Apologies for a seemingly inane question. But I have spent the whole day trying to figure it out and it drives me up the walls. I'm trying to write a seemingly simple bash script that would take a list of files in the directory from ls, replace part of the file names using sed, get unique names from the list and pass them onto some command. Like so:
inputs=`ls *.ext`
echo $inputs
test1_R1.ext test1_R2.ext test2_R1.ext test2_R2.ext
Now I would like to put it through sed to replace 1.ext and 2.ext with * to get test1_R* etc. Then I'd like to remove resulting duplicates by running sort -u to arrive to the following $outputs variable:
echo $outputs
test1_R* test2_R*
And pass this onto a command, like so
cat $outputs
I can do something like this in a command line:
ls *.ext | sed s/..ext/\*/g | sort -u
But if I try to assign the above to a variable in the script it just returns the output from the ls. I have tried several ways to do it: including the whole pipe in the script. Running each command separately and assigning it to a variable, then passing that variable to the next command and writing the outputs to files then passing the file to the next command. But so far none of this managed to achieve what I aimed to. I think my problem lies in (except general cluelessness aroung bash scripting) inability to run seq on a variable within script. There seems to be a lot of advice around in how to pass variables to pattern or replacement string in sed, but they all seem to take files as input. But I understand that it might not be the proper way of doing it anyway. Therefore I would really appreciate if someone could suggest an elegant way to achieve, what I'm trying to.
Many thanks!
Update 2/06/2014
Hi Barmar, thanks for your answer. Can't say it solved the problem, but it helped pin-pointing it. Seems like the problem is in me using the asterisk. I have to say, I'm very puzzled. The actual file names I've got are:
test1_R1.fastq.gz test1_R2.fastq.gz test2_R1.fastq.gz test2_R2.fastq.gz
If I'm using the code you suggested, which seems to me the right way do to it:
ins=$(ls *.fastq.gz | sed 's/..fastq.gz/\*/g' | sort -u)
Sed doesn't seem to do anything and I'm getting the output of ls:
test1_R1.fastq.gz test1_R2.fastq.gz test2_R1.fastq.gz test2_R2.fastq.gz
Now if I replace that backslash with anything else, the sed works, but it also returns whatever character I'm putting in front (or after) the asteriks:
ins=$(ls *.fastq.gz | sed 's/..fastq.gz/"*/g' | sort -u)
test1_R"* test2_R"*
That's odd enough, but surely I can just put an "R" in front of the asteriks and then replace R in the search pattern string, right? Wrong! If I do that whichever way: 's/R..fastq.gz/R*/g' 's/...fastq.gz/R*/g' 's/[A-Z]..fastq.gz/R*/g' I'm back to the original names! And even if I end up with something like test1_RR* test2_RR* and try to run it through sed again and replace "_R" for "_" or "RR" for "R", I'm having no luck and I'm back to the original names. And yet I can replace the rest of the file name no problem, just not to get me test1_R* I need.
I have a feeling I should be escaping that * in some very clever way, but nothing I've tried seems to work. Thanks again for your help!
This is how you capture the result of the whole pipeline in a variable:
var=$(ls *.ext | sed s/..ext/\*/g | sort -u)
Related
I did check the ABS, but it was hard to find a reference to my problem/question there.
Here it is. Consider the following code (Which extracts the first character of OtherVar and then converts MyVar to uppercase):
OtherVar=foobar
MyChar=${OtherVar:0:1} # get first character of OtherVar string variable
MyChar=${MyChar^} # first character to upper case
Could I somehow condense the second and third line into one statement?
P.S.: As was pointed out below, not needs to have a named variable. I should add, I would like to not add any sub-shells or so and would also accept a somehow hacky way to achieve the desired result.
P.P.S.: The question is purely educational.
You could do it all-in-one without forking sub-shell or running external command:
printf -v MyChar %1s "${OtherVar^}"
Or:
read -n1 MyChar <<<"${OtherVar^}"
Another option:
declare -u MyChar=${OtherVar:0:1}
But I can't see the point in such optimization in a bash script.
There are more suitable text processing interpreters, like awk, sed, even perl or python if performance matters.
You could use the cut command and put it in a complex expression to get it on one line, but I'm not sure it makes the code too much clearer:
OtherVar=foobar
MyChar=$(echo ${OtherVar^} | cut -c1-1) # uppercase first character and cut string
this is my very first post on Stackoverflow, and I should probably point out that I am EXTREMELY new to a lot of programming. I'm currently a postgraduate student doing projects involving a lot of coding in various programs, everything from LaTeX to bash, MATLAB etc etc.
If you could explicitly explain your answers that would be much appreciated as I'm trying to learn as I go. I apologise if there is an answer else where that does what I'm trying to do, but I have spent a couple of days looking now.
So to the problem I'm trying to solve: I'm currently using a selection of bioinformatics tools to analyse a range of genomes, and I'm trying to somewhat automate the process.
I have a few sequences with names that look like this for instance (all contained in folders of their own currently as paired files):
SOL2511_S5_L001_R1_001.fastq
SOL2511_S5_L001_R2_001.fastq
SOL2510_S4_L001_R1_001.fastq
SOL2510_S4_L001_R2_001.fastq
...and so on...
I basically wish to automate the process by turning these in to variables and passing these variables to each of the programs I use in turn. So for example my idea thus far was to assign them as wildcards, using the R1 and R2 (which appears in all the file names, as they represent each strand of DNA) as follows:
#!/bin/bash
seq1=*R1_001*
seq2=*R2_001*
On a rudimentary level this works, as it returns the correct files, so now I pass these variables to my first function which trims the DNA sequences down by a specified amount, like so:
# seqtk is the program suite, trimfq is a function within it,
# and the options -b -e specify how many bases to trim from the beginning and end of
# the DNA sequence respectively.
seqtk trimfq -b 10 -e 20 $seq1 >
seqtk trimfq -b 10 -e 20 $seq2 >
So now my problem is I wish to be able to append something like "_trim" to the output file which appears after the >, but I can't find anything that seems like it will work online.
Alternatively, I've been hunting for a script that will take the name of the folder that the files are in, and create a variable for the folder name which I can then give to the functions in question so that all the output files are named correctly for use later on.
Many thanks in advance for any help, and I apologise that this isn't really much of a minimum working example to go on, as I'm only just getting going on all this stuff!
Joe
EDIT
So I modified #ghoti 's for loop (does the job wonderfully I might add, rep for you :D ) and now I append trim_, as the loop as it was before ended up giving me a .fastq.trim which will cause errors later.
Is there any way I can append _trim to the end of the filename, but before the extension?
Explicit is usually better than implied, when matching filenames. Your wildcards may match more than you expect, especially if you have versions of the files with "_trim" appended to the end!
I would be more precise with the wildcards, and use for loops to process the files instead of relying on seqtk to handle multiple files. That way, you can do your own processing on the filenames.
Here's an example:
#!/bin/bash
# Define an array of sequences
sequences=(R1_001 R2_001)
# Step through the array...
for seq in ${sequences[#]}; do
# Step through the files in this sequence...
for file in SOL*_${seq}.fastq; do
seqtk trimfq -b 10 -e 20 "$file" > "${file}.trim"
done
done
I don't know how your folders are set up, so I haven't addressed that in this script. But the basic idea is that if you want the script to be able to manipulate individual filenames, you need something like a for loop to handle the that manipulation on a per-filename basis.
Does this help?
UPDATE:
To put _trim before the extension, replace the seqtk line with the following:
seqtk trimfq -b 10 -e 20 "$file" > "${file%.fastq}_trim.fastq"
This uses something documented in the Bash man page under Parameter Expansion if you want to read up on it. Basically, the ${file%.fastq} takes the $file variable and strips off a suffix. Then we add your extra text, along with the suffix.
You could also strip an extension using basename(1), but there's no need to call something external when you can use something built in to the shell.
Instead of setting variables with the filenames, you could pipe the output of ls to the command you want to run with these filenames, like this:
ls *R{1,2}_001* | xargs -I# sh -c 'seqtk trimfq -b 10 -e 20 "$1" > "${1}_trim"' -- #
xargs -I# will grab the output of the previous command and store it in # to be used by seqtk
I am essentially trying to use sed to remove a few lines within a text document. To clean it up. But I'm not getting it right at all. Missing something and I have no idea what...
#!/bin/bash
items[0]='X-Received:'
items[1]='Path:'
items[2]='NNTP-Posting-Date:'
items[3]='Organization:'
items[4]='MIME-Version:'
items[5]='References:'
items[6]='In-Reply-To:'
items[7]='Message-ID:'
items[8]='Lines:'
items[9]='X-Trace:'
items[10]='X-Complaints-To:'
items[11]='X-DMCA-Complaints-To:'
items[12]='X-Abuse-and-DMCA-Info:'
items[13]='X-Postfilter:'
items[14]='Bytes:'
items[15]='X-Original-Bytes:'
items[16]='Content-Type:'
items[17]='Content-Transfer-Encoding:'
items[18]='Xref:'
for f in "${items[#]}"; do
sed '/${f}/d' "$1"
done
What I am thinking, incorrectly it seems, is that I can setup a for loop to check each item in the array that I want removed from the text file. But it's simply not working. Any idea. Sure this is basic and simple and yet I can't figure it out.
Thanks,
Marek
Much better to create a single sed script, rather than generate 19 small scripts in sequence.
Fortunately, generating a script by joining the array elements is moderately easy in Bash:
regex=$(printf '\|%s' "${items[#]}")
regex=${regex#'\|'}
sed "/^$regex/d" "$1"
(Notice also the addition of ^ to the final regex -- I assume you only want to match at beginning of line.)
Properly, you should not delete any lines from the message body, so the script should leave anything after the first empty line alone:
sed "1,/^\$/!b;/$regex/d" "$1"
Add -i if you want in-place editing of the target file.
I am trying to make heads or tails of a shell script. Could someone please explain this line?
$FILEDIR is a directory containing files. F is a marker in an array of files that is returned from this command:
files=$( find $FILEDIR -type f | grep -v .rpmsave\$ | grep -v .swp\$ )
The confusing line is within a for loop.
for f in $files; do
target=${f:${#FILEDIR}}
<<do some more stuff>>
done
I've never seen the colon, and the hash before in a shell script for loop. I haven't been able to find any documentation on them... could someone try and enlighten me? I'd appreciate it.
There are no arrays involved here. POSIX sh doesn't have arrays (assuming you're not using another shell based upon the tags).
The colon indicates a Bash/Ksh substring expansion. These are also not POSIX. The # prefix expands to the number of characters in the parameter. I imagine they intended to chop off the directory part and assign it to target.
To explain the rest of that: first find is run and hilariously piped into two greps which do what could have been done with find alone (except breaking on possible filenames containing newlines), and the output saved into files. This is also something that can't really be done correctly if restricted only to POSIX tools, but there are better ways.
Next, files is expanded unquoted and mutalated by the shell in more ridiculous ways for the for loop to iterate over the meaningless results. If the rest of the script is this bad, probably throw it out and start over. There's no way that will do what's expected.
The colon can be as a substring. So:
A=abcdefg
echo ${A:4}
will print the output:
efg
I'm not sure why they would use a file directory as the 2nd parameter though...
If you are having problems understanding the for loop section, try http://www.dreamsyssoft.com/unix-shell-scripting/loop-tutorial.php
I'm trying to make a script that will go into a directory and run my own application with each file matching a regular expression, specifically Test[0-9]*.txt.
My input filenames look like this TestXX.txt. Now, I could just use cut and chop off the Test and .txt, but how would I do this if XX wasn't predefined to be two digits? What would I do if I had Test1.txt, ..., Test10.txt? In other words, How would I get the [0-9]* part?
Just so you know, I want to be able to make a OutputXX.txt :)
EDIT:
I have files with filename Test[0-9]*.txt and I want to manipulate the string into Output[0-9]*.txt
Would something like this help?
#!/bin/bash
for f in Test*.txt ;
do
process < $f > ${f/Test/Output}
done
Bash Shell Parameter Expansion
A good tutorial on regexes in bash is here. Summarizing, you need something like:
if [[$filenamein =~ "^Test([0-9]*).txt$"]]; then
filenameout = "Output${BASH_REMATCH[1]}.txt"
and so on. The key is that, when you perform the =~" regex-match, the "sub-matches" to parentheses-enclosed groups in the RE are set in the entries of arrayBASH_REMATCH(the[0]entry is the whole match,1` the first parentheses-enclosed group, etc).
You need to use rounded brackets around the part you want to keep.
i.e. "Test([0-9]*).txt"
The syntax for replacing these bracketed groups varies between programs, but you'll probably find you can use \1 , something like this:
s/Test(0-9*).txt/Output\1.txt/
If you're using a unix shell, then 'sed' might be your best bet for performing the transformation.
http://www.grymoire.com/Unix/Sed.html#uh-4
Hope that helps
for file in Test[0-9]*.txt;
do
num=${file//[^0-9]/}
process $file > "Output${num}.txt"
done