Auto-Detect Tab Width in Atom? - format

I know I can specify the tab-width for all documents and I can have Atom auto-detect the usage of tab characters versus spaces but is there any way to auto-detect tab-width?
I am working with files that use both 2-space width and 4-space width. Combined with how Atom interacts with tabs (automatically prepending multiples of four when I make a new line and treating four contiguous spaces as a single character) this makes for a pretty frustrating experience.
Is there any simple way of having Atom switch between 4- and 2-width tabs automatically?

I put together a script for converting files from one tab-width to another. (Assuming "tabs" are spaces.)
I think the first few lines describe its usage well enough but just in case; the first argument must specify the file's current tab-width. (You'll have to check this yourself.) The second argument specifies the desired tab-width. Third argument is the filename and the final argument is the destination for the modified file.
E.g. To change from 2-width to 4.
chtabwidth 2 4 "./file.py" "./moddedFile.py"
Note: Do not save the file to itself. It appends to the end of the file it is reading and will run forever. (This was the first thing I did and I made a 20MB file before I realized why it was hanging.) Actually, you know what, I'll add a condition to ensure it never happens. There, done.
#!/bin/bash
old_width="$1"
new_width="$2"
file="$3"
newfile="$4"
if [[ "$file" == "$newfile" ]]; then
echo "Don't save to the same file!!"
exit
fi
IFS=
while read -r p || [[ -n $p ]]; do
indent_len=$(echo "$p" | egrep -o "^ *" | tr -d '\012\015' | wc -m)
tab_num=$(( indent_len / old_width ))
new_indent_len=$(( tab_num * new_width ))
new_indent=$(printf '%*s' $new_indent_len '')
revised=$(echo ${new_indent}$(echo "$p" | egrep -o "[^ ].*$"))
echo "$revised" >> "$newfile"
done <"$file"
PS. I hate bash programming.
PPS. Zero warranty; don't blame me if random code you downloaded from the Internet sets your lunch on fire.

Related

Bash script MV is disappearing files

I've written a script to go through all the files in the directory the script is located in, identify if a file name contains a certain string and then modify the filename. When I run this script, the files that are supposed to be modified are disappearing. It appears my usage of the mv command is incorrect and the files are likely going to an unknown directory.
#!/bin/bash
string_contains="dummy_axial_y_position"
string_dontwant="dummy_axial_y_position_time"
file_extension=".csv"
for FILE in *
do
if [[ "$FILE" == *"$string_contains"* ]];then
if [[ "$FILE" != *"$string_dontwant"* ]];then
filename= echo $FILE | head -c 15
combined_name="$filename$file_extension"
echo $combined_name
mv $FILE $combined_name
echo $FILE
fi
fi
done
I've done my best to go through the possible errors I've made in the MV command but I haven't had any success so far.
There are a couple of problems and several places where your script can be improved.
filename= echo $FILE | head -c 15
This pipeline runs echo $FILE adding the variable filename having the null string as value in its environment. This value of the variable is visible only to the echo command, the variable is not set in the current shell. echo does not care about it anyway.
You probably want to capture the output of echo $FILE | head -c 15 into the variable filename but this is not the way to do it.
You need to use command substitution for this purpose:
filename=$(echo $FILE | head -c 15)
head -c outputs only the first 15 characters of the input file (they can be on multiple lines but this does not happen here). head is not the most appropriate way for this. Use cut -c-15 instead.
But for what you need (extract the first 15 characters of the value stored in the variable $FILE), there is a much simpler way; use a form of parameter expansion called "substring expansion":
filename=${FILE:0:15}
mv $FILE $combined_name
Before running mv, the variables $FILE and $combined_name are expanded (it is called "parameter expansion"). This means that the variable are replaced by their values.
For example, if the value of FILE is abc def and the value of combined_name is mnp opq, the line above becomes:
mv abc def mnp opq
The mv command receives 4 arguments and it attempts to move the files denoted by the first three arguments into the directory denoted by the fourth argument (and it probably fails).
In order to keep the values of the variables as single words (if they contain spaces), always enclose them in double quotes. The correct command is:
mv "$FILE" "$combined_name"
This way, in the example above, the command becomes:
mv "abc def" "mnp opq"
... and mv is invoked with two arguments: abc def and mnp opq.
combined_name="$filename$file_extension"
There isn't any problem in this line. The quotes are simply not needed.
The variables filename and file_extension are expanded (replaced by their values) but on assignments word splitting is not applied. The value resulted after the replacement is the value assigned to variable combined_name, even if it contains spaces or other word separator characters (spaces, tabs, newlines).
The quotes are also not needed here because the values do not contain spaces or other characters that are special in the command line. They must be quoted if they contain such characters.
string_contains="dummy_axial_y_position"
string_dontwant="dummy_axial_y_position_time"
file_extension=".csv"
It is not not incorrect to quote the values though.
for FILE in *
do
if [[ "$FILE" == *"$string_contains"* ]];then
if [[ "$FILE" != *"$string_dontwant"* ]]; then
This is also not wrong but it is inefficient.
You can use the expression from the if condition directly in the for statement (and get rid of the if statement):
for FILE in *"$string_contains"*; do
if [[ "$FILE" != *"$string_dontwant"* ]]; then
...
If you have read and understood the above (and some of the linked documentation) you will be able to figure out yourself where were your files moved :-)

Delete duplicate commands of zsh_history keeping last occurence

I'm trying to write a shell script that deletes duplicate commands from my zsh_history file. Having no real shell script experience and given my C background I wrote this monstrosity that seems to work (only on Mac though), but takes a couple of lifetimes to end:
#!/bin/sh
history=./.zsh_history
currentLines=$(grep -c '^' $history)
wordToBeSearched=""
currentWord=""
contrastor=0
searchdex=""
echo "Currently handling a grand total of: $currentLines lines. Please stand by..."
while (( $currentLines - $contrastor > 0 ))
do
searchdex=1
wordToBeSearched=$(awk "NR==$currentLines - $contrastor" $history | cut -d ";" -f 2)
echo "$wordToBeSearched A BUSCAR"
while (( $currentLines - $contrastor - $searchdex > 0 ))
do
currentWord=$(awk "NR==$currentLines - $contrastor - $searchdex" $history | cut -d ";" -f 2)
echo $currentWord
if test "$currentWord" == "$wordToBeSearched"
then
sed -i .bak "$((currentLines - $contrastor - $searchdex)) d" $history
currentLines=$(grep -c '^' $history)
echo "Line deleted. New number of lines: $currentLines"
let "searchdex--"
fi
let "searchdex++"
done
let "contrastor++"
done
^THIS IS HORRIBLE CODE NOONE SHOULD USE^
I'm now looking for a less life-consuming approach using more shell-like conventions, mainly sed at this point. Thing is, zsh_history stores commands in a very specific way:
: 1652789298:0;man sed
Where the command itself is always preceded by ":0;".
I'd like to find a way to delete duplicate commands while keeping the last occurrence of each command intact and in order.
Currently I'm at a point where I have a functional line that will delete strange lines that find their way into the file (newlines and such):
#sed -i '/^:/!d' $history
But that's about it. Not really sure how get the expression to look for into a sed without falling back into everlasting whiles or how to delete the duplicates while keeping the last-occurring command.
The zsh option hist_ignore_all_dups should do what you want. Just add setopt hist_ignore_all_dups to your zshrc.
I wanted something similar, but I dont care about preserving the last one as you mentioned. This is just finding duplicates and removing them.
I used this command and then removed my .zsh_history and replacing it with the .zhistory that this command outputs
So from your home folder:
cat -n .zsh_history | sort -t ';' -uk2 | sort -nk1 | cut -f2- > .zhistory
This effectively will give you the file .zhistory containing the changed list, in my case it went from 9000 lines to 3000, you can check it with wc -l .zhistory to count the number of lines it has.
Please double check and make a backup of your zsh history before doing anything with it.
The sort command might be able to be modified to sort it by numerical value and somehow archieve what you want, but you will have to investigate further about that.
I found the script here, along with some commands to avoid saving duplicates in the future
I didn't want to rename the history file.
# dedupe_lines.zsh
if [ $# -eq 0 ]; then
echo "Error: No file specified" >&2
exit 1
fi
if [ ! -f $1 ]; then
echo "Error: File not found" >&2
exit 1
fi
sort $1 | uniq >temp.txt
mv temp.txt $1
Add dedupe_lines.zsh to your home directory, then make it executable.
chmod +x dedupe_lines.zsh
Run it.
./dedupe_lines.zsh .zsh_history

How to parse out specific filenames from basename in bash

I'm working on the following script for a research project with my school
for f in $(ls Illumina_Data/Aphyllon/PE150_2016_04_05* ); do
if [[ "${f}" == *"_R1"* ]] ;then
echo "INITIALIZE THE SEQUENCE"
echo `basename " ${f%%_R1*}"`
get_organelle_from_reads.py -1 ${f%%_R1*}_R1_001.fastq.gz \
-2 ${f%%_R1*}_R2_001.fastq.gz \
-o Sequenced_Aphyllon_Data/`basename "${f%%_R1*}"` \
-R 15 -k 21,45,65,85,105 -F embplant_pt
fi
done
What we're getting with this script right now is kinda of a long name and we're wanting it to be shorter for organization sake. If you take a look at the -o command and the section that says Sequenced_Aphyllon_Data/'basename "${f%%_R1*}"'. What this is spitting out is the entire fastq file name that we originally used of the following format
A_speciesname_IDtag_(some set of number and letters)_(some set of numbers and letters)_(some set of number and letters)_(some set of numbers and letters)
The issue I'm having is that we're wanting the A_speciesname_IDtag section to remain, though sometimes our reads don't contain the IDtag section which makes it so we need to parse at either the second or third _ from the left. However there are always four _ from the right without fail.
So is there a way to specifically target an _ from the right of a string? From the right the amount of _ separating what we need will always remain the same but will change from the left.
grep with a lookahead assertion?
$ s1=dog_ID1_a000_b111_c222_d333
$ s2=cat_a000_b111_c222_d333
$ grep -oP ".+(?=_\w+_\w+_\w+_\w+)" <<<$s1
dog_ID1
$ grep -oP ".+(?=_\w+_\w+_\w+_\w+)" <<<$s2
cat

Script which will move non-ASCII files

I need help. I should write a script,whih will move all non-ASCII files from one directory to another. I got this code,but i dont know why it is not working.
#!/bin/bash
for file in "/home/osboxes/Parkhom"/*
do
if [ -eq "$( echo "$(file $file)" | grep -nP '[\x80-\xFF]' )" ];
then
if test -e "$1"; then
mv $file $1
fi
fi
done
exit 0
It's not clear which one you are after, but:
• To test if the variable $file contains a non-ASCII character, you can do:
if [[ $file == *[^[:ascii:]]* ]]; then
• To test if the file $file contains a non-ASCII character, you can do:
if grep -qP '[^[:ascii:]]' "$file"; then
So for example your code would look like:
for file in "/some/path"/*; do
if grep -qP '[^[:ascii:]]' "$file"; then
test -d "$1" && mv "$file" "$1"
fi
done
The first problem is that your first if statement has an invalid test clause. The -eq operator of [ needs to take one argument before and one after; your before argument is gone or empty.
The second problem is that I think the echo is redundant.
The third problem is that the file command always has ASCII output but you're checking for binary output, which you'll never see.
Using file pretty smart for this application, although there are two ways you can go on this; file says a variety of things and what you're interested in are data and ASCII, but not all files that don't identify as data are ASCII and not all files that don't identify as ASCII are data. You might be better off going with the original idea of using grep, unless you need to support Unicode files. Your grep is a bit strange to me so I don't know what your environment is but I might try this:
#!/bin/bash
for file in "/home/osboxes/Parkhom"/*
do
if grep -qP '[\0x80-\0xFF]' $file; then
[ -e "$1" ] && mv $file $1
fi
done
The -q option means be quiet, only return a return code, don't show the matches. (It might be -s in your grep.) The return code is tested directly by the if statement (no need to use [ or test). The && in the next line is just a quick way of saying if the left-hand side is true, then execute the right-hand side. You could also form this as an if statement if you find that clearer. [ is a synonym for test. Personally if $1 is a directory and doesn't change, I'd check it once at the beginning of the script instead of on each file, it would be faster.
If you mean you want to know if something is not a plain text file then you can use the file command which returns information about the type of a file.
[[ ! $( file -b "$file" ) =~ (^| )text($| ) ]]
The -b simply tells it not to bother returning the filename.
The returned value will be something like:
ASCII text
HTML document text
POSIX shell script text executable
PNG image data, 21 x 34, 8-bit/color RGBA, non-interlaced
gzip compressed data, from Unix, last modified: Mon Oct 31 14:29:59 2016
The regular expression will check whether the returned file information includes the word "text" that is included for all plain text file types.
You can instead filter for specific file types like "ASCII text" if that is all you need.

In a small script to monitor a folder for new files, the script seems to be finding the wrong files

I'm using this script to monitor the downloads folder for new .bin files being created. However, it doesn't seem to be working. If I remove the grep, I can make it copy any file created in the Downloads folder, but with the grep it's not working. I suspect the problem is how I'm trying to compare the two values, but I'm really not sure what to do.
#!/bin/sh
downloadDir="$HOME/Downloads/"
mbedDir="/media/mbed"
inotifywait -m --format %f -e create $downloadDir -q | \
while read line; do
if [ $(ls $downloadDir -a1 | grep '[^.].*bin' | head -1) == $line ]; then
cp "$downloadDir/$line" "$mbedDir/$line"
fi
done
The ls $downloadDir -a1 | grep '[^.].*bin' | head -1 is the wrong way to go about this. To see why, suppose you had files named a.txt and b.bin in the download directory, and then c.bin was added. inotifywait would print c.bin, ls would print a.txt\nb.bin\nc.bin (with actual newlines, not \n), grep would thin that to b.bin\nc.bin, head would remove all but the first line leaving b.bin, which would not match c.bin. You need to be checking $line to see if it ends in .bin, not scanning a directory listing. I'll give you three ways to do this:
First option, use grep to check $line, not the listing:
if echo "$line" | grep -q '[.]bin$'; then
Note that I'm using the -q option to supress grep's output, and instead simply letting the if command check its exit status (success if it found a match, failure if not). Also, the RE is anchored to the end of the line, and the period is in brackets so it'll only match an actual period (normally, . in a regular expression matches any single character). \.bin$ would also work here.
Second option, use the shell's ability to edit variable contents to see if $line ends in .bin:
if [ "${line%.bin}" != "$line" ]; then
the "${line%.bin}" part gives the value of $line with .bin trimmed from the end if it's there. If that's not the same as $line itself, then $line must've ended with .bin.
Third option, use bash's [[ ]] expression to do pattern matching directly:
if [[ "$line" == *.bin ]]; then
This is (IMHO) the simplest and clearest of the bunch, but it only works in bash (i.e. you must start the script with #!/bin/bash).
Other notes: to avoid some possible issues with whitespace and backslashes in filenames, use while IFS= read -r line; do and follow #shellter's recommendation about double-quotes religiously.
Also, I'm not very familiar with inotifywait, but AIUI its -e create option will notify you when the file is created, not when its contents are fully written out. Depending on the timing, you may wind up copying partially-written files.
Finally, you don't have any checking for duplicate filenames. What should happen if you download a file named foo.bin, it gets copied, you delete the original, then download a different file named foo.bin. As the script is now, it'll silently overwrite the first foo.bin. If this isn't what you want, you should add something like:
if [ ! -e "$mbedDir/$line" ]; then
cp "$downloadDir/$line" "$mbedDir/$line"
elif ! cmp -s "$downloadDir/$line" "$mbedDir/$line"; then
echo "Eeek, a duplicate filename!" >&2
# or possibly something more constructive than that...
fi

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