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comparison tools/unix_tools/grep_wrapper.sh @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 #!/bin/sh
2
3 ##
4 ## Galaxy wrapper for GREP command.
5 ##
6
7 ##
8 ## command line arguments:
9 ## input_file
10 ## output_file
11 ## regex
12 ## COLOR or NOCOLOR
13 ## [other parameters passed on to grep]
14
15 INPUT="$1"
16 OUTPUT="$2"
17 REGEX="$3"
18 COLOR="$4"
19
20 shift 4
21
22 if [ -z "$COLOR" ]; then
23 echo usage: $0 INPUTFILE OUTPUTFILE REGEX COLOR\|NOCOLOR [other grep patameters] >&2
24 exit 1
25 fi
26
27 if [ ! -r "$INPUT" ]; then
28 echo "error: input file ($INPUT) not found!" >&2
29 exit 1
30 fi
31
32 # Messages printed to STDOUT will be displayed in the "INFO" field in the galaxy dataset.
33 # This way the user can tell what was the command
34 echo "grep" "$@" "$REGEX"
35
36 if [ "$COLOR" == "COLOR" ]; then
37 #
38 # What the heck is going on here???
39 # 1. "GREP_COLORS" is an environment variable, telling GREP which ANSI colors to use.
40 # 2. "--colors=always" tells grep to actually use colors (according to the GREP_COLORS variable)
41 # 3. first sed command translates the ANSI color to a <FONT> tag with blue color (and a <B> tag, too)
42 # 4. second sed command translates the no-color ANSI command to a </FONT> tag (and a </B> tag, too)
43 # 5. htmlize_pre scripts takes a text input and wraps it in <HTML><BODY><PRE> tags, making it a fixed-font HTML file.
44
45 GREP_COLORS="ms=31" grep --color=always "$@" -- "$REGEX" "$INPUT" | \
46 grep -v "^\[36m\[K--\[m\[K$" | \
47 sed -r 's/\[[0123456789;]+m\[K?/<font color="blue"><b>/g' | \
48 sed -r 's/\[m\[K?/<\/b><\/font>/g' | \
49 htmlize_pre.sh > "$OUTPUT"
50
51
52 if (( $? )); then exit; fi
53
54 elif [ "$COLOR" == "NOCOLOR" ]; then
55 grep "$@" -- "$REGEX" "$INPUT" | grep -v "^--$" > "$OUTPUT"
56 if (( $? )); then exit; fi
57 else
58 echo Error: third parameter must be "COLOR" or "NOCOLOR" >&2
59 exit 1
60 fi
61
62 exit 0