1## 2# 3# script to add links to postscript file that was produced using the plot.awk script from ROIs. 4# usage : gawk -v roiFile=infile.roi \ 5# -f ps2pswLinks.gawk \ 6# infile.roi.ps > outfile.ps 7# infile.roi.ps was created using plot.awk 8# infile.roi is the same file that was used to generate the infile.roi.ps 9# 10# the link to the localhost, i.e. the genome browser to be used can be changed at the end of the script. 11# current version is using the default for IGV on localhost. 12# 13 14 15BEGIN{ 16longstring="\ 17[ /Rect [124 87 240 257]\n\ 18/Border [0 0 0]\n\ 19/Color [0 0 1]\n\ 20/Action << /Subtype /URI /URI (__URI1__) >>\n\ 21/Subtype /Link\n\ 22/ANN pdfmark\n\ 23[ /Rect [275 87 391 257]\n\ 24/Border [0 0 0]\n\ 25/Color [0 0 1]\n\ 26/Action << /Subtype /URI /URI (__URI4__) >>\n\ 27/Subtype /Link\n\ 28/ANN pdfmark\n\ 29[ /Rect [426 87 542 257]\n\ 30/Border [0 0 0]\n\ 31/Color [0 0 1]\n\ 32/Action << /Subtype /URI /URI (__URI7__) >>\n\ 33/Subtype /Link\n\ 34/ANN pdfmark\n\ 35[ /Rect [124 297 240 473]\n\ 36/Border [0 0 0]\n\ 37/Color [0 0 1]\n\ 38/Action << /Subtype /URI /URI (__URI2__) >>\n\ 39/Subtype /Link\n\ 40/ANN pdfmark\n\ 41[ /Rect [275 297 391 473]\n\ 42/Border [0 0 0]\n\ 43/Color [0 0 1]\n\ 44/Action << /Subtype /URI /URI (__URI5__) >>\n\ 45/Subtype /Link\n\ 46/ANN pdfmark\n\ 47[ /Rect [426 297 542 473]\n\ 48/Border [0 0 0]\n\ 49/Color [0 0 1]\n\ 50/Action << /Subtype /URI /URI (__URI8__) >>\n\ 51/Subtype /Link\n\ 52/ANN pdfmark\n\ 53[ /Rect [124 507 240 689]\n\ 54/Border [0 0 0]\n\ 55/Color [0 0 1]\n\ 56/Action << /Subtype /URI /URI (__URI3__) >>\n\ 57/Subtype /Link\n\ 58/ANN pdfmark\n\ 59[ /Rect [275 507 391 689]\n\ 60/Border [0 0 0]\n\ 61/Color [0 0 1]\n\ 62/Action << /Subtype /URI /URI (__URI6__) >>\n\ 63/Subtype /Link\n\ 64/ANN pdfmark\n\ 65[ /Rect [426 507 542 689]\n\ 66/Border [0 0 0]\n\ 67/Color [0 0 1]\n\ 68/Action << /Subtype /URI /URI (__URI9__) >>\n\ 69/Subtype /Link\n\ 70/ANN pdfmark\n\ 71showpage\n\ 72" 73if(roiFile==""){ 74 print "Error: I need the variable roiFile to be set (-v roiFile=filename)" > "/dev/stderr" 75 exit -1 76} 77} 78/showpage/{ 79 outstring = longstring 80 for(i=1;i<=9;i++){ 81 roiLine="" 82 while(roiLine==""){ 83 if( (getline roiLine < roiFile) <= 0){ 84 break 85 } 86 if(substr(roiLine,1,1)=="#"){ 87 roiLine="" 88 } 89 } 90 split(roiLine,roiArr, "\t") 91 gsub("__URI"i"__","http://localhost:60151/goto?locus="roiArr[1]":"roiArr[2]"-"roiArr[3],outstring) 92 } 93 print outstring 94 next 95} 96{print} 97