src/sabdab_downloader_fixed.py

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