Thank you very much, I never thought of just taking that out!
For the completeness of this thread in case others are interested it has also been pointed out by someone on the other thread that all the way over on page *2* of the referenced thread there is a working script for this purpose, which also takes the path as command line arg.
Hi all,
I've been trying to get this to work for ages to no avail. I've searched this site and googled but cannot find a satisfactory answer.
I've got a while loop, like this
while read line
do
echo "$line"
done < file_name
Now, my problem is that most of the lines in the file... (3 Replies)
Hmmm... Bash doesn't parse whitespace with a read.
lev@sys09:~$ read line; echo "$line"
test
test
You can imagine what this does if you're using a shell script to read a list of unknown file names containing unknown spaces.
lev@sys09:~$ read word1 word2; echo "$word1,$word2"
123 456... (2 Replies)
I obviously haven't learned my lesson with shell and whitespace.
find /path/to/some/where/ -name "*.pdf" | awk '{print $5}'| uniq -d
results:
some Corporation
other Corporate junk
firmx
Works fine from cmdline but the whitespace turns into another FS in a for loop.
for... (7 Replies)
Hi,
I have a for loop which iterates over a list of strings, separated by whitespace:
$ list="1 2 3"
$ for i in $list; do echo $i; done
1
2
3
I now want to introduce some strings containing whitespace themselves ... This is straightforward if I directly iterate over the list:
$ for... (4 Replies)
I want to create a temp file which is named based on a search string. The search string may contain spaces or characters that aren't supposed to be used in filenames so I want to strip those out.
My thought was to use 'tr' with but the result is the opposite of what I want:
$ echo "test... (5 Replies)
Hi
Following is an example line.
echo "192.22.22.22 \"33dffwef\" 200 300 dsdsd" | sed "s:\(\ *\ \):\1:"
I want it's output to be
200
However this is not the case. Can you tell me how to do it? I don't want to use AWK for this. Secondly, how can i fetch just 300? Should I use "\2"... (3 Replies)
Daily stupid question. I want to increment the file name everytime the script is run. So for example if the filename is manager.log and I run the script, I want the next sequence to be manager.log1. So to be clear I only want it to increment when the script is executed. So
./script... (10 Replies)
Having issues with an expect script. I've been scripting bash, python, etc... for a couple years now, but just started to try and use Expect. Trying to create a script that takes in some arguments, and then for now, just runs a pwd command(for testing, final will be command I pass).
Here is... (0 Replies)
I am trying to do in a single line to take a list of paths separated by whitespace and then loop thru all the paths that were wrote but my regex is not working,
I have
echo {3} | sed 's/ //g' | while read EACHFILE
do
.....
But for some reason is only taking always the first path that I... (7 Replies)
Create a single bash script that does the following:
a. Print out the number of occurrences for each motif that is found in the bacterial genome and output to a file called motif_count.txt
b. Create a fasta file for each motif (so 3 in total) which contains all of the genes and their... (6 Replies)
Discussion started by: dre
6 Replies
LEARN ABOUT DEBIAN
gmt_shell_functions
GMT_SHELL_FUNCTIONS.SH(1gmt) Generic Mapping Tools GMT_SHELL_FUNCTIONS.SH(1gmt)NAME
gmt_shell_functions.sh - Practical functions to be used in GMT bourne shell scripts
SYNOPSIS
gmt_init_tmpdir
gmt_remove_tmpdir
gmt_clean_up [prefix]
gmt_message message
gmt_abort message
gmt_nrecords file(s)
gmt_nfields string
gmt_get_field string
gmt_get_region file(s) [options]
gmt_get_gridregion file [options]
gmt_get_map_width -R -J
gmt_get_map_height -R -J
gmt_set_psfile file
gmt_set_framename prefix framenumber
gmt_set_framenext framenumber
DESCRIPTION
gmt_shell_functions.sh provides a set of functions to Bourne (again) shell scripts in support of GMT. The calling shell script should
include the following line, before the functions can be used:
. gmt_shell_functions.sh
Once included in a shell script, gmt_shell_functions.sh allows GMT users to do some scripting more easily than otherwise. The functions
made available are:
gmt_init_tmpdir
Creates a temporary directory in /tmp or (when defined) in the directory specified by the environment variable TMPDIR. The name of
the temporary directory is returned as environment variable GMT_TMPDIR. This function also causes GMT to run in `isolation mode',
i.e. all temporary files will be created in GMT_TMPDIR and the .gmtdefaults file will not be adjusted.
gmt_remove_tmpdir
Removes the temporary directory and unsets the GMT_TMPDIR environment variable.
gmt_cleanup
Remove all files and directories in which the current process number is part of the file name. If the optional prefix is given then
we also delete all files and directories that begins with the given prefix.
gmt_message
Send a message to standard error.
gmt_abort
Send a message to standard error and exit the shell.
gmt_nrecords
Returns the total number of lines in file(s)
gmt_nfields
Returns the number of fields or words in string
gmt_get_field
Returns the given field in a string. Must pass string between double quotes to preserve it as one item.
gmt_get_region
Returns the region in the form w/e/s/n based on the data in table file(s). Optionally add -Idx/dy to round off the answer.
gmt_get_gridregion
Returns the region in the form w/e/s/n based on the header of a grid file. Optionally add -Idx/dy to round off the answer.
gmt_map_width
Expects the user to give the desired -R -J settings and returns the map width in the current measurement unit.
gmt_map_height
Expects the user to give the desired -R -J settings and returns the map height in the current measurement unit.
gmt_set_psfile
Create the output PostScript file name based on the base name of a given file (usually the script name $0).
gmt_set_framename
Returns a lexically ordered filename stem (i.e., no extension) given the file prefix and the current frame number, using a width of
6 for the integer including leading zeros. Useful when creating animations and lexically sorted filenames are required.
gmt_set_framenext
Accepts the current frame integer counter and returns the next integer counter.
NOTES
1. These functions only work in the bourne shell (sh) and their derivatives (like ash, bash, ksh and zsh). These functions do not work in
the C shell (csh) or their derivatives (like tcsh), and cannot be used in DOS batch scripts either.
2. gmt_shell_functions.sh were first introduced in GMT version 4.2.2 and have since been regularly expanded with other practical scripting
short-cuts. If you want to suggest other functions, please do so by mailing to the GMT mailing list: gmt-help@lists.hawaii.edu.
SEE ALSO GMT(1), sh(1), bash(1), minmax(1), grdinfo(1)GMT 4.5.7 15 Jul 2011 GMT_SHELL_FUNCTIONS.SH(1gmt)