:78 Function create_function() is deprecated [8192]
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core/table.sh |
diff --git a/core/table.sh b/core/table.sh index 116a7ca..55d2cc7 100755 --- a/core/table.sh +++ b/core/table.sh @@ -8,7 +8,7 @@ FILE=$1 ##################################################################### ##################################################################### -## The folllowing two sections: +## The following two sections: ## ## "FILTERS AND DELIMITERS" ## @@ -52,24 +52,29 @@ delim3="Note=" ################## selection ... ##################################### # grab scafold and genes' range -grep $filter1 $FILE | grep $filter2 | awk '{print $1" "$4"-"$5}' > tmp0 +grep $filter1 $FILE | grep $filter2 | awk '{print $1" "$4"-"$5}' > tmp0.$FILE # grab "TTHERM", ie. *delim1* -# grep $filter1 $FILE | grep $filter2 | awk 'BEGIN{FS="TTHERM"} {print $2}' | awk 'BEGIN{FS=";Note"} {print "TTHERM"$1}' > tmp1 -grep $filter1 $FILE | grep $filter2 | awk -v d1="$delim1" 'BEGIN{FS=d1} {print $2}' | awk -v d1="$delim1" -v d2="$delim2" 'BEGIN{FS=d2} {print d1$1}' > tmp1 +# grep $filter1 $FILE | grep $filter2 | awk 'BEGIN{FS="TTHERM"} {print $2}' | awk 'BEGIN{FS=";Note"} {print "TTHERM"$1}' > tmp1.$FILE +grep $filter1 $FILE | grep $filter2 | awk -v d1="$delim1" 'BEGIN{FS=d1} {print $2}' | awk -v d1="$delim1" -v d2="$delim2" 'BEGIN{FS=d2} {print d1$1}' > tmp1.$FILE # grab 'Note' and replace 'spaces' with 'underscores (_)' -#grep $filter1 $FILE | grep $filter2 | awk 'BEGIN{FS="Note="} {print "Note="$2}' | sed 's/ /_/g' > tmp2 -grep $filter1 $FILE | grep $filter2 | awk -v d3="$delim3" 'BEGIN{FS=d3} {print d3$2}' | sed 's/ /_/g' > tmp2 +#grep $filter1 $FILE | grep $filter2 | awk 'BEGIN{FS="Note="} {print "Note="$2}' | sed 's/ /_/g' > tmp2.$FILE +grep $filter1 $FILE | grep $filter2 | awk -v d3="$delim3" 'BEGIN{FS=d3} {print d3$2}' | sed 's/ /_/g' > tmp2.$FILE # compute gene size -grep $filter1 $FILE | grep $filter2 | awk '{print $5-$4+1}' > tmp3 +grep $filter1 $FILE | grep $filter2 | awk '{print $5-$4+1}' > tmp3.$FILE ####################################################################### # join sliced data (tmp.files) to generate a combined table -paste tmp0 tmp1 tmp2 tmp3 | sort -k 1 | sort -t: -n -k 2 | awk '{print $1":"$2"\t"$3"\t"$4"\t"$5"\t"$6}' > table.$FILE +#paste tmp0 tmp1 tmp2 tmp3 +paste tmp0.$FILE tmp1.$FILE tmp2.$FILE tmp3.$FILE | sort -k 1 | sort -t: -n -k 2 | awk '{print $1":"$2"\t"$3"\t"$4"\t"$5"\t"$6}' > table.$FILE # cleanup: remove temporary files... -rm tmp0 tmp1 tmp2 tmp3 +#rm tmp0 tmp1 tmp2 tmp3 +rm -v tmp?.$FILE + +####################################################################### +#######################################################################