I am trying to write a loop with which I want to extract text file names in all sub-directories and append certain strings to it. Additionally, I want the text file name sorted for numbers after ^.
For example, I have three sub directories mydir1, mydir2, mydir3. I have,
in mydir1,
file223^1.txt
file221^2.txt
file666^3.txt
in mydir2,
file111^1.txt
file4^2.txt
In mydir3,
file1^4.txt
file5^5.txt
The expected result final.csv:
STRINGmydir1file223^1
STRINGmydir1file221^2
STRINGmydir1file666^3
STRINGmydir2file111^1
STRINGmydir2file4^2
STRINGmydir3file1^4
STRINGmydir3file5^5
This is the code I tried:
for dir in my*/; do
array=(${dir}/*.txt)
IFS=$'\n' RGBASE=($(sort <<<"${array[#]}"));
for RG in ${RGBASE[#]}; do
RGTAG=$(basename ${RG/.txt//})
echo "STRING${dir}${RGTAG}" >> final.csv
done
done
Can someone please explain what is wrong with my code? Also, there could be other better ways to do this, but I want to use the for-loop.
The output with this code:
$ cat final.csv
STRINGdir1file666^3.txt
STRINGdir2file4^2.txt
STRINGdir3file5^5.txt
As a starting point which works for your special case, I got a two liner for this.
mapfile -t array < <( find my* -name "*.txt" -printf "STRING^^%H^^%f\n" | cut -d"." -f1 | LANG=C sort -t"^" -k3,3 -k6 )
printf "%s\n" "${array[#]//^^/}"
To restrict the directory depth, you can add -maxdepth with the number of subdirs to search. The find command can also use regex in the search, which is applied to the whole path, which can be used to work on a more complex directory-tree.
The difficulty was the sort on two positions and the delimiter.
My idea was to add a delimiter, which easily can be removed afterwards.
The sort command can only handle one delimiter, therefore I had to use the double hat as delimiter which can be removed without removing the single hat in the filename.
A solution using decorate-sort-undecorate idiom could be:
printf "%s\n" my*/*.txt |
sed -E 's_(.*)/(.*)\^([0-9]+).*_\1\t\3\tSTRING\1\2^\3_' |
sort -t$'\t' -k1,1 -k2,2n |
cut -f3
assuming filenames don't contain tab or newline characters.
A basic explanation: The printf prints each pathname on a separate line. The sed converts the pathname dir/file^number.txt into dir\tnumber\tSTRINGdirfile^number (\t represents a tab character). The aim is to use the tab character as a field separator in the sort command. The sort sorts the lines by the first (lexicographically) and second fields (numerically). The cut discards the first and second fields; the remaining field is what we want.
Related
I have over 100 files in a directory with format xxx_1_sequence.fastq.gz and xxx_2_sequence.fastq.gz
The goal is to create a TAB file with 3 columns in this format:
xxx ---> xxx_1_sequence.fastq.gz ---> xxx_2_sequence.fastq.gz
where ---> is a tab.
I was thinking of creating a for loop or maybe using string manipulation in order to achieve this. My knowledge is rudimentary at this stage, so any help would be much appreciated.
Would you please try the following:
shopt -s extglob # enable extended pattern matching
suffix="sequence.fastq.gz"
for f in !(*"$suffix"); do # files which does not match the pattern
if [[ -f ${f}_1_$suffix && -f ${f}_2_$suffix ]]; then
# check the existence of the files just in case
printf "%s\t%s\t%s\n" "$f" "${f}_1_$suffix" "${f}_2_$suffix"
fi
done
If your files are in a directory called files:
paste -d '\t' \
<(printf "%s\n" files/*_1_sequence.fastq.gz | sort) \
<(printf "%s\n" files/*_2_sequence.fastq.gz | sort) \
| sed 's/\(.*\)_1_sequence.fastq.gz/\1\t\1_1_sequence.fastq.gz/' \
> out.tsv
Explanation:
printf "%s\n" will print every argument in a new line. So:
printf "%s\n" files/*_1_sequence.fastq.gz | sort
prints a sorted list of the first type of files (the second column in your output). And of course it's symmetrical with *_2_sequence.fastq.gz (the third column).
(We probably don't need the sort part, but it helps clarify the intention.)
The syntax <(some shell command) runs some shell command, puts its output into a temporary input file, and passes that file as an argument. You can see the temporary file like so:
$ echo <(echo a) <(echo b)
/dev/fd/63 /dev/fd/62
So we are passing 2 (temporary) files to paste. If each output file has N lines, then paste outputs N lines, where line number K is a concatenation of line K of each of the files, in order.
For example, if line 4 of the first file is hello and line 4 if the second file is world, paste will have hello\tworld as line 4 of the output. But instead of trusting the default, we're setting the delimiter to TAB explicitly with -d '\t'.
That gives us the last 2 columns of our tab-separated-values file, but the first column is the * part of *_1_sequence.fastq.gz, which is where sed comes in.
We tell sed to replace \(.*\)_1_sequence.fastq.gz with \1\t\1_1_sequence.fastq.gz. .* will match anything, and \(some-pattern\) tells sed to remember the text that matched the pattern.
The first parentheses in sed's regex are can be read back into the replacement pattern as \1, which is why we have \1_1_sequence.fastq.gz in the replacement pattern.
But now we can also use \1 to create the first column of our tsv, which is why we have \1\t.
Thankyou for the help guys- I was thrown into a coding position a week ago with no prior experience and have been struggling.
I ended up with this printf "%s\n" *_1_sequence.fastq.gz | sort | sed 's/\(.*\)_1_sequence.fastq.gz/\1\t\1_1_sequence.fastq.gz\t\1_2_sequence.fastq.gz/ ' > NULLARBORformat.tab
and it does the job perfectly!
I have the following format for filenames: filename_1234.svg
How can I retrieve the numbers preceded by an underscore and followed by a dot. There can be between one to four numbers before the .svg
I have tried:
width=${fileName//[^0-9]/}
but if the fileName contains a number as well, it will return all numbers in the filename, e.g.
file6name_1234.svg
I found solutions for two underscores (and splitting it into an array), but I am looking for a way to check for the underscore as well as the dot.
You can use simple parameter expansion with substring removal to simply trim from the right up to, and including, the '.', then trim from the left up to, and including, the '_', leaving the number you desire, e.g.
$ width=filename_1234.svg; val="${width%.*}"; val="${val##*_}"; echo $val
1234
note: # trims from left to first-occurrence while ## trims to last-occurrence. % and %% work the same way from the right.
Explained:
width=filename_1234.svg - width holds your filename
val="${width%.*}" - val holds filename_1234
val="${val##*_}" - finally val holds 1234
Of course, there is no need to use a temporary value like val if your intent is that width should hold the width. I just used a temp to protect against changing the original contents of width. If you want the resulting number in width, just replace val with width everywhere above and operate directly on width.
note 2: using shell capabilities like parameter expansion prevents creating a separate subshell and spawning a separate process that occurs when using a utility like sed, grep or awk (or anything that isn't part of the shell for that matter).
Try the following code :
filename="filename_6_1234.svg"
if [[ "$filename" =~ ^(.*)_([^.]*)\..*$ ]];
then
echo "${BASH_REMATCH[0]}" #will display 'filename_6_1234.svg'
echo "${BASH_REMATCH[1]}" #will display 'filename_6'
echo "${BASH_REMATCH[2]}" #will display '1234'
fi
Explanation :
=~ : bash operator for regex comparison
^(.*)_([^.])\..*$ : we look for any character, followed by an underscore, followed by any character, followed by a dot and an extension. We create 2 capture groups, one for before the last underscore, one for after
BASH_REMATCH : array containing the captured groups
Some more way
[akshay#localhost tmp]$ filename=file1b2aname_1234.svg
[akshay#localhost tmp]$ after=${filename##*_}
[akshay#localhost tmp]$ echo ${after//[^0-9]}
1234
Using awk
[akshay#localhost tmp]$ awk -F'[_.]' '{print $2}' <<< "$filename"
1234
I would use
sed 's!_! !g' | awk '{print "_" $NF}'
to get from filename_1234.svg to _1234.svg then
sed 's!svg!!g'
to get rid of the extension.
If you set IFS, you can use Bash's build-in read.
This splits the filename by underscores and dots and stores the result in the array a.
IFS='_.' read -a a <<<'file1b2aname_1234.svg'
And this takes the second last element from the array.
echo ${a[-2]}
There's a solution using cut:
name="file6name_1234.svg"
num=$(echo "$name" | cut -d '_' -f 2 | cut -d '.' -f 1)
echo "$num"
-d is for specifying a delimiter.
-f refers to the desired field.
I don't know anything about performance but it's simple to understand and simple to maintain.
in a text file I have the following entries:
10.1.0.10-15
10.1.0.20-25
10.1.0.30-35
10.1.0.40-45
I would like to print 10.1.0.10,15, 20, 25,30
cat file | grep 10.1.0.[1,2,3][0.5] -- prints 10,15,20,25,30, 35.
How do I suppress 35?
I do not want to use grep -v .35 ...just want to print specific IPs or #s.
You can use:
grep -E '10\.1\.0\.([12][05]|30)' file
However awk will be more readable:
awk -F '[.-]' '$4%5 == 0 && $4 >= 10 && $4 <= 30' file
10.1.0.10-15
10.1.0.20-25
10.1.0.30-35
Note that the , and . in the character classes are not needed — in fact, they match data that you don't want the pattern to match. Also, the . outside the character classes match any character (digit, letter, or . as you intend) — you need to escape them with a backslash so that they only match an actual ..
Also, you are making Useless Use of cat (UUoC) errors; grep can perfectly well read from a file.
As to what to do, probably use:
grep -E '10\.1\.0\.([12][05]|30)' file
This uses the extended regular expressions (formerly for egrep, now grep -E). It also avoids the dots from matching any character.
I'm not sure if what you want is just printing the first two IPs, excluding that one with 35. In that case cat file | grep '10.1.0.[1-3]0.[15|25]' does the job.
Remember that you can use conditional expressions such as | to help you.
Suppose I have setA.txt:
a|b|0.1
c|d|0.2
b|a|0.3
and I also have setB.txt:
c|d|200
a|b|100
Now I want to delete from setA.txt lines that have the same first 2 fields with setB.txt, so the output should be:
b|a|0.3
I tried:
comm -23 <(sort setA.txt) <(sort setB.txt)
But the equality is defined for whole line, so it won't work. How can I do this?
$ awk -F\| 'FNR==NR{seen[$1,$2]=1;next;} !seen[$1,$2]' setB.txt setA.txt
b|a|0.3
This reads through setB.txt just once, extracts the needed information from it, and then reads through setA.txt while deciding which lines to print.
How it works
-F\|
This sets the field separator to a vertical bar, |.
FNR==NR{seen[$1,$2]=1;next;}
FNR is the number of lines read so far from the current file and NR is the total number of lines read. Thus, when FNR==NR, we are reading the first file, setB.txt. If so, set the value of associative array seen to true, 1, for the key consisting of fields one and two. Lastly, skip the rest of the commands and start over on the next line.
!seen[$1,$2]
If we get to this command, we are working on the second file, setA.txt. Since ! means negation, the condition is true if seen[$1,$2] is false which means that this combination of fields one and two was not in setB.txt. If so, then the default action is performed which is to print the line.
This should work:
sed -n 's#\(^[^|]*|[^|]*\)|.*#/^\1/d#p' setB.txt |sed -f- setA.txt
How this works:
sed -n 's#\(^[^|]*|[^|]*\)|.*#/^\1/d#p'
generates an output:
/^c|d/d
/^a|b/d
which is then used as a sed script for the next sed after the pipe and outputs:
b|a|0.3
(IFS=$'|'; cat setA.txt | while read x y z; do grep -q -P "\Q$x|$y|\E" setB.txt || echo "$x|$y|$z"; done; )
explanation: grep -q means only test if grep can find the regexp, but do not output, -P means use Perl syntax, so that the | is matched as is because the \Q..\E struct.
IFS=$'|' will make bash to use | instead of the spaces (SPC, TAB, etc.) as token separator.
Okay so what I am trying to figure out is how do I count the number of periods in a string and then cut everything up to that point but minus 2. Meaning like this:
string="aaa.bbb.ccc.ddd.google.com"
number_of_periods="5"
number_of_periods=`expr $number_of_periods-2`
string=`echo $string | cut -d"." -f$number_of_periods`
echo $string
result: "aaa.bbb.ccc.ddd"
The way that I was thinking of doing it was sending the string to a text file and then just greping for the number of times like this:
grep -c "." infile
The reason I don't want to do that is because I want to avoid creating another text file for I do not have permission to do so. It would also be simpler for the code I am trying to build right now.
EDIT
I don't think I made it clear but I want to make finding the number of periods more dynamic because the address I will be looking at will change as the script moves forward.
If you don't need to count the dots, but just remove the penultimate dot and everything afterwards, you can use Bash's built-in string manuipulation.
${string%substring}
Deletes shortest match of $substring from back of $string.
Example:
$ string="aaa.bbb.ccc.ddd.google.com"
$ echo ${string%.*.*}
aaa.bbb.ccc.ddd
Nice and simple and no need for sed, awk or cut!
What about this:
echo "aaa.bbb.ccc.ddd.google.com"|awk 'BEGIN{FS=OFS="."}{NF=NF-2}1'
(further shortened by helpful comment from #steve)
gives:
aaa.bbb.ccc.ddd
The awk command:
awk 'BEGIN{FS=OFS="."}{NF=NF-2}1'
works by separating the input line into fields (FS) by ., then joining them as output (OFS) with ., but the number of fields (NF) has been reduced by 2. The final 1 in the command is responsible for the print.
This will reduce a given input line by eliminating the last two period separated items.
This approach is "shell-agnostic" :)
Perhaps this will help:
#!/bin/sh
input="aaa.bbb.ccc.ddd.google.com"
number_of_fields=$(echo $input | tr "." "\n" | wc -l)
interesting_fields=$(($number_of_fields-2))
echo $input | cut -d. -f-${interesting_fields}
grep -o "\." <<<"aaa.bbb.ccc.ddd.google.com" | wc -l
5