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1 #!/bin/bash
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2
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3 # This tool creates a UCSC track line given a bigWig or bedGraph input file, a track name and genome assembly.
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4
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5 ## Define URL prefix
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6
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7 URL="http://data.bric.dk/galaxy/UCSC"
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8
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9 #parse input
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10 while getopts hi:t:n:o: myarg
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11 do case "$myarg" in
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12 h) echo "Usage: create UCSC track line -i <INPUT_FILE> -t <FILE_TYPE> -n <TRACK_NAME> -o <ASSEMBLY>"
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13 exit ;;
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14 i) input_file="$OPTARG" ;;
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15 t) file_type="$OPTARG" ;;
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16 n) track_name="$OPTARG" ;;
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17 o) org_assembly="$OPTARG" ;;
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18 [?]) echo "Usage: create UCSC track line -i <INPUT_FILE> -t <FILE_TYPE> -n <TRACK_NAME> -o <ASSEMBLY>"
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19
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20 exit 1 ;;
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21 esac
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22 done
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23
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24 ####################################################################
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25 # Check if a link to that file exists in the UCSC webfolder
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26 flag=0
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27
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28 for link in `ls -1 $UCSCPATH`
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29 do
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30 if [ `readlink -f $input_file` == `readlink -f $UCSCPATH/$link` ] ; then
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31 link_path=/$link # use already existing link
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32 flag=1
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33 fi
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34 done
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35
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36 # If link to input file doesn't exist, create anonymous soft-link for input file in a folder accessible from the web.
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37
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38 if [ $flag == 0 ]; then
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39
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40 link_path=`mktemp -u --tmpdir=/`
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41 ln -s $input_file $UCSCPATH$link_path
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42 fi
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43
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44 ####################################################################
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45 ##Convert 4th character of file_type to uppercase (e.g. bigwig -> bigWig). UCSC browser doesn't recognize the file type otherwise.
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46
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47 ##Split file_type string to prefix (big) and suffix (wig, bed) and uppercase the first character of the latter.
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48 prefix=`echo ${file_type:0:3}`
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49 suffix=`echo ${file_type:3} | sed -e "s/\b\(.\)/\u\1/g"`
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50
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51 file_type=`echo ${prefix}${suffix}`
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52
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53 ####################################################################
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54 #Contruct URL
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55 bigURL=`echo ${URL}${link_path}`
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56
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57 ####################################################################
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58 ## Print track line
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59 echo "track name='$track_name' db=$org_assembly type=$file_type visibility=full alwaysZero=ON bigDataUrl=$bigURL"
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