9108ce75f1
Former-commit-id: d733a46f4e92f755f38e452f03a28062de6739f1 Former-commit-id: 36bdc324d2b9a0491d07d40a7e68a4cf7ea73984
94 lines
2.0 KiB
Bash
Executable File
94 lines
2.0 KiB
Bash
Executable File
#!/bin/csh -f
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#
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# compare CDS annotation in reference file to predicted file
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# annotation file are in Genbank/Embl format
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#
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# usage: go_compare reference predicted
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#
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# output on stdout
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#
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unsetenv ORG_SOURCED
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setenv ORG_HOME `dirname $0`/../../../..
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source $ORG_HOME/scripts/csh_init.sh
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NeedArg 2
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set RefFile = $Argv[1]
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set PrdFile = $Argv[2]
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NeedFile $RefFile
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NeedFile $PrdFile
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set RefType = $RefFile:e
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set PrdType = $PrdFile:e
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if ((! -e $LIB_DIR/$RefType.oneliner.awk) || (! -e $LIB_DIR/$PrdType.oneliner.awk)) then
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Error 1 "file extension should be 'gbk' or 'embl'"
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endif
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#
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# parse ref and prediction
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#
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Notify "get genome info from $RefFile"
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$AwkCmd -f $LIB_DIR/$RefType.oneliner.awk $RefFile |\
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$AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/$RefType.cds_short.awk > R_$$
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Notify "get prediction info from $PrdFile"
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$AwkCmd -f $LIB_DIR/$PrdType.oneliner.awk $PrdFile |\
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$AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/$PrdType.cds_short.awk > P_$$
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#
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# compare
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#
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Notify "compare bank to predictions"
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$AwkCmd -f $LIB_DIR/libnws.awk \
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-f $LIB_DIR/compareCds.awk \
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R_$$ P_$$ > S_$$
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# base statistics
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egrep "^MATCH" S_$$ | tr '.' ' ' | awk '{print $5}' |\
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sort | uniq -c | sort -nr | awk '{print "#",$0}' > U_$$
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# add chlorodb/core statistics
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if (-d $DATA_DIR/cds/chlorodb/core) then
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ls $DATA_DIR/cds/chlorodb/core/*.fst |\
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sed -e 's@^.*core/@@1' | sed -e 's/.fst$//g' |\
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sort > C_$$
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egrep "^MATCH" S_$$ | grep "MISSED" | awk '{print $2}' | sort | uniq > D_$$
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join D_$$ C_$$ > E_$$
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@ nc = `cat C_$$ | wc -l`
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@ mt = `cat D_$$ | wc -l`
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@ mc = `cat E_$$ | wc -l`
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@ mn = $mt - $mc
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set LC = `cat E_$$`
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echo "#" >> U_$$
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echo "# $mc MISSED in ChloroDB-Core ($LC)" >> U_$$
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echo "# $mn MISSED not in ChloroDB-Core" >> U_$$
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echo "#" >> U_$$
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echo "" >> U_$$
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endif
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cat S_$$ >> U_$$
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cat U_$$
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#
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# end
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#
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(\rm -f ?_$$) >> /dev/null
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Exit 0
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