_file = os.path.join( out_path, "%s_%s_VL.fa"%(entry,Lchain) )
-            try:
-                urllib.request.urlretrieve("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/sequences/%s_%s_VL.fa"%(entry,entry,Lchain), out_file)
-            except Exception as e:
-                Lchain = Lchain.lower()
-                out_file = os.path.join( out_path, "%s_%s_VL.fa"%(entry,Lchain) )
-                try:
-                    urllib.request.urlretrieve("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/sequences/%s_%s_VL.fa"%(entry,entry,Lchain), out_file)
-                except Exception as e:
-                    print("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/sequences/%s_%s_VL.fa failed"%(entry,entry,Lchain))
-                    return False
-            if os.path.isfile(out_file):
-                Retrieved = open(out_file).read()
-                if not Retrieved.count(">%s"%entry):
-                    print("Failed to retrieve sequence file from SAbDab.")
-                    os.remove(out_file)
-                    return False
-            else:
-                return False
-
-    return True
-
-def getannotation(entry, fab_list, out_path):
-    """
-    Get the annotation files for the antibody sequences.
-    These are for the variable region of the sequences only.
-    """
-    for fab in fab_list:
-        Hchain = fab[1].upper()
-        if Hchain!="NA":
-            out_file = os.path.join( out_path, "%s_%s_VH.ann"%(entry,Hchain) )
-            try:
-                urllib.request.urlretrieve("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/annotation/%s_%s_VH.ann"%(entry,entry,Hchain), out_file)
-            except Exception as e:
-                Hchain = Hchain.lower()
-                out_file = os.path.join( out_path, "%s_%s_VH.ann"%(entry,Hchain) )
-                try:
-                    urllib.request.urlretrieve("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/annotation/%s_%s_VH.ann"%(entry,entry,Hchain), out_file)
-                except Exception as e:
-                    print("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/annotation/%s_%s_VH.ann failed"%(entry,entry,Hchain))
-                    return False
-            if os.path.isfile(out_file):
-                Retrieved = open(out_file).read()
-                if not Retrieved.count("H3"):
-                    print("Failed to retrieve annotation file from SAbDab.")
-                    os.remove(out_file)
-                    return False
-            else:
-                return False
-
-        Lchain = fab[2].upper()
-        if Lchain!="NA":
-            out_file = os.path.join( out_path, "%s_%s_VL.ann"%(entry,Lchain) )
-            try:
-                urllib.request.urlretrieve("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/annotation/%s_%s_VL.ann"%(entry,entry,Lchain), out_file)
-            except Exception as e:
-                Lchain = Lchain.lower()
-                out_file = os.path.join( out_path, "%s_%s_VL.ann"%(entry,Lchain) )
-                try:
-                    urllib.request.urlretrieve("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/annotation/%s_%s_VL.ann"%(entry,entry,Lchain), out_file)
-                except Exception as e:
-                    print("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/annotation/%s_%s_VL.ann failed"%(entry,entry,Lchain))
-                    return False
-            if os.path.isfile(out_file):
-                Retrieved = open(out_file).read()
-                if not Retrieved.count("L3"):
-                    print("Failed to retrieve annotation file from SAbDab.")
-                    os.remove(out_file)
-                    return False
-            else:
-                return False
-    return True
-
-def getabangle(entry, fab_list, out_path):
-    """
-    Get the orientation angles for any of the fabs in the pdb.
-    A non-paired antibody chain e.g VHH will have NA as the other chain identifier.
-    """
-    for fab in fab_list:
-        if "NA" in fab:
-            continue
-        else:
-            out_file = os.path.join( out_path, "%s.abangle"%(entry) )
-            try:
-                urllib.request.urlretrieve("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/abangle/%s.abangle"%(entry,entry), out_file)
-            except Exception as e:
-                print("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/abangle/%s.abangle failed"%(entry,entry))
-                return False
-            if os.path.isfile(out_file):
-                Retrieved = open(out_file).read()
-                if not Retrieved.count(entry):
-                    print("Failed to retrieve abangle file from SAbDab.")
-                    os.remove(out_file)
-                    return False
-            else:
-                return False
-            return True
-    return True
-
-def getimgt(entry, fab_list, out_path):
-    """
-    Get the imgt files for the antibody sequences.
-    """
-    for fab in fab_list:
-        Hchain = fab[1].upper()
-        if Hchain!="NA":
-            out_file = os.path.join( out_path, "%s_%s_H.ann"%(entry,Hchain) )
-            try:
-                urllib.request.urlretrieve("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/imgt/%s_%s_H.imgt"%(entry,entry,Hchain), out_file)
-            except Exception as e:
-                Hchain = Hchain.lower()
-                out_file = os.path.join( out_path, "%s_%s_H.ann"%(entry,Hchain) )
-                try:
-                    urllib.request.urlretrieve("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/imgt/%s_%s_H.imgt"%(entry,entry,Hchain), out_file)
-                except Exception as e:
-                    print("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/imgt/%s_%s_H.imgt failed"%(entry,entry,Hchain))
-                    return False
-            
-            if os.path.isfile(out_file):
-                Retrieved = open(out_file).read()
-                if not Retrieved.count("gene_type"):
-                    print("Failed to retrieve imgt file from SAbDab.")
-                    os.remove(out_file)
-                    return False
-            else:
-                return False
-
-        Lchain = fab[2].upper()
-        if Lchain!="NA":
-            out_file = os.path.join( out_path, "%s_%s_L.ann"%(entry,Lchain) )
-            try:
-                urllib.request.urlretrieve("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/imgt/%s_%s_L.imgt"%(entry,entry,Lchain), out_file)
-            except Exception as e:
-                Lchain = Lchain.lower()
-                out_file = os.path.join( out_path, "%s_%s_L.ann"%(entry,Lchain) )
-                try:
-                    urllib.request.urlretrieve("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/imgt/%s_%s_L.imgt"%(entry,entry,Lchain), out_file)
-                except Exception as e:
-                    print("https://opig.stats.ox.ac.uk/webapps/abdb/entries/%s/imgt/%s_%s_L.imgt failed"%(entry,entry,Lchain))
-                    return False
-            if os.path.isfile(out_file):
-                Retrieved = open(out_file).read()
-                if not Retrieved.count("gene_type"):
-                    print("Failed to retrieve imgt file from SAbDab.")
-                    os.remove(out_file)
-                    return False
-            else:
-                return False
-
-    return True
-
-if __name__ == "__main__":
-
-    parser = argparse.ArgumentParser(prog="sabdab_downloader", description=description, epilog=epilogue,formatter_class=argparse.RawDescriptionHelpFormatter)
-    parser.add_argument( '--summary_file','-s',type=str, help="A tab-separated csv downloaded from SAbDab - https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab.", dest="summary_file")
-    parser.add_argument( '--output_path','-o',type=str, help="The path to the output directory.", dest="output_path")
-    parser.add_argument( '--original_pdb',action="store_true", help="Download the pdb structure(s).", dest="original_pdb")
-    parser.add_argument( '--chothia_pdb', action="store_true", help="Download the chothia re-numbered pdb structure(s).", dest="chothia_pdb")
-    parser.add_argument( '--sequences',action="store_true", help="Download the sequence information.", dest="sequence")
-    parser.add_argument( '--annotation',action="store_true", help="Download the chothia numbered sequence information.", dest="annotation")
-    parser.add_argument( '--abangle',action="store_true", help="Download the abangle angles.", dest="abangle")
-    parser.add_argument( '--imgt',action="store_true", help="Download the imgt information for the structure.", dest="imgt")
-
-    args= parser.parse_args()
-
-    if len(sys.argv)<2:
-        parser.print_help()
-        sys.exit(0)
-
-    #####################
-    #  Check the inputs #
-    #####################
-
-    if not args.summary_file:
-        print("No summary file found.")
-        sys.exit(1)
-    if not args.output_path:
-        print("No output path given.")
-        sys.exit(1)
-
-    if not (args.original_pdb or args.chothia_pdb or args.sequence or args.annotation or args.abangle or args.imgt):
-        print("No requested data type given. Please choose at least one.")
-
-    if not os.path.exists(args.output_path):
-        print("Output path does not exist.")
-        sys.exit(1)
-
-    if not os.path.isdir(args.output_path):
-        print("Output path is not a directory.")
-        sys.exit(1)
-
-    if not os.access(args.output_path, os.W_OK):
-        print("Output path is not writable.")
-        sys.exit(1)
-
-    # Set up output directory
-    output_path = os.path.join(args.output_path,"sabdab_dataset")
-    try:
-        os.mkdir(output_path)
-    except OSError:
-        print("A 'sabdab_dataset' already exists in the output directory. Please rename it or provide a new output directory.")
-        sys.exit(1)
-
-    # Get the summary data    
-    try:
-        with open(args.summary_file,'r') as input_file:
-            lines = input_file.readlines()
-            header = lines[0].strip().split("\t")[:4]
-            if header != ["pdb", "Hchain", "Lchain", "model"]:
-                raise IndexError
-            data={}
-            for line in lines[1:]:
-                if not line.strip(): continue
-                entry = line.strip().split("\t")[:4]
-                if len(entry) < 4 and not entry[0].isalnum():
-                    raise IndexError
-                try:
-                    data[entry[0].lower()].append(entry)
-                except KeyError:
-                    data[entry[0].lower()] = [entry]
-    except IOError:
-        print("Could not open summary file.")
-        sys.exit(1)
-    except IndexError:
-        print("Summary file in incorrect format.")
-        sys.exit(1)
-
-    for pdb_entry in data:
-        print("Getting data for %s"%pdb_entry)
-        got_data=False
-        pdb_entry_dir = os.path.join(output_path, pdb_entry)
-        os.mkdir(pdb_entry_dir)
-        if args.original_pdb or args.chothia_pdb:
-            struc_out_path = os.path.join(pdb_entry_dir,"structure")
-            os.mkdir(struc_out_path)
-            if args.original_pdb:
-                if getpdb(pdb_entry, struc_out_path):
-                    got_data=True
-                else:
-                    print(f"removed {struc_out_path}")
-                    # os.rmdir(struc_out_path)
-
-            if args.chothia_pdb:
-                choth_struc_out_path = os.path.join(struc_out_path,"chothia")
-                os.mkdir(choth_struc_out_path)
-                if getchothpdb(pdb_entry, choth_struc_out_path):
-                    got_data=True
-                else:
-                    print(f"removed {choth_struc_out_path}")
-                    # os.rmdir(choth_struc_out_path)
-
-        if args.sequence:
-            seq_out_path = os.path.join(pdb_entry_dir,"sequence")
-            os.mkdir(seq_out_path)
-            if getsequence(pdb_entry, data[pdb_entry] , seq_out_path):
-                got_data=True
-            else:
-                print(f"removed {seq_out_path}")
-                # os.rmdir(seq_out_path)
-
-        if args.annotation:
-            annotation_out_path = os.path.join(pdb_entry_dir,"annotation")
-            os.mkdir(annotation_out_path)
-            if getannotation(pdb_entry, data[pdb_entry] , annotation_out_path):
-                got_data=True
-            else:
-                print(f"removed {annotation_out_path}")
-                # os.rmdir(annotation_out_path)
-
-        if args.abangle:
-            abangle_out_path = os.path.join(pdb_entry_dir,"abangle")
-            os.mkdir(abangle_out_path)
-            if getabangle(pdb_entry, data[pdb_entry] , abangle_out_path):
-                got_data=True
-            else:
-                print(f"removed {abangle_out_path}")
-                # os.rmdir(abangle_out_path)
-
-        if args.imgt:
-            imgt_out_path = os.path.join(pdb_entry_dir,"imgt")
-            os.mkdir(imgt_out_path)
-            if getimgt(pdb_entry, data[pdb_entry] , imgt_out_path):
-                got_data=True
-            else:
-                print(f"removed {imgt_out_path}")
-                # os.rmdir(imgt_out_path)
-
-        if not got_data:
-            print(f"deleted {pdb_entry}")
-            # os.rmdir(pdb_entry_dir)
-
-# Failed or failed or deleted or removed