Mercurial > repos > xuebing > sharplabtool
diff tools/unix_tools/grep_wrapper.sh @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/unix_tools/grep_wrapper.sh Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,62 @@ +#!/bin/sh + +## +## Galaxy wrapper for GREP command. +## + +## +## command line arguments: +## input_file +## output_file +## regex +## COLOR or NOCOLOR +## [other parameters passed on to grep] + +INPUT="$1" +OUTPUT="$2" +REGEX="$3" +COLOR="$4" + +shift 4 + +if [ -z "$COLOR" ]; then + echo usage: $0 INPUTFILE OUTPUTFILE REGEX COLOR\|NOCOLOR [other grep patameters] >&2 + exit 1 +fi + +if [ ! -r "$INPUT" ]; then + echo "error: input file ($INPUT) not found!" >&2 + exit 1 +fi + +# Messages printed to STDOUT will be displayed in the "INFO" field in the galaxy dataset. +# This way the user can tell what was the command +echo "grep" "$@" "$REGEX" + +if [ "$COLOR" == "COLOR" ]; then + # + # What the heck is going on here??? + # 1. "GREP_COLORS" is an environment variable, telling GREP which ANSI colors to use. + # 2. "--colors=always" tells grep to actually use colors (according to the GREP_COLORS variable) + # 3. first sed command translates the ANSI color to a <FONT> tag with blue color (and a <B> tag, too) + # 4. second sed command translates the no-color ANSI command to a </FONT> tag (and a </B> tag, too) + # 5. htmlize_pre scripts takes a text input and wraps it in <HTML><BODY><PRE> tags, making it a fixed-font HTML file. + + GREP_COLORS="ms=31" grep --color=always "$@" -- "$REGEX" "$INPUT" | \ + grep -v "^\[36m\[K--\[m\[K$" | \ + sed -r 's/\[[0123456789;]+m\[K?/<font color="blue"><b>/g' | \ + sed -r 's/\[m\[K?/<\/b><\/font>/g' | \ + htmlize_pre.sh > "$OUTPUT" + + + if (( $? )); then exit; fi + +elif [ "$COLOR" == "NOCOLOR" ]; then + grep "$@" -- "$REGEX" "$INPUT" | grep -v "^--$" > "$OUTPUT" + if (( $? )); then exit; fi +else + echo Error: third parameter must be "COLOR" or "NOCOLOR" >&2 + exit 1 +fi + +exit 0