#!/usr/bin/expect -f
set MZEF "/usr/local/mzef";

# SET THE FIRST LINE TO POINT TO YOUR COPY OF EXPECT
# SET THE SECOND LINE TO THE FULL PATH TO YOUR MZEF ROOT DIRECTORY

set VERSION .20
set DEFAULT_ORG         "human"
set DEFAULT_PROBABILITY .04
set DEFAULT_OVERLAPPING 0

proc usage {} {
    puts "usage: There are 3 ways to run mzef.expect"
    puts "mzef.expect FASTA"
    puts "mzef.expect FASTA ORGANISM"
    puts "mzef.expect FASTA ORGANISM PROBABILITY OVERLAPPING"
}

proc run_mzef {SEQ_FILE FORWARD_REVERSE PROBABILITY OVERLAPPING} {
    set timeout -1
    spawn ./mzef
    expect *SEQUENCE*
    send "'$SEQ_FILE'\n"
    expect *REVERSE*
    send "$FORWARD_REVERSE\n"
    expect *PROBABILITY*
    send "$PROBABILITY\n"
    expect *LAPPING*
    send "$OVERLAPPING\n"
    expect *prompt*
}

proc get_full_path_to_seq {SEQ_FILE} {
    set cwd [pwd]
    set first_char [string index $SEQ_FILE 0]

    if {[string match $first_char /]} {
        return $SEQ_FILE;
    } elseif {[string match $first_char ~]} {
        return $env(HOME)/$SEQ_FILE";
    } else {
        return "$cwd/$SEQ_FILE";
    }
}

proc chdir_to_org_directory {ORG MZEF} {
    if {[string match human $ORG]} {
        cd "$MZEF/human";
    } elseif {[string match mouse $ORG]} {
        cd "$MZEF/mouse";     
    } elseif {[string match arab $ORG]} {
        cd "$MZEF/arab";     
    } else {
        cd "$MZEF/human";     
    }
}
 
if {$argc < 1} {
    usage 
    exit
} elseif {$argc == 3} {
    usage 
    exit
} elseif {$argc > 4} {
    usage
    exit
}

set SEQ_FILE [lindex $argv 0]
set ORG      [lindex $argv 1]
set PROBABILITY $DEFAULT_PROBABILITY
set OVERLAPPING $DEFAULT_OVERLAPPING

set prob [lindex $argv 2]
set over [lindex $argv 3]

if {$prob == ""} {
    set PROBABILITY $DEFAULT_PROBABILITY
    set OVERLAPPING $DEFAULT_OVERLAPPING
} else {
    set PROBABILITY $prob
    set OVERLAPPING $over
}

set SEQ_FILE [get_full_path_to_seq $SEQ_FILE]

chdir_to_org_directory $ORG $MZEF
run_mzef $SEQ_FILE 1 $PROBABILITY $OVERLAPPING
run_mzef $SEQ_FILE 2 $PROBABILITY $OVERLAPPING