scripting

Some practical scripting tricks for computing scientists not for programmers: perl, python and R etc

Perl Some tricks on perl.
R tricks Miscellaneous R tricks

@perrykid A reminder to any biologist interested in learning Unix & Perl. We have a free online course available: http://bradn.am/LsDla

Unix awk, sed, cut, paste

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3 comments on “scripting

  1. Removing first character from each filename/string
    $ cat files |sed ‘s/.\(.*\)/\1/’
    Removing the last three characters from every filename
    $ cat files | sed ‘s/\(.*\)…/\1/’
    Find all large files on a Linux machine
    find / -type f -size +20000k -exec ls -lh {} \; | awk ‘{ print $9 “: ” $5 }’

    Change permission of all files or all directories separately from a set starting point.
    // Directories:
    find . -type d -exec chmod XXX {} \;
    // Files:
    find . -type f -exec chmod XXX {} \;

  2. sed:
    USEFUL ONE-LINE SCRIPTS FOR SED (Unix stream editor) Dec. 29, 2005
    Compiled by Eric Pement – pemente[at]northpark[dot]edu version 5.5
    Latest version of this file (in English) is usually at:
    http://sed.sourceforge.net/sed1line.txt
    http://www.pement.org/sed/sed1line.txt

    FILE SPACING:

    # double space a file
    sed G

    # double space a file which already has blank lines in it. Output file
    # should contain no more than one blank line between lines of text.
    sed ‘/^$/d;G’

    # triple space a file
    sed ‘G;G’

    # undo double-spacing (assumes even-numbered lines are always blank)
    sed ‘n;d’

    # insert a blank line above every line which matches “regex”
    sed ‘/regex/{x;p;x;}’

    # insert a blank line below every line which matches “regex”
    sed ‘/regex/G’

    # insert a blank line above and below every line which matches “regex”
    sed ‘/regex/{x;p;x;G;}’

    NUMBERING:

    # number each line of a file (simple left alignment). Using a tab (see
    # note on ‘\t’ at end of file) instead of space will preserve margins.
    sed = filename | sed ‘N;s/\n/\t/’

    # number each line of a file (number on left, right-aligned)
    sed = filename | sed ‘N; s/^/ /; s/ *\(.\{6,\}\)\n/\1 /’

    # number each line of file, but only print numbers if line is not blank
    sed ‘/./=’ filename | sed ‘/./N; s/\n/ /’

    # count lines (emulates “wc -l”)
    sed -n ‘$=’

    TEXT CONVERSION AND SUBSTITUTION:

    # IN UNIX ENVIRONMENT: convert DOS newlines (CR/LF) to Unix format.
    sed ‘s/.$//’ # assumes that all lines end with CR/LF
    sed ‘s/^M$//’ # in bash/tcsh, press Ctrl-V then Ctrl-M
    sed ‘s/\x0D$//’ # works on ssed, gsed 3.02.80 or higher

    # IN UNIX ENVIRONMENT: convert Unix newlines (LF) to DOS format.
    sed “s/$/`echo -e \\\r`/” # command line under ksh
    sed ‘s/$'”/`echo \\\r`/” # command line under bash
    sed “s/$/`echo \\\r`/” # command line under zsh
    sed ‘s/$/\r/’ # gsed 3.02.80 or higher

    # IN DOS ENVIRONMENT: convert Unix newlines (LF) to DOS format.
    sed “s/$//” # method 1
    sed -n p # method 2

    # IN DOS ENVIRONMENT: convert DOS newlines (CR/LF) to Unix format.
    # Can only be done with UnxUtils sed, version 4.0.7 or higher. The
    # UnxUtils version can be identified by the custom “–text” switch
    # which appears when you use the “–help” switch. Otherwise, changing
    # DOS newlines to Unix newlines cannot be done with sed in a DOS
    # environment. Use “tr” instead.
    sed “s/\r//” infile >outfile # UnxUtils sed v4.0.7 or higher
    tr -d \r outfile # GNU tr version 1.22 or higher

    # delete leading whitespace (spaces, tabs) from front of each line
    # aligns all text flush left
    sed ‘s/^[ \t]*//’ # see note on ‘\t’ at end of file

    # delete trailing whitespace (spaces, tabs) from end of each line
    sed ‘s/[ \t]*$//’ # see note on ‘\t’ at end of file

    # delete BOTH leading and trailing whitespace from each line
    sed ‘s/^[ \t]*//;s/[ \t]*$//’

    # insert 5 blank spaces at beginning of each line (make page offset)
    sed ‘s/^/ /’

    # align all text flush right on a 79-column width
    sed -e :a -e ‘s/^.\{1,78\}$/ &/;ta’ # set at 78 plus 1 space

    # center all text in the middle of 79-column width. In method 1,
    # spaces at the beginning of the line are significant, and trailing
    # spaces are appended at the end of the line. In method 2, spaces at
    # the beginning of the line are discarded in centering the line, and
    # no trailing spaces appear at the end of lines.
    sed -e :a -e ‘s/^.\{1,77\}$/ & /;ta’ # method 1
    sed -e :a -e ‘s/^.\{1,77\}$/ &/;ta’ -e ‘s/\( *\)\1/\1/’ # method 2

    # substitute (find and replace) “foo” with “bar” on each line
    sed ‘s/foo/bar/’ # replaces only 1st instance in a line
    sed ‘s/foo/bar/4’ # replaces only 4th instance in a line
    sed ‘s/foo/bar/g’ # replaces ALL instances in a line
    sed ‘s/\(.*\)foo\(.*foo\)/\1bar\2/’ # replace the next-to-last case
    sed ‘s/\(.*\)foo/\1bar/’ # replace only the last case

    # substitute “foo” with “bar” ONLY for lines which contain “baz”
    sed ‘/baz/s/foo/bar/g’

    # substitute “foo” with “bar” EXCEPT for lines which contain “baz”
    sed ‘/baz/!s/foo/bar/g’

    # change “scarlet” or “ruby” or “puce” to “red”
    sed ‘s/scarlet/red/g;s/ruby/red/g;s/puce/red/g’ # most seds
    gsed ‘s/scarlet\|ruby\|puce/red/g’ # GNU sed only

    # reverse order of lines (emulates “tac”)
    # bug/feature in HHsed v1.5 causes blank lines to be deleted
    sed ‘1!G;h;$!d’ # method 1
    sed -n ‘1!G;h;$p’ # method 2

    # reverse each character on the line (emulates “rev”)
    sed ‘/\n/!G;s/\(.\)\(.*\n\)/&\2\1/;//D;s/.//’

    # join pairs of lines side-by-side (like “paste”)
    sed ‘$!N;s/\n/ /’

    # if a line ends with a backslash, append the next line to it
    sed -e :a -e ‘/\\$/N; s/\\\n//; ta’

    # if a line begins with an equal sign, append it to the previous line
    # and replace the “=” with a single space
    sed -e :a -e ‘$!N;s/\n=/ /;ta’ -e ‘P;D’

    # add commas to numeric strings, changing “1234567” to “1,234,567”
    gsed ‘:a;s/\B[0-9]\{3\}\>/,&/;ta’ # GNU sed
    sed -e :a -e ‘s/\(.*[0-9]\)\([0-9]\{3\}\)/\1,\2/;ta’ # other seds

    # add commas to numbers with decimal points and minus signs (GNU sed)
    gsed -r ‘:a;s/(^|[^0-9.])([0-9]+)([0-9]{3})/\1\2,\3/g;ta’

    # add a blank line every 5 lines (after lines 5, 10, 15, 20, etc.)
    gsed ‘0~5G’ # GNU sed only
    sed ‘n;n;n;n;G;’ # other seds

    SELECTIVE PRINTING OF CERTAIN LINES:

    # print first 10 lines of file (emulates behavior of “head”)
    sed 10q

    # print first line of file (emulates “head -1”)
    sed q

    # print the last 10 lines of a file (emulates “tail”)
    sed -e :a -e ‘$q;N;11,$D;ba’

    # print the last 2 lines of a file (emulates “tail -2”)
    sed ‘$!N;$!D’

    # print the last line of a file (emulates “tail -1”)
    sed ‘$!d’ # method 1
    sed -n ‘$p’ # method 2

    # print the next-to-the-last line of a file
    sed -e ‘$!{h;d;}’ -e x # for 1-line files, print blank line
    sed -e ‘1{$q;}’ -e ‘$!{h;d;}’ -e x # for 1-line files, print the line
    sed -e ‘1{$d;}’ -e ‘$!{h;d;}’ -e x # for 1-line files, print nothing

    # print only lines which match regular expression (emulates “grep”)
    sed -n ‘/regexp/p’ # method 1
    sed ‘/regexp/!d’ # method 2

    # print only lines which do NOT match regexp (emulates “grep -v”)
    sed -n ‘/regexp/!p’ # method 1, corresponds to above
    sed ‘/regexp/d’ # method 2, simpler syntax

    # print the line immediately before a regexp, but not the line
    # containing the regexp
    sed -n ‘/regexp/{g;1!p;};h’

    # print the line immediately after a regexp, but not the line
    # containing the regexp
    sed -n ‘/regexp/{n;p;}’

    # print 1 line of context before and after regexp, with line number
    # indicating where the regexp occurred (similar to “grep -A1 -B1”)
    sed -n -e ‘/regexp/{=;x;1!p;g;$!N;p;D;}’ -e h

    # grep for AAA and BBB and CCC (in any order)
    sed ‘/AAA/!d; /BBB/!d; /CCC/!d’

    # grep for AAA and BBB and CCC (in that order)
    sed ‘/AAA.*BBB.*CCC/!d’

    # grep for AAA or BBB or CCC (emulates “egrep”)
    sed -e ‘/AAA/b’ -e ‘/BBB/b’ -e ‘/CCC/b’ -e d # most seds
    gsed ‘/AAA\|BBB\|CCC/!d’ # GNU sed only

    # print paragraph if it contains AAA (blank lines separate paragraphs)
    # HHsed v1.5 must insert a ‘G;’ after ‘x;’ in the next 3 scripts below
    sed -e ‘/./{H;$!d;}’ -e ‘x;/AAA/!d;’

    # print paragraph if it contains AAA and BBB and CCC (in any order)
    sed -e ‘/./{H;$!d;}’ -e ‘x;/AAA/!d;/BBB/!d;/CCC/!d’

    # print paragraph if it contains AAA or BBB or CCC
    sed -e ‘/./{H;$!d;}’ -e ‘x;/AAA/b’ -e ‘/BBB/b’ -e ‘/CCC/b’ -e d
    gsed ‘/./{H;$!d;};x;/AAA\|BBB\|CCC/b;d’ # GNU sed only

    # print only lines of 65 characters or longer
    sed -n ‘/^.\{65\}/p’

    # print only lines of less than 65 characters
    sed -n ‘/^.\{65\}/!p’ # method 1, corresponds to above
    sed ‘/^.\{65\}/d’ # method 2, simpler syntax

    # print section of file from regular expression to end of file
    sed -n ‘/regexp/,$p’

    # print section of file based on line numbers (lines 8-12, inclusive)
    sed -n ‘8,12p’ # method 1
    sed ‘8,12!d’ # method 2

    # print line number 52
    sed -n ’52p’ # method 1
    sed ’52!d’ # method 2
    sed ’52q;d’ # method 3, efficient on large files

    # beginning at line 3, print every 7th line
    gsed -n ‘3~7p’ # GNU sed only
    sed -n ‘3,${p;n;n;n;n;n;n;}’ # other seds

    # print section of file between two regular expressions (inclusive)
    sed -n ‘/Iowa/,/Montana/p’ # case sensitive

    SELECTIVE DELETION OF CERTAIN LINES:

    # print all of file EXCEPT section between 2 regular expressions
    sed ‘/Iowa/,/Montana/d’

    # delete duplicate, consecutive lines from a file (emulates “uniq”).
    # First line in a set of duplicate lines is kept, rest are deleted.
    sed ‘$!N; /^\(.*\)\n\1$/!P; D’

    # delete duplicate, nonconsecutive lines from a file. Beware not to
    # overflow the buffer size of the hold space, or else use GNU sed.
    sed -n ‘G; s/\n/&&/; /^\([ -~]*\n\).*\n\1/d; s/\n//; h; P’

    # delete all lines except duplicate lines (emulates “uniq -d”).
    sed ‘$!N; s/^\(.*\)\n\1$/\1/; t; D’

    # delete the first 10 lines of a file
    sed ‘1,10d’

    # delete the last line of a file
    sed ‘$d’

    # delete the last 2 lines of a file
    sed ‘N;$!P;$!D;$d’

    # delete the last 10 lines of a file
    sed -e :a -e ‘$d;N;2,10ba’ -e ‘P;D’ # method 1
    sed -n -e :a -e ‘1,10!{P;N;D;};N;ba’ # method 2

    # delete every 8th line
    gsed ‘0~8d’ # GNU sed only
    sed ‘n;n;n;n;n;n;n;d;’ # other seds

    # delete lines matching pattern
    sed ‘/pattern/d’

    # delete ALL blank lines from a file (same as “grep ‘.’ “)
    sed ‘/^$/d’ # method 1
    sed ‘/./!d’ # method 2

    # delete all CONSECUTIVE blank lines from file except the first; also
    # deletes all blank lines from top and end of file (emulates “cat -s”)
    sed ‘/./,/^$/!d’ # method 1, allows 0 blanks at top, 1 at EOF
    sed ‘/^$/N;/\n$/D’ # method 2, allows 1 blank at top, 0 at EOF

    # delete all CONSECUTIVE blank lines from file except the first 2:
    sed ‘/^$/N;/\n$/N;//D’

    # delete all leading blank lines at top of file
    sed ‘/./,$!d’

    # delete all trailing blank lines at end of file
    sed -e :a -e ‘/^\n*$/{$d;N;ba’ -e ‘}’ # works on all seds
    sed -e :a -e ‘/^\n*$/N;/\n$/ba’ # ditto, except for gsed 3.02.*

    # delete the last line of each paragraph
    sed -n ‘/^$/{p;h;};/./{x;/./p;}’

    SPECIAL APPLICATIONS:

    # remove nroff overstrikes (char, backspace) from man pages. The ‘echo’
    # command may need an -e switch if you use Unix System V or bash shell.
    sed “s/.`echo \\\b`//g” # double quotes required for Unix environment
    sed ‘s/.^H//g’ # in bash/tcsh, press Ctrl-V and then Ctrl-H
    sed ‘s/.\x08//g’ # hex expression for sed 1.5, GNU sed, ssed

    # get Usenet/e-mail message header
    sed ‘/^$/q’ # deletes everything after first blank line

    # get Usenet/e-mail message body
    sed ‘1,/^$/d’ # deletes everything up to first blank line

    # get Subject header, but remove initial “Subject: ” portion
    sed ‘/^Subject: */!d; s///;q’

    # get return address header
    sed ‘/^Reply-To:/q; /^From:/h; /./d;g;q’

    # parse out the address proper. Pulls out the e-mail address by itself
    # from the 1-line return address header (see preceding script)
    sed ‘s/ *(.*)//; s/>.*//; s/.*[: /’

    # delete leading angle bracket & space from each line (unquote a message)
    sed ‘s/^> //’

    # remove most HTML tags (accommodates multiple-line tags)
    sed -e :a -e ‘s/]*>//g;/zipup.bat
    dir /b *.txt | sed “s/^\(.*\)\.TXT/pkzip -mo \1 \1.TXT/” >>zipup.bat

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