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diff parsedb.sh @ 6:3ddd933dd7a2 draft default tip

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Uploaded
author davidvanzessen
date Thu, 15 Sep 2016 03:54:33 -0400
parents dda9b2e72e2b
children
line wrap: on
line diff
--- a/parsedb.sh	Mon Aug 15 10:06:24 2016 -0400
+++ b/parsedb.sh	Thu Sep 15 03:54:33 2016 -0400
@@ -12,21 +12,21 @@
 mkdir $PWD/outdir
 
 if [ "fasta" == "$action" ] ; then
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py fasta -d $input --outdir $PWD/outdir --outname output
+	python3 $dir/ParseDb.py fasta -d $input --outdir $PWD/outdir --outname output
 	mv $PWD/outdir/output_sequences.fasta $output
 elif [ "clip" == "$action" ] ; then
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py clip -d $input --outdir $PWD/outdir --outname output
+	python3 $dir/ParseDb.py clip -d $input --outdir $PWD/outdir --outname output
 	mv $PWD/outdir/output_sequences.fasta $output
 elif [ "split" == "$action" ] ; then
 	field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
 	label=$5
 	mkdir $PWD/split
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py split -d $input --outdir $PWD/split --outname output -f $field 
+	python3 $dir/ParseDb.py split -d $input --outdir $PWD/split --outname output -f $field 
 	#rename "s/output_${field}/$label/" $PWD/split/*
 elif [ "add" == "$action" ] ; then
 	field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
 	value=$5
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py add -d $input --outdir $PWD/outdir --outname output -f $field -u $value
+	python3 $dir/ParseDb.py add -d $input --outdir $PWD/outdir --outname output -f $field -u $value
 	mv $PWD/outdir/output_parse-add.tab $output
 elif [ "delete" == "$action" ] ; then
 	field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
@@ -37,20 +37,20 @@
 	else
 		regex=""
 	fi
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py delete -d $input --outdir $PWD/outdir --outname output -f $field -u $value --logic any $regex
+	python3 $dir/ParseDb.py delete -d $input --outdir $PWD/outdir --outname output -f $field -u $value --logic any $regex
 	mv $PWD/outdir/output_parse-delete.tab $output
 elif [ "drop" == "$action" ] ; then
 	field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py drop -d $input --outdir $PWD/outdir --outname output -f $field
+	python3 $dir/ParseDb.py drop -d $input --outdir $PWD/outdir --outname output -f $field
 	mv $PWD/outdir/output_parse-drop.tab $output
 elif [ "index" == "$action" ] ; then
 	field=$4
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py index -d $input --outdir $PWD/outdir --outname output -f $field
+	python3 $dir/ParseDb.py index -d $input --outdir $PWD/outdir --outname output -f $field
 	mv $PWD/outdir/output_parse-index.tab $output
 elif [ "rename" == "$action" ] ; then
 	field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
 	newname=$5
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py rename -d $input --outdir $PWD/outdir --outname output -f $field -k $newname
+	python3 $dir/ParseDb.py rename -d $input --outdir $PWD/outdir --outname output -f $field -k $newname
 	mv $PWD/outdir/output_parse-rename.tab $output
 elif [ "select" == "$action" ] ; then
 	field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
@@ -61,7 +61,7 @@
 	else
 		regex=""
 	fi
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py select -d $input --outdir $PWD/outdir --outname output -f $field -u $value --logic any $regex
+	python3 $dir/ParseDb.py select -d $input --outdir $PWD/outdir --outname output -f $field -u $value --logic any $regex
 	mv $PWD/outdir/output_parse-select.tab $output
 elif [ "sort" == "$action" ] ; then
 	field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
@@ -74,7 +74,7 @@
 	if [ "true" == "$desc" ] ; then
 		tmp="--descend $tmp"
 	fi	
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py sort -d $input --outdir $PWD/outdir --outname output -f $field $tmp
+	python3 $dir/ParseDb.py sort -d $input --outdir $PWD/outdir --outname output -f $field $tmp
 	mv $PWD/outdir/output_parse-sort.tab $output
 elif [ "update" == "$action" ] ; then
 	field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
@@ -86,7 +86,7 @@
 	else
 		regex=""
 	fi
-	/data/users/david/anaconda3/bin/python $dir/ParseDb.py update -d $input --outdir $PWD/outdir --outname output -f $field -u $value -t $replace $regex
+	python3 $dir/ParseDb.py update -d $input --outdir $PWD/outdir --outname output -f $field -u $value -t $replace $regex
 	mv $PWD/outdir/output_parse-update.tab $output
 fi