#!/bin/bash
#AUTHOR: Malvika Sharan <malvika.sharan@uni-wuerzburg.de>

## This installation will skip the third party tools for additional annotations
# Tools that are skipped: PsortB, RaptorX, Biojs, openpyxl
# It assumes that User's environment has Java installed, it is required to run InterProScan

PYTHON_PATH=python

APRICOT_PATH=$1

## full path where you have cloned/save APRICOT from git
apricot_lib=../$APRICOT_PATH/apricotlib

## path where the source files will be stored
apricot_files=source_files/reference_db_files

main(){
        get_python_modules
        create_main_path
        
        ### CDD-MODULES ###
        create_cdd_inpath
        check_and_download_cdd
        
        ### InterProScan-MODULES ###
        create_interpro_inpath
        check_and_download_interpro
        uniprot_species_to_taxid
        
        ### Other-requirements ###
        get_blast_executables
        ontology_mapping_to_domains
        get_pfam_domain_file

        ### PDB-MODULES ###
        create_pdb_inpath
        download_uniprot_map
        download_pdb_sec_str
        sort_and_format_pdb_data
        
        ### EMBOSS: needle commandline ###
        ## please skip if it is already installed ##
        get_emboss
}

get_python_modules(){
    pip3 install --user bio-apricot
}

create_main_path(){
    mkdir -p $apricot_files
    for FOLDER in cdd interpro blast go_mapping pdb all_taxids pfam
    do
        mkdir -p $apricot_files/$FOLDER
    done
}

create_cdd_inpath(){
    for FOLDER in cdd_annotation_data Cdd
    do
        mkdir -p $apricot_files/cdd/$FOLDER
    done
}

check_and_download_cdd(){
    rm -rf $apricot_files/cdd/cdd_flat_files/*
    wget -c -P $apricot_files/cdd ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/cdd.info
    if diff $apricot_files/cdd/cdd.info $apricot_files/cdd/cdd_current.info >/dev/null ; then
        echo '\n**'updated vesion of cdd is present in path $apricot_files/cdd.'**\n'
    else
        wget -c -P $apricot_files/cdd/Cdd ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/*
        
        for binary_files in $(ls $apricot_files/cdd/Cdd)
        do
            tar xvf $apricot_files/cdd/Cdd/$binary_files -C $apricot_files/cdd/Cdd
        done
        rm $apricot_files/cdd/Cdd/*.gz
        cat $apricot_files/cdd/cdd.info > $apricot_files/cdd/cdd_current.info
    fi
    rm $apricot_files/cdd/cdd_annotation_data/*
    wget -c -P $apricot_files/cdd/cdd_annotation_data ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/cddid.tbl.gz
    gunzip $apricot_files/cdd/cdd_annotation_data/*
}

create_interpro_inpath(){
    for FOLDER in interpro_annotation_data interproscan
    do
        mkdir -p $apricot_files/interpro/$FOLDER
    done
}

check_and_download_interpro(){
    wget -O - ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/ > $apricot_files/interpro/ipr_info.html
    $PYTHON_PATH $apricot_lib/current_interpro_version.py $apricot_files/interpro/ipr_info.html $apricot_files/interpro/current_version_ipr
    if diff $apricot_files/interpro/ipr_info.html $apricot_files/interpro/ipr_current.html >/dev/null ; then
        echo '\n**'updated vesion of InterPro is present in path $apricot_files/interpro $(cat $apricot_files/interpro/current_version_ipr)'**\n'
    else
        wget -c -P $apricot_files/interpro ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/$(cat $apricot_files/interpro/current_version_ipr)/*-64-bit.tar*
        for files in $(ls $apricot_files/interpro/*.tar.gz)
        do
            tar xvf $files -C $apricot_files/interpro
        done
        mv $apricot_files/interpro/interproscan-*/* $apricot_files/interpro/interproscan
        cat $apricot_files/interpro/ipr_info.html > $apricot_files/interpro/ipr_current.html
    fi
    
    rm -rf $apricot_files/interpro/interpro_annotation_data/*
    wget -O - ftp://ftp.ebi.ac.uk/pub/databases/interpro/ > $apricot_files/interpro/ipr_flatfile.html
    $PYTHON_PATH $apricot_lib/current_interpro_version.py $apricot_files/interpro/ipr_flatfile.html $apricot_files/interpro/current_version_flatfiles
    version_info=$(cat $apricot_files/interpro/current_version_flatfiles)
    ipr_flatfile_server=ftp://ftp.ebi.ac.uk/pub/databases/interpro/$version_info
    echo $ipr_flatfile_server
    wget -c -P $apricot_files/interpro/interpro_annotation_data $ipr_flatfile_server/interpro2go
    wget -c -P $apricot_files/interpro/interpro_annotation_data $ipr_flatfile_server/interpro.xml.gz
    gunzip $apricot_files/interpro/interpro_annotation_data/interpro.xml.gz
    $PYTHON_PATH $apricot_lib/interpro_xml_to_table.py $apricot_files/interpro/interpro_annotation_data $apricot_files/interpro/interpro_annotation_data/interpro.xml
}

uniprot_species_to_taxid(){
    wget -c -P $apricot_files/all_taxids http://www.uniprot.org/docs/speclist.txt
}

create_pdb_inpath(){
    for FOLDER in pdb_sequence pdb_secstr pdb2uniprot
    do
        mkdir -p $apricot_files/pdb/$FOLDER
    done
}

download_uniprot_map(){
    wget -P $apricot_files/pdb/pdb2uniprot http://www.uniprot.org/docs/pdbtosp.txt
}

download_pdb_sec_str(){
    wget -c -P $apricot_files/pdb/pdb_secstr http://www.rcsb.org/pdb/files/ss.txt
}

sort_and_format_pdb_data(){
    $PYTHON_PATH $apricot_lib/sort_sec_struc_pdb_data.py \
    -i $apricot_files/pdb/pdb_secstr/ss.txt -seq $apricot_files/pdb/pdb_sequence -str $apricot_files/pdb/pdb_secstr
    $apricot_files/blast/makeblastdb -in $apricot_files/pdb/pdb_sequence/pdb_sequence.txt -dbtype prot
}

get_pfam_domain_file(){
    wget -O - ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/ > $apricot_files/pfam/index.html
    current_release=$(cut -d'>' -f2 $apricot_files/pfam/index.html | cut -d'/' -f1 | cut -d'm' -f2 | sort -g | tail -n1)
    echo $current_release
    wget -c -P $apricot_files/pfam ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam$current_release/database_files/pfamA.txt.gz
    gunzip $apricot_files'/pfam/pfamA.txt.gz'
}

get_blast_executables(){
    wget -c -P $apricot_files/blast ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.4.0/*x64-linux*
    tar -xvzf $apricot_files/blast/*x64-linux* -C $apricot_files/blast
    rm -rf $apricot_files/blast/*x64-linux*.gz
    for exepath in $(ls $apricot_files/blast)
    do
        if [ ! -p $apricot_files/blast/makeblastdb ]
        then
            if [ 'ncbi' = $(echo $exepath | cut -d \- -f 1) ]
            then
                cp -r $apricot_files/blast/$exepath/* $apricot_files/blast
            fi
        fi
        install $apricot_files/blast/bin/psiblast $apricot_files/blast
        install $apricot_files/blast/bin/blastp $apricot_files/blast
        install $apricot_files/blast/bin/makeblastdb $apricot_files/blast
    done
}

ontology_mapping_to_domains(){
    GO_PATH=$apricot_files/go_mapping
    rm $GO_PATH/go.obo*
    wget -P $GO_PATH http://www.geneontology.org/ontology/go.obo
    interpro_to_go=$apricot_files/interpro/interpro_annotation_data/interpro2go
    interpro_data=$apricot_files/interpro/interpro_annotation_data/interproid.tbl
    cdd_data=$apricot_files/cdd/cdd_annotation_data/cddid.tbl
    $PYTHON_PATH $apricot_lib/map_domain_to_go.py $GO_PATH $interpro_to_go $interpro_data $cdd_data
}

get_emboss(){
    mkdir -p emboss/needle
    wget -P emboss/needle ftp://emboss.open-bio.org/pub/EMBOSS/old/6.5.0/emboss-latest.tar.gz
    tar -xvzf emboss/needle/emboss-latest.tar.gz -C emboss/needle
    mv emboss/needle/EMBOSS*/* emboss/needle
    cd emboss/needle && ./configure && make && cd -
    echo "In order to re-install please delete (rm) config.log file from your present working directory"
}

main