48 lines
962 B
Tcsh
48 lines
962 B
Tcsh
#! /bin/csh -f
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#
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# getMCHfof
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# Run all the files in a file of file names through "getMCH -SCF"
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#
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# This program was written for Bill Rawlinson, and is intended for
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# his use only.
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#
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# Usage: getMCHfof file_of_file_names
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#
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if ( $#argv != 1 ) then
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echo "Usage: getMCHfof file_of_file_names"
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exit 2
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endif
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if (! -e $1 ) then
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echo "No such file of file names"
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exit 2
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endif
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echo "Processing a file of file names through getMCH"
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echo ""
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# New fofn
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set seq_fofn = ${1:r}.fofn
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if (-e $seq_fofn) /bin/mv $seq_fofn ${seq_fofn}.$$
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touch $seq_fofn
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echo "Processing:"
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foreach x ( `cat $1` )
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# This file of file name contains the sequence file names
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# Determine chromatogram file
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echo -n " " $x
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set trace = ${x}.scf
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if (-e $x) /bin/mv $x ${x}.$$
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getMCH -SCF $trace -output $x -header 1
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if ($status != 0) then
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echo " - error in getMCH\!"
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else
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echo " - done"
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echo $x >> $seq_fofn
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endif
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end
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echo
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echo "File of file names created:" $seq_fofn
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