|
0
|
1 # Get igv screenshot
|
|
|
2
|
|
|
3 echo $@
|
|
|
4
|
|
|
5 # parse input parameters
|
|
|
6 set -- `getopt -n$0 -u -a --longoptions="track: region: archive: build: outfile: scriptdir: ftype: index: label: viewaspairs: view:" "h:" "$@"` || usage
|
|
|
7 [ $# -eq 0 ] && usage
|
|
|
8
|
|
|
9 while [ $# -gt 0 ]
|
|
|
10 do
|
|
|
11 case "$1" in
|
|
|
12 --track) tracks+=",$2";shift;;
|
|
|
13 --region) region=$2;shift;;
|
|
|
14 --build) build=$2;shift;;
|
|
|
15 --outfile) outfile=$2;shift;;
|
|
|
16 --scriptdir) scriptdir=$2;shift;;
|
|
|
17 --ftype) ftypes+=",$2";shift;;
|
|
|
18 --index) indexfiles+=",$2";shift;;
|
|
|
19 --label) tracklabels+=",$2";shift;;
|
|
|
20 --view) view+=",$2";shift;;
|
|
|
21 --viewaspairs) viewaspairs+=",$2";shift;;
|
|
|
22 -h) shift;;
|
|
|
23 --) shift;break;;
|
|
|
24 -*) usage;;
|
|
|
25 *) break;;
|
|
|
26 esac
|
|
|
27 shift
|
|
|
28 done
|
|
|
29
|
|
|
30 # location of IGV installation
|
|
|
31 igvlocation="${scriptdir}/IGV_2.1.28"
|
|
|
32
|
|
|
33 # set preferences properly
|
|
|
34 echo -e "IGV.track.show.attribute.views=true
|
|
|
35 LAST_CHROMOSOME_VIEWED_KEY=All
|
|
|
36 DEFAULT_GENOME_KEY=${build}" > prefs.properties
|
|
|
37
|
|
|
38 #IGV.Bounds=0,0,$width,$height
|
|
|
39 #SHOW_SEQUENCE_TRANSLATION=true
|
|
|
40 #IGV.Frame.ExtendedState=0
|
|
|
41
|
|
|
42 # parse track, filetype and indexfile strings
|
|
|
43 tracks=${tracks/,/} # remove leading comma from list
|
|
|
44 tracks=${tracks//,/ } # replace commas with spaces
|
|
|
45 ftypes=${ftypes/,/} # remove leading comma from list
|
|
|
46 indexfiles=${indexfiles/,/} # remove leading comma from list
|
|
|
47 tracklabels=${tracklabels/,/} # remove leading comma from list
|
|
|
48 tracklabels=${tracklabels// /_} # replace spaces with underscores for track labels
|
|
|
49 view=${view/,/} # remove leading comma from list
|
|
|
50 viewaspairs=${viewaspairs/,/} # remove leading comma from list
|
|
|
51
|
|
|
52 # generate batch file recipe for igv
|
|
|
53 echo -e "new
|
|
|
54 genome ${build}" > recipe.txt
|
|
|
55
|
|
|
56 # add tracks to recipe
|
|
|
57 IFS=',' read -a ftypearray <<< "$ftypes"
|
|
|
58 IFS=',' read -a indexarray <<< "$indexfiles"
|
|
|
59 IFS=',' read -a labelarray <<< "$tracklabels"
|
|
|
60 IFS=',' read -a viewarray <<< "$view"
|
|
|
61 IFS=',' read -a viewaspairsarray <<< "$viewaspairs"
|
|
|
62 count=0
|
|
|
63 for track in $tracks
|
|
|
64 do
|
|
|
65
|
|
|
66 # make symlink to file with the proper extension (or IGV will not work)
|
|
|
67 ftype=${ftypearray[count]}
|
|
|
68 label=${labelarray[count]}
|
|
|
69 ltrack="${label}.${ftype}"
|
|
|
70 ln -s ${track} ${ltrack}
|
|
|
71
|
|
|
72 # link the index file too if needed
|
|
|
73 if [[ $ftype == "bam" ]]
|
|
|
74 then
|
|
|
75 indexltrack="${label}.bam.bai"
|
|
|
76 ln -s ${indexarray[count]} ${indexltrack}
|
|
|
77 fi
|
|
|
78
|
|
|
79 # add track to recipe
|
|
|
80 echo -e "load ${ltrack}" >>recipe.txt
|
|
|
81
|
|
|
82 # set view for track (collapsed/expanded/squished)
|
|
|
83 echo -e "${viewarray[count]} ${ltrack}" >> recipe.txt
|
|
|
84
|
|
|
85 # set to view as pairs if requested
|
|
|
86 if [[ ${viewaspairsarray[count]} == "yes" ]]
|
|
|
87 then
|
|
|
88 echo -e "viewaspairs ${ltrack}" >> recipe.txt
|
|
|
89 fi
|
|
|
90
|
|
|
91
|
|
|
92 count=$[$count+1]
|
|
|
93
|
|
|
94 done
|
|
|
95
|
|
|
96
|
|
|
97 echo -e "snapshotDirectory .
|
|
|
98 goto ${region//,/ }
|
|
|
99 sort base
|
|
|
100 snapshot screenshot.png
|
|
|
101 exit" >> recipe.txt
|
|
|
102
|
|
|
103 # for debugging purposes:
|
|
|
104 echo -e "\nIGV batch recipe is:\n"
|
|
|
105 cat recipe.txt
|
|
|
106
|
|
|
107 # setup X environment
|
|
|
108 echo -e "\nsetting up Xvfb:\n"
|
|
|
109 Xvfb :0 2>&1 &
|
|
|
110 export DISPLAY=:0
|
|
|
111
|
|
|
112 # run igv
|
|
|
113 echo -e "\nrunning IGV:\n"
|
|
|
114 igv.sh -b recipe.txt -o prefs.properties 2>&1
|
|
|
115
|
