I have many fq.gz files in a directory and I want to loop through each filename, delete the last 8 characters and print this to a sample name text file
eg.
984674-TAATGAGC-GCTGTAGA--R1.fq.gz
984674-TAATGAGC-GCTGTAGA--R2.fq.gz
will become:
984674-TAATGAGC-GCTGTAGA--
984674-TAATGAGC-GCTGTAGA--
At the moment I have a bash script to put each filename into an array and then print the array to a sample.txt file. I have then tried to mv the filename to the new desired filename:
#!/bin/bash
declare -a FILELIST
for f in *.gz; do
#FILELIST[length_of_FILELIST + 1]=filename
FILELIST[${#FILELIST[#]}+1]=$(echo "$f");
done
printf '%s\n' "${FILELIST[#]:1:10}" > sample.txt
sample_info=sample.txt
sample_files=($(cut -f 1 "$sample_info"))
for file in "${sample_files[#]}"
do
mv "$file" "${file::(-8)}"
echo $file
done
But the script isn't removing any characters. Can you help?
to loop through each filename, delete the last 8 characters and print this to a sample name, would this work for you:
for i in *fq.gz
do
echo ${i:0:-8}
done
Using substring removal, here. Assuming you want exactly 8 characters out from the end:
for n in *.fq.gz
do
echo "${n%%??.fq.gz}"
done
For a test,
$ n="984674-TAATGAGC-GCTGTAGA--R1.fq.gz"
$ echo "${n%%??.fq.gz}"
984674-TAATGAGC-GCTGTAGA--
OR
$ echo "${n%%????????}"
984674-TAATGAGC-GCTGTAGA--
Related
I have a directory with files, some have the same ID, which is given in the first part of the file name before the first underscore (always). e.g.:
S100_R1.txt
S100_R2.txt
S111_1_R1.txt
S111_R1.txt
S111_R2.txt
S333_R1.txt
I want to concatenate those identical IDs (and if possible placing the original files in another dir, e.g. output:
original files (folder)
S100_merged.txt
S111_merged.txt
S333_R1.txt
Small note: I imaging that perhaps a solution would be to place all files which will be processed by the code in a new directory and than in a second step move the files with the appended "merged" back to the original dir or something like this...
I am extremely new to bash scripting, so I really can't produce this code. I am use to R language and I can think how it should be but can't write it.
My pitiful attempt is something like this:
while IFS= read -r -d '' id; do
cat *"$id" > "./${id%.txt}_grouped.txt"
done < <(printf '%s\0' *.txt | cut -zd_ -f1- | sort -uz)
or this:
for ((k=100;k<400;k=k+1));
do
IDList= echo "S${k}_S*.txt" | awk -F'[_.]' '{$1}'
while [ IDList${k} == IDList${k+n} ]; do
cat IDList${k}_S*.txt IDList${k+n}_S*.txt S${k}_S*.txt S${k}_S*.txt >cat/S${k}_merged.txt &;
done
Sometimes there are only one version of the file (e.g. S333_R1.txt) sometime two (S100*), three (S111*) or more of the same.
I am prepared for harsh critique for this question because I am so far from a solution, but if someone would be willing to help me out I would greatly appreciate it!
while read $fil;
do
if [[ "$(find . -maxdepth 1 -name $line"_*.txt" | wc -l)" -gt "1" ]]
then
cat $line_*.txt >> "$line_merged.txt"
fi
done <<< "$(for i in *_*.txt;do echo $i;done | awk -F_ '{ print $1 }')"
Search for files with _.txt and run the output into awk, printing the strings before "_". Run this through a while loop. Check if the number of files for each prefix pattern is greater than 1 using find and if it is, cat the files with that prefix pattern into a merged file.
for id in $(ls | grep -Po '^[^_]+' | uniq) ; do
if [ $(ls ${id}_*.txt 2> /dev/null | wc -l) -gt 1 ] ; then
cat ${id}_*.txt > _${id}_merged.txt
mv ${id}_*.txt folder
fi
done
for f in _*_merged.txt ; do
mv ${f} ${f:1}
done
A plain bash loop with preprocessing:
# first get the list of files
find . -type f |
# then extract the prefix
sed 's#./\([^_]*\)_#\1\t&#' |
# then in a loop merge the files
while IFS=$'\t' read prefix file; do
cat "$file" >> "${prefix}_merged.txt"
done
That script is iterative - one file at a time. To detect if there is one file of specific prefix, we have to look at all files at a time. So first an awk script to join list of filenames with common prefix:
find . -type f | # maybe `sort |` ?
# join filenames with common prefix
awk '{
f=$0; # remember the file path
gsub(/.*\//,"");gsub(/_.*/,""); # extract prefix from filepath and store it in $0
a[$0]=a[$0]" "f # Join path with leading space in associative array indexed with prefix
}
# Output prefix and filanames separated by spaces.
# TBH a tab would be a better separator..
END{for (i in a) print i a[i]}
' |
# Read input separated by spaces into a bash array
while IFS=' ' read -ra files; do
#first array element is the prefix
prefix=${files[0]}
unset files[0]
# rest is the files
case "${#files[#]}" in
0) echo super error; ;;
# one file - preserve the filename
1) cat "${files[#]}" > "$outdir"/"${files[1]}"; ;;
# more files - do a _merged.txt suffix
*) cat "${files[#]}" > "$outdir"/"${prefix}_merged.txt"; ;;
esac
done
Tested on repl.
IDList= echo "S${k}_S*.txt"
Executes the command echo with the environment variable IDList exported and set to empty with one argument equal to S<insert value of k here>_S*.txt.
Filename expansion (ie. * -> list of files) is not executed inside " double quotes.
To assign a result of execution into a variable, use command substitution var=$( something seomthing | seomthing )
IDList${k+n}_S*.txt
The ${var+pattern} is a variable expansion that does not add two variables together. It uses pattern when var is set and does nothing when var is unset. See shell parameter expansion and this my answer on ${var-pattern}, but it's similar.
To add two numbers use arithemtic expansion $((k + n)).
awk -F'[_.]' '{$1}'
$1 is just invalid here. To print a line, print it {print %1}.
Remember to check your scripts with http://shellcheck.net
A pure bash way below. It uses only globs (no need for external commands like ls or find for this question) to enumerate filenames and an associative array (which is supported by bash since the version 4.0) in order to compute frequencies of ids. Parsing ls output to list files is questionable in bash. You may consider reading ParsingLs.
#!/bin/bash
backupdir=original_files # The directory to move the original files
declare -A count # Associative array to hold id counts
# If it is assumed that the backup directory exists prior to call, then
# drop the line below
mkdir "$backupdir" || exit
for file in [^_]*_*; do ((++count[${file%%_*}])); done
for id in "${!count[#]}"; do
if ((count[$id] > 1)); then
mv "$id"_* "$backupdir"
cat "$backupdir/$id"_* > "$id"_merged.txt
fi
done
I have many files not having consistent filenames.
For example
IMG_20200823_1.jpg
IMG_20200823_10.jpg
IMG_20200823_12.jpg
IMG_20200823_9.jpg
I would like to rename all of them and ensure they all follow same naming convention
IMG_20200823_0001.jpg
IMG_20200823_0010.jpg
IMG_20200823_0012.jpg
IMG_20200823_0009.jpg
Found out it's possible to change for file having only a number using below
printf "%04d\n"
However am not able to do with my files considering they mix string + "_" + different numbers.
Could anyone help me ?
Thanks !
With Perl's standalone rename or prename command:
rename -n 's/(\d+)(\.jpg$)/sprintf("%04d%s",$1,$2)/e' *.jpg
Output:
rename(IMG_20200823_10.jpg, IMG_20200823_0010.jpg)
rename(IMG_20200823_12.jpg, IMG_20200823_0012.jpg)
rename(IMG_20200823_1.jpg, IMG_20200823_0001.jpg)
rename(IMG_20200823_9.jpg, IMG_20200823_0009.jpg)
if everything looks fine, remove -n.
With Bash regular expressions:
re='(IMG_[[:digit:]]+)_([[:digit:]]+)'
for f in *.jpg; do
[[ $f =~ $re ]]
mv "$f" "$(printf '%s_%04d.jpg' "${BASH_REMATCH[1]}" "${BASH_REMATCH[2]}")"
done
where BASH_REMATCH is an array containing the capture groups of the regular expression. At index 0 is the whole match; index 1 contains IMG_ and the first group of digits; index 2 contains the second group of digits. The printf command is used to format the second group with zero padding, four digits wide.
Use a regex to extract the relevant sub-strings from the input and then pad it...
For each file.
Extract the prefix, number and suffix from the filename.
Pad the number with zeros.
Create the new filename.
Move files
The following code for bash:
echo 'IMG_20200823_1.jpg
IMG_20200823_10.jpg
IMG_20200823_12.jpg
IMG_20200823_9.jpg' |
while IFS= read -r file; do # foreach file
# Use GNU sed to extract parts on separate lines
tmp=$(<<<"$file" sed 's/\(.*_\)\([0-9]*\)\(\..*\)/\1\n\2\n\3\n/')
# Read the separate parts separated by newlines
{
IFS= read -r prefix
IFS= read -r number
IFS= read -r suffix
} <<<"$tmp"
# create new filename
newfilename="$prefix$(printf "%04d" "$number")$suffix"
# move the files
echo mv "$file" "$newfilename"
done
outputs:
mv IMG_20200823_1.jpg IMG_20200823_0001.jpg
mv IMG_20200823_10.jpg IMG_20200823_0010.jpg
mv IMG_20200823_12.jpg IMG_20200823_0012.jpg
mv IMG_20200823_9.jpg IMG_20200823_0009.jpg
Being puzzled by your hint at printf...
Current folder content:
$ ls -1 IMG_*
IMG_20200823_1.jpg
IMG_20200823_21.jpg
Surely is not a good solution but with printf and sed we can do that:
$ printf "mv %3s_%8s_%d.%3s %3s_%8s_%04d.%3s\n" $(ls -1 IMG_* IMG_* | sed 's/_/ /g; s/\./ /')
mv IMG_20200823_1.jpg IMG_20200823_0001.jpg
mv IMG_20200823_21.jpg IMG_20200823_0021.jpg
I have a directory that I'm reading from and I want to save only the date representation as a string.
I am close to getting it , although I know there is probably an easier way. Here is what I have so far:
#files are in the format of "THIS_20200420.csv" so I want only "20200420"
declare -a arr
declare -a arr2
FILES=test2/*.csv
for file in $FILES
do
arr=(${arr[*]} "${file##*/}")
done
for i in "${arr[#]}"
do
arr2+=$(echo $i | cut -c6-13)
done
for item in "${arr2[#]}"
do
echo $item
done
the output shows the array only having one element which is all the strings concatenated:
20200110202001202020021920200220202004202020042220200110202001202020021920200220202004202020042220200219202002202020042020200422
Im bashing my head against my computer at this point.
arr=(
"THIS_20200420.csv"
"THIS_20200421.csv"
"THIS_20200422.csv"
"THIS_20200423.csv"
"THIS_20200424.csv"
"THIS_20200425.csv"
"THIS_20200426.csv"
"THIS_20200427.csv"
"THIS_20200428.csv"
"THIS_20200429.csv"
"THIS_20200430.csv" )
arr=( ${arr[#]//*_} )
arr=( ${arr[#]//.*} )
echo "arr: ${arr[#]}"
Explanation:
arr=( ${arr[#]//*_} ) will match all char up to '_' for each element, and replace them with empty string.
arr=( ${arr[#]//.*} ) will match all char after '.' for each element, and replace them with empty string.
For more information on parameter expansion, a good reference is TLDP's guide on parameter expansion.
Try this
declare -a arrayname=($(ls -1 test2/*.csv | grep -o '[0-9]*'))
Demo:
$ls -1 *csv
THIS_20200420.csv
THIS_20200421.csv
THIS_20200422.csv
THIS_20200423.csv
THIS_20200424.csv
THIS_20200425.csv
THIS_20200426.csv
THIS_20200427.csv
THIS_20200428.csv
THIS_20200429.csv
THIS_20200430.csv
$declare -a arrayname=($(ls -1 *csv | grep -o '[0-9]*'))
$echo ${arrayname[#]}
20200420 20200421 20200422 20200423 20200424 20200425 20200426 20200427 20200428 20200429 20200430
$echo ${arrayname[2]}
20200422
$
You could achieve this using a loop with awk:
$ for file in *.csv; do echo $file | awk -F '[^[:alnum:]]' '{print $2}'; done
The -F '[^[:alnum:]]' tells awk to use non alphanumeric characters as the delimiter.
Another way to do this is to use bash shell parameter expansion to echo only the part of the filename you want. This obviously only works if your filenames have consistent formatting:
$ for file in *.csv; do echo "${file:5:8}"; done
I thought it would be nice to use bash parameter expansion to strip the unwanted prefix and suffix but you can't have nested expansion (afaict) so this is the best I could come up with:
$ for file in *.csv; do echo "$(tmp=${file%.csv}; echo ${tmp#THIS_})"; done
Meet Cut! A good friend of Linux Users
for file in ./*.csv; do echo $file | cut -d "_" -f 2 | cut -d "." -f 1 ; done
This one line should do the trick!
Example:
Use an array for the files assignment and parameter expansion.
#!/usr/bin/env bash
shopt -s nullglob
##: Save the files ending in *.csv in an array
## so it expands properly, variable assignment does not expand the glob *
files=(test2/*.csv)
##: Remain only the files that end with .csv without the pathname, longest match
files=("${files[#]##*/}")
##: Remain only the file names without the .csv extention
files=("${files[#]%.csv}")
##: Remain only the filename after the _ from the beginning, shortest match.
files=("${files[#]#*_}")
printf '%s ' "${files[#]}"
Suppose there are two files:
File1.txt
My name is Anamika.
File2.txt
My name is Anamitra.
I want result file storing:
Result.txt
Anamika
Anamitra
I use putty so can't use wdiff, any other alternative.
not my greatest script, but it works. Other might come up with something more elegant.
#!/bin/bash
if [ $# != 2 ]
then
echo "Arguments: file1 file2"
exit 1
fi
file1=$1
file2=$2
# Do this for both files
for F in $file1 $file2
do
if [ ! -f $F ]
then
echo "ERROR: $F does not exist."
exit 2
else
# Create a temporary file with every word from the file
for w in $(cat $F)
do
echo $w >> ${F}.tmp
done
fi
done
# Compare the temporary files, since they are now 1 word per line
# The egrep keeps only the lines diff starts with > or <
# The awk keeps only the word (i.e. removes < or >)
# The sed removes any character that is not alphanumeric.
# Removes a . at the end for example
diff ${file1}.tmp ${file2}.tmp | egrep -E "<|>" | awk '{print $2}' | sed 's/[^a-zA-Z0-9]//g' > Result.txt
# Cleanup!
rm -f ${file1}.tmp ${file2}.tmp
This uses a trick with the for loop. If you use a for to loop on a file, it will loop on each word. NOT each line like beginners in bash tend to believe. Here it is actually a nice thing to know, since it transforms the files into 1 word per line.
Ex: file content == This is a sentence.
After the for loop is done, the temporary file will contain:
This
is
a
sentence.
Then it is trivial to run diff on the files.
One last detail, your sample output did not include a . at the end, hence the sed command to keep only alphanumeric charactes.
I have been working in bash, and need to create a string argument. bash is a newish for me, to the point that I dont know how to build a string in bash from a list.
// foo.txt is a list of abs file names.
/foo/bar/a.txt
/foo/bar/b.txt
/delta/test/b.txt
should turn into: a.txt,b.txt,b.txt
OR: /foo/bar/a.txt,/foo/bar/b.txt,/delta/test/b.txt
code
s = ""
for file in $(cat foo.txt);
do
#what goes here? s += $file ?
done
myShellScript --script $s
I figure there was an easy way to do this.
with for loop:
for file in $(cat foo.txt);do echo -n "$file",;done|sed 's/,$/\n/g'
with tr:
cat foo.txt|tr '\n' ','|sed 's/,$/\n/g'
only sed:
sed ':a;N;$!ba;s/\n/,/g' foo.txt
This seems to work:
#!/bin/bash
input="foo.txt"
while IFS= read -r var
do
basename $var >> tmp
done < "$input"
paste -d, -s tmp > result.txt
output: a.txt,b.txt,b.txt
basename gets you the file names you need and paste will put them in the order you seem to need.
The input field separator can be used with set to create split/join functionality:
# split the lines of foo.txt into positional parameters
IFS=$'\n'
set $(< foo.txt)
# join with commas
IFS=,
echo "$*"
For just the file names, add some sed:
IFS=$'\n'; set $(sed 's|.*/||' foo.txt); IFS=,; echo "$*"