89 lines
2.5 KiB
Bash
89 lines
2.5 KiB
Bash
#! /bin/sh
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# shell script to process a batch of ABI data.
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# it assumes that the raw data is in ~/Mac-files-$USER/'Results date',
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# where date is e.g. 10_28_90.
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# after preliminary checks it runs ted on each file
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# then forces the user to back up on tape
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# then copies everything across to the project directory
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# (latter two steps are done in abibackup, so they can be executed on a
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# remote machine - cele in our case)
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#
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# RMD 6/12/90, based on an original of JES
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#
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# define machine on which qic drive resides
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QIC_MACH=dumpy
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if test ! -n "$DISPLAY"
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then
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echo "Sorry - you must run abiprocess under X windows"
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exit 1
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fi
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case $# in
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2) ;;
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*) echo 'Usage: abiprocess machine_letter date' 1>&2; exit 2
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esac
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if test ! -d $HOME/Mac-files-$USER/Results?$1?$2
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then
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echo "Bad folder machine or date"
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exit 1
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fi
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cd $HOME/Mac-files-$USER/Results?$1?$2
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echo "abiprocess: runs ted, backs up on tape, and transfers to project"
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echo " To abort, type CTRL/C in the xterm window while in ted"
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echo " If you do this, or you don't backup, just rerun abiprocess; you"
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echo " will not have to run ted again on traces you have already processed."
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echo " You can not transfer to your project without backing up."
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# next loop runs ted on each eligible file
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filenames=${2}${1}fn # file of filenames
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for i in 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
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do
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oldname=Sample?$i
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if test ! -f $oldname
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then continue
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fi
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# sed in next line replaces spaces in sample name by '_', since
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# spaces mess things up badly (they shouldn't be there!)
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newname=`echo \`getABISampleName $oldname\` | sed 's/ /_/g'`
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echo $i $newname
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if test $newname
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then if test -f $oldname.Seq
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then
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ted -ABI $oldname -output $newname -raw $newname"RES"
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if test ! $? = 0
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then
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echo "ted failed - am exiting without changing that clone"
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exit 1
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fi
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# 2rs -abi < "Sample $i.Seq" > $newname"MCH"
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rm $oldname.Seq
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if test -f $newname
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then
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mv $oldname $newname"RES"
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cat >> $filenames << EOF
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$newname
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EOF
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else
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mv $oldname $newname"FLD"
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fi
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else mv $oldname $newname"FLD"
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fi
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# if they didn't attach a name to their clone then destroy the data
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else
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if test -f "Sample $i.Seq"
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then
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echo "Can't find name for sample $i - get help!"
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exit 1
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else
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rm $oldname
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fi
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fi
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done
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rsh $QIC_MACH /usr/local/bin/abibackup "\"${1}?${2}\""
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