--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/human_genome_variation/sift_variants_wrapper.sh	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,184 @@
+#!/usr/bin/env bash
+
+input_file=$1
+output_file=$2
+org=$3
+db_loc=$4
+chrom_col=$5
+pos_col=$6
+base=$7
+allele_col=$8
+strand_col=$9
+comment_col=${10}
+output_opts=${11}
+
+working_dir=$PWD
+sift_input="$working_dir/sift_input.txt"
+sift_output="$working_dir/sift_output.txt"
+
+################################################################################
+## make sure input file column selections are mutually exclusive              ##
+################################################################################
+ERROR=0
+declare -a col_use
+
+function check_col () {
+    local col=$1
+    local use=$2
+    local int=$3
+
+    if [ -n "${col//[0-9]}" ]; then
+        if [ $int -eq 1 ]; then
+            echo "ERROR: invalid value for $use column: $col" 1>&2
+            ERROR=1
+        fi
+        return
+    fi
+
+    local cur=${col_use[$col]}
+    if [ -n "$cur" ]; then
+        echo "ERROR: $use column is the same as $cur column" 1>&2
+        col_use[$col]="${cur},$use"
+        ERROR=1
+    else
+        col_use[$col]=$use
+    fi
+}
+
+check_col $chrom_col   'chromosome' 1
+check_col $pos_col     'position'   1
+check_col $allele_col  'allele'     1
+check_col $strand_col  'strand'     0
+check_col $comment_col 'comment'    0
+
+if [ $ERROR -ne 0 ]; then
+    exit 1
+fi
+
+################################################################################
+## get/check the db directory from the argument org,db_loc                    ##
+################################################################################
+db_dir=$( awk '$1 == org { print $2 }' org=$org $db_loc )
+
+if [ -z "$db_dir" ]; then
+    echo "Can't find dbkey \"$org\" in loc file \"$db_loc\"" 1>&2
+    exit 1
+fi
+
+if [ ! -d "$db_dir" ]; then
+    echo "Can't access SIFT database directory \"$db_dir\"" 1>&2
+    exit 1
+fi
+
+################################################################################
+## create input file for SIFT_exome_nssnvs.pl                                 ##
+################################################################################
+if [ ! -r "$input_file" ]; then
+    echo "Can't read input file \"$input_file\"" 1>&2
+    exit 1
+fi
+
+if [ $base -eq 0 ]; then
+    beg_col="$pos_col"
+    end_col="$pos_col + 1"
+    pos_adj='$2 = $2 - 1'
+else
+    beg_col="$pos_col - 1"
+    end_col="$pos_col"
+    pos_adj=''
+fi
+
+strand_cvt=''
+if [ \( "$strand_col" = "+" \) ]; then
+    strand='"1"'
+elif [ \( "$strand_col" = "-" \) ]; then
+    strand='"-1"'
+else
+    strand="\$$strand_col"
+    strand_cvt='if ('"${strand}"' == "+") {'"${strand}"' = "1"} else if ('"${strand}"' == "-") {'"${strand}"' = "-1"}'
+fi
+
+print_row='print $'"${chrom_col}"', $'"${beg_col}"', $'"${end_col}"', '"${strand}"', $'"${allele_col}"''
+if [ "$comment_col" != "-" ]; then
+    print_row=''"${print_row}"', $'"${comment_col}"''
+fi
+
+awk '
+BEGIN {FS="\t";OFS=","}
+$'"${chrom_col}"' ~ /^[cC][hH][rR]/ {$'"${chrom_col}"' = substr($'"${chrom_col}"',4)}
+{
+    '"${strand_cvt}"'
+    '"${print_row}"'
+}
+' "$input_file" > "$sift_input"
+
+################################################################################
+## run SIFT_exome_nssnvs.pl command line program                              ##
+################################################################################
+if [ "$output_opts" = "None" ]; then
+    output_opts=""
+else
+    output_opts=$( echo "$output_opts" | sed -e 's/,/ 1 -/g' )
+    output_opts="-$output_opts 1"
+fi
+
+SIFT_exome_nssnvs.pl -i "$sift_input" -d "$db_dir" -o "$working_dir" $output_opts &> "$sift_output"
+if [ $? -ne 0 ]; then
+    echo "failed: SIFT_exome_nssnvs.pl -i \"$sift_input\" -d \"$db_dir\" -o \"$working_dir\" $output_opts"
+    exit 1
+fi
+
+################################################################################
+## locate the SIFT_exome_nssnvs.pl output file                                ##
+################################################################################
+sift_pid=$( sed -n -e 's/^.*Your job id is \([0-9][0-9]*\) and is currently running.*$/\1/p' "$sift_output" )
+
+if [ -z "$sift_pid" ]; then
+    echo "Can't find SIFT pid in \"$sift_output\"" 1>&2
+    exit 1
+fi
+
+sift_outdir="$working_dir/$sift_pid"
+if [ ! -d "$sift_outdir" ]; then
+    echo "Can't access SIFT output directory \"$sift_outdir\"" 1>&2
+    exit 1
+fi
+
+sift_outfile="$sift_outdir/${sift_pid}_predictions.tsv"
+if [ ! -r "$sift_outfile" ]; then
+    echo "Can't access SIFT output file \"$sift_outfile\"" 1>&2
+    exit 1
+fi
+
+################################################################################
+## create galaxy output file                                                  ##
+################################################################################
+awk '
+BEGIN {FS="\t";OFS="\t"}
+NR == 1 {
+    $12 = "Num seqs at position"
+    $1 = "Chrom\tPosition\tStrand\tAllele"
+    print
+}
+NR != 1 {
+    $1 = "chr" $1
+    gsub(/,/, "\t", $1)
+    print
+}
+' "$sift_outfile" | awk '
+BEGIN {FS="\t";OFS="\t"}
+NR == 1 {
+    print "#" $0
+}
+NR != 1 {
+    if ($3 == "1") {$3 = "+"} else if ($3 == "-1") {$3 = "-"}
+    '"${pos_adj}"'
+    print
+}
+' > "$output_file"
+
+################################################################################
+## cleanup                                                                    ##
+################################################################################
+rm -rf "$sift_outdir" "$sift_input" "$sift_output"
+