I wrote the following bash code in order to create CSV path with disks partitions , so each partition will get new increment dev disk
number_of_disks=5
mount_p=({a..z})
path=` for i in \`seq 1 $number_of_disks \`; do mount_p="$(echo $mount_p| tr '[a-z]' '[b-z]a')"; echo /home/sd$mount_p/oop/app/data","; done `
but when I print the $path we get space between each partion
echo $path
/home/sdb/oop/app/data, /home/sdc/oop/app/data,
/home/sdd/oop/app/data, /home/sde/oop/app/data,
/home/sdf/oop/app/data,
Second problem is the unnecessary "," at the end of the line
Based on my code how to create the path variable without space and without "," at the end of the CSV line
You are using a very complex way (hacky as hell) to achieve something rather simple:
path=$(echo /home/sd{a..e}/oop/app/data | tr ' ' ,)
You can change your path variable like tihs:
echo $path | sed 's/ //g;s/,$//g'
It will remove last ',' and spaces.
UPD.
Or:
path=( $(echo /home/sd{b..z}/oop/app/data | tr ' ' ',') ); echo "${path[#]}"
Related
I have a FASTA file test.fasta which has the following information:
>QWE2J2_DEFR00000200123 DEFR00000560077.11 DEFR00000100333.7 3:444563-33443(-
)
acccaaagggagggagagagggctattatcatggaaaactaatttttcccagagaatttcctttcaaacctcccagtatc
tatgatcactcccaacgggaggtttaagtgcaacaccaggctgtgtctttctatcacggatttccacccggacacgtgga
acccggcctggtctgtctccaccatcctgactgggctcctgagcttcatggtggagaagggccccaccctgggcagtata
gagacgtcggacttcacgaaaagacaactggcagtgcagagaaaaggggggggggggggggataaagtcttttgtgaatt
atttcctgaagtcgtggaggagattaaacaaaaacagaaagcacaagacgaactcagtagcagaccccagactctcccct
tgccagacgtggttccagaaaaaaaaaaaaacctcgtccagaacgggattcagctgctcaacgggcatgcgccgggggcc
gtcccaaacctcgcagggctccagcaggccaaccggcaccacggactcctgggtggcgccctggcgaacttgtttgtgat
agttgggtttgcagcctttgcttacacggtcaagtaggggggggggggggcgcaggagtg
I need to convert it to CSV in the following format:
>QWE2J2_DEFR00000200123,DEFR00000560077.11,DEFR00000100333.7,3:444563-33443(-),acccaaagggagggagagagggctattatcatggaaaactaatttttcccagagaatttcctttcaaacctcccagtatctatgatcactcccaacgggaggtttaagtgcaacaccaggctgtgtctttctatcacggatttccacccggacacgtggaacccggcctggtctgtctccaccatcctgactgggctcctgagcttcatggtggagaagggccccaccctgggcagtatagagacgtcggacttcacgaaaagacaactggcagtgcagagaaaaggggggggggggggggataaagtcttttgtgaattatttcctgaagtcgtggaggagattaaacaaaaacagaaagcacaagacgaactcagtagcagaccccagactctccccttgccagacgtggttccagaaaaaaaaaaaaacctcgtccagaacgggattcagctgctcaacgggcatgcgccgggggccgtcccaaacctcgcagggctccagcaggccaaccggcaccacggactcctgggtggcgccctggcgaacttgtttgtgatagttgggtttgcagcctttgcttacacggtcaagtaggggggggggggggcgcaggagtg
I have tried in Linux terminal:
input_file=test.fasta; vim -c '0,$s/>\(.*\)\n/>\1,/' -c '0,$s/\(.*\)\n\([^>]\)/\1\2/' -c 'w! my-tmp.fasta.csv' -c 'q!' $input_file; mv my-tmp.fasta.csv $input_file.csv
However, it gives me wrong output:
>QWE2J2_DEFR00000200123 DEFR00000560077.11 DEFR00000100333.7 3:444563-33443(-,)acccaaagggagggagagagggctattatcatggaaaactaatttttcccagagaatttcctttcaaacctcccagtatctatgatcactcccaacgggaggtttaagtgcaacaccaggctgtgtctttctatcacggatttccacccggacacgtggaacccggcctggtctgtctccaccatcctgactgggctcctgagcttcatggtggagaagggccccaccctgggcagtatagagacgtcggacttcacgaaaagacaactggcagtgcagagaaaaggggggggggggggggataaagtcttttgtgaattatttcctgaagtcgtggaggagattaaacaaaaacagaaagcacaagacgaactcagtagcagaccccagactctccccttgccagacgtggttccagaaaaaaaaaaaaacctcgtccagaacgggattcagctgctcaacgggcatgcgccgggggccgtcccaaacctcgcagggctccagcaggccaaccggcaccacggactcctgggtggcgccctggcgaacttgtttgtgatagttgggtttgcagcctttgcttacacggtcaagtaggggggggggggggcgcaggagtg
How can I create this CSV file?
Using awk with RS set to > is just simple:
awk -vRS='>' 'NR>1{
gsub(/ /, ",")
sub(/\)\n/, "),")
gsub("\n", "")
print RS $0
}' file
GNU sed with -z looks simple too:
sed -z '
s/ /,/g
s/)\n/),/g
s/\n//g
s/>/\n>/g
s/^\n//
' file
The following sed script should also work:
sed -n '
# if line does not start with >
/^>/!{
# append the line to hold space
H
# if its not the end of file, start over
$!b
}
# switch pattern space with hold space
x
# add a comma after )
s/)/),/
# remove all the newlines
s/\n//g
# print it all, if hold space not empty
/^$/!p
# switch pattern space with hold space
x
# replace spaces with comma
s/ /,/g
# hold the line
h
' file
Scripts written and tested on repl:
>QWE2J2_DEFR00000200123,DEFR00000560077.11,DEFR00000100333.7,3:444563-33443(-),acccaaagggagggagagagggctattatcatggaaaactaatttttcccagagaatttcctttcaaacctcccagtatcacccggcctggtctgtctccaccatcctgactgggctcctgagcttcatggtggagaagggccccaccctgggcagtataatttcctgaagtcgtggaggagattaaacaaaaacagaaagcacaagacgaactcagtagcagaccccagactctcccctgtcccaaacctcgcagggctccagcaggccaaccggcaccacggactcctgggtggcgccctggcgaacttgtttgtgat
Prefer sed instead of vim.
I am trying to use this script to create a list of files names (including their path) and have each path separated by a comma so ideally, an output would look like: file1.txt,file2.txt,file3.txt ...etc. How do I go about this?
#!/bin/bash
LEFT=/home/ndevon/USER/SRA/PE/*_1.fastq.gz
for f in $LEFT; do
cat "${f}," >> /home/ndevon/USER/left_list.txt
done
What you want is probably
echo /home/ndevon/USER/SRA/PE/*_1.fastq.gz | tr ' ' ,
which translates spaces to commas. This works as long as your file names don't contain spaces.
Try this:
# read the filenames into an array
files=( /home/ndevon/USER/SRA/PE/*_1.fastq.gz )
# print the filenames comma-separated
IFS=,
echo "${files[*]}" > output_file
I want the spaces to be removed between two columns.
After running a sql query from shell, I'm getting the output as below:
23554402243 0584940772;2TZ0584940772001U;
23554402272 0423721840;7TT0423721840001B;
23554402303 0110770863;BBTU500248822001Q;
23554402305 02311301;BTB02311301001J;
23554402563 0550503408;PPTU004984208001O;
23554402605 0457553223;Q0T0457553223001I;
23554367602 0454542427;TB8U501674990001V;
23554378584 0383071261;HTHU500374797001Y;
23554404965 059792244;ST3059792244005C;
23554405503 0571632586;QTO0571632586001D;
But the desired output should be like below:
23554400043 0117601738;22TU003719388001V;
23554402883 0823973229;TTT0823973229001C;
23554402950 024071080;MNT024071080001D;
23554405827 0415260614;TL20415260614001R;
23554405828 08119270800;TL2U003010407001G;
23554406553 011306895;VBT011306895001E;
23554406557 054121509;TL2054121509001M;
23554406563 065069209;TL2065069209005M;
23554409085 0803434328;QTO0803434328001B;
23553396219 062004063;G6T062004063001C;
Remember, there should be only one tabspace between two columns in the desired output.
Assuming you need to remove space between all the columns:
If you need tab spaced result between first two columns. Put g to apply changes between all the columns.
sed -r 's/\s+/\t/' inputfile
if -r is not available:
sed 's/\s\+/\t/'
or If you need single space between every multi-space
tr -s ' '
Easy to do using this awk:
awk -v OFS='\t' '{$1=$1} 1' file
23554402243 0584940772;2TZ0584940772001U;
23554402272 0423721840;7TT0423721840001B;
23554402303 0110770863;BBTU500248822001Q;
23554402305 02311301;BTB02311301001J;
23554402563 0550503408;PPTU004984208001O;
23554402605 0457553223;Q0T0457553223001I;
23554367602 0454542427;TB8U501674990001V;
23554378584 0383071261;HTHU500374797001Y;
23554404965 059792244;ST3059792244005C;
23554405503 0571632586;QTO0571632586001D;
Alternatively this tr will also work:
tr -s ' ' < file | tr ' ' '\t'
or this sed:
sed -i.bak $'s/ \{1,\}/\t/g' file
what about the following perl one-liner?
perl -ne '/(.*?)\s+(.*)/; print "$1\t$2\n"' your_input_file
I have a file like this (tens of variables) :
PLAY="play"
APPS="/opt/play/apps"
LD_FILER="/data/mysql"
DATA_LOG="/data/log"
I need a script that will output the variables into another file like this (with space between them):
PLAY=${PLAY} APPS=${APPS} LD_FILER=${LD_FILER}
Is it possible ?
I would say:
$ awk -F= '{printf "%s=${%s} ", $1,$1} END {print ""}' file
PLAY=${PLAY} APPS=${APPS} LD_FILER=${LD_FILER} DATA_LOG=${DATA_LOG}
This loops through the file and prints the content before = in a format var=${var} together with a space. At the end, it prints a new line.
Note this leaves a trailing space at the end of the line. If this matters, we can check how to improve it.
< input sed -e 's/\(.*\)=.*/\1=${\1}/' | tr \\n \ ; echo
sed 's/"\([^"]*"\)"/={\1}/;H;$!d
x;y/\n/ /;s/.//' YourFile
your sample exclude last line so if this is important
sed '/DATA_LOG=/ d
s/"\([^"]*"\)"/={\1}/;H;$!d
x;y/\n/ /;s/.//' YourFile
I have some data which is being returned by some SQL query which looks as below.I am trying to separate the lines based on a delimiter and send it to the new line.How can I do this in UNIX.. I tried using shell-scripting but couldn't make through...
ALB|1001|2012-04-15 ALB|1001|2012-04-14 ALB|1001|2012-04-16 ALB|1001|2012-04-17
ALB|1001|2012-04-15
ALB|1001|2012-04-14
ALB|1001|2012-04-16
ALB|1001|2012-04-17
For that particular example, tr ' ' '\n' < file ought to work:
echo "ALB|1001|2012-04-15 ALB|1001|2012-04-14 ALB|1001|2012-04-16 ALB|1001|2012-04-17" | tr ' ' '\n'
xargs is a simple single program you can use to do this, as in:
$ echo "ALB|1001|2012-04-15 ALB|1001|2012-04-14 ALB|1001|2012-04-16 ALB|1001|2012-04-17"|xargs -d' ' -n1
ALB|1001|2012-04-15
ALB|1001|2012-04-14
ALB|1001|2012-04-16
ALB|1001|2012-04-17