I am trying to combine a for loop inside a while read command. If run alone, this for loop works as needed:
for file in *postp*/*;
do;
ls $file/*/*/sequences/*/*_supercontig.fasta | xargs cat > My_New_File.txt;
done;
However, I only want to cat the files (*.fasta) that are named based on a given input list (Files_to_cat.txt). Here is the code I am trying, but returns an empty file so I have something wrong.
while read -r name;
do;
for file in *postp*/*;
do;
ls $file/*/*/sequences/*/"$name"_supercontig.fasta | xargs cat > My_New_File.txt;
done;
done<Files_to_cat.txt
Note the the list in Files_to_cat.txt matches the prefix of *_supercontig.fasta
Any help would be greatly appreciated.
I can't spot any mistake in the way you use while read.
You probably get this result because you use overwrite redirection > My_New_File.txt. If the last file which is cat-ed to My_New_File.txt is empty, then My_New_File.txt will be empty as well.
I expect what you want to do is either:
Append to file: >> My_New_File.txt;
Have a different file name for each output: > "Copy_of_${file##*/}_$name"
${file##*/} matches */ against the beginning of the string and removes it, so we get the basename of the file. We could as well do ${file//\//-} to replace all slashes by dashes.
Related
I need to see the last characters of bunch of text files (or alternatively test whether they are "}" and give a list of files that test negative ). Is there an easy way to do this from the command line.
(Ideally the solution works without reading the whole file from the start because in addition to there being many they can also be quite large.
P.S.: Any answer would be great but I would really appreciate if the function and syntax of everything in the answer can be fully explained.
It can be done fairly easily with tail and then string indexing in bash. For example, you obtain the last line in a file with, tail -n1 file. You will need to store the line in a variable using command-substitution, e.g.
lastln=$(tail -n1 file)
Then it is simply a matter of indexing the last characters, e.g.
echo ${lastln:(-1)}
(note: when indexing from the end of the string, you must put the offset (e.g. -1 in parenthesis (-1) -- or -- you must leave a space before the -1, e.g. echo ${lastln: -1} is also valid.)
You can try this:
for file in file1 file2; do tail -n 1 "$file" | grep -q '}$' || echo "$file"; done
where you should replace file1 file2 with the list of files you want to analyze, e.g. * or the like. Now what happens here? The outer part
for file in file1 file2; do ...; done
is a simple loop over the files, where inside the loop, you can refer to the current file as $file. Then,
tail -n 1 "$file"
prints the last line of the given file and
| grep -q '}$'
redirects the output to grep (turned into silent mode with -q), which looks for '}' immediatly followed by the end of the line ($). The return value of this command can be used to chain another action: when grep returns non-zero (indicating failure, i.e., the pattern is not matched), the last part
|| echo "$file"
is executed, resulting in the list of files you need.
I have a directory containing files numbered like this
1>chr1:2111-1111_mask.txt
1>chr1:2111-1111_mask2.txt
1>chr1:2111-1111_mask3.txt
2>chr2:345-678_mask.txt
2>chr2:345-678_mask2.txt
2>chr2:345-678_mask3.txt
100>chr19:444-555_mask.txt
100>chr19:444-555_mask2.txt
100>chr19:444-555_mask3.txt
each file contains a name like >chr1:2111-1111 in the first line and a series of characters in the second line.
I need to sort files in this directory numerically using the number before the > as guide, the execute the command for each one of the files with _mask3 and using.
I have this code
ls ./"$INPUT"_temp/*_mask3.txt | sort -n | for f in ./"$INPUT"_temp/*_mask3.txt
do
read FILE
Do something with each file and list the results in output file including the name of the string
done
It works, but when I check the list of the strings inside the output file they are like this
>chr19:444-555
>chr1:2111-1111
>chr2:345-678
why?
So... I'm not sure what "Works" here like your question stated.
It seems like you have two problems.
Your files are not in sorted order
The file names have the leading digits removed
Addressing 1, your command ls ./"$INPUT"_temp/*_mask3.txt | sort -n | for f in ./"$INPUT"_temp/*_mask3.txt here doesn't make a whole lot of sense. You are getting a list of files from ls, and then piping that to sort. That probably gives you the output you are looking for, but then you pipe that to for, which doesn't make any sense.
In fact you can rewrite your entire script to
for f in ./"$INPUT"_temp/*_mask3.txt
do
read FILE
Do something with each file and list the results in output file including the name of the string
done
And you'll have the exact same output. To get this sorted you could do something like:
for f in `ls ./"$INPUT"_temp/*_mask3.txt | sort -n`
do
read FILE
Do something with each file and list the results in output file including the name of the string
done
As for the unexpected truncation, that > character in your file name is important in your bash shell since it directs the stdout of the preceding command to a specified file. You'll need to insure that when you use variable $f from your loop that you stick quotes around that thing to keep bash from misinterpreting the file name a command > file type of thing.
I have a folder filled with ~300 files. They are named in this form username#mail.com.pdf. I need about 40 of them, and I have a list of usernames (saved in a file called names.txt). Each username is one line in the file. I need about 40 of these files, and would like to copy over the files I need into a new folder that has only the ones I need.
Where the file names.txt has as its first line the username only:
(eg, eternalmothra), the PDF file I want to copy over is named eternalmothra#mail.com.pdf.
while read p; do
ls | grep $p > file_names.txt
done <names.txt
This seems like it should read from the list, and for each line turns username into username#mail.com.pdf. Unfortunately, it seems like only the last one is saved to file_names.txt.
The second part of this is to copy all the files over:
while read p; do
mv $p foldername
done <file_names.txt
(I haven't tried that second part yet because the first part isn't working).
I'm doing all this with Cygwin, by the way.
1) What is wrong with the first script that it won't copy everything over?
2) If I get that to work, will the second script correctly copy them over? (Actually, I think it's preferable if they just get copied, not moved over).
Edit:
I would like to add that I figured out how to read lines from a txt file from here: Looping through content of a file in bash
Solution from comment: Your problem is just, that echo a > b is overwriting file, while echo a >> b is appending to file, so replace
ls | grep $p > file_names.txt
with
ls | grep $p >> file_names.txt
There might be more efficient solutions if the task runs everyday, but for a one-shot of 300 files your script is good.
Assuming you don't have file names with newlines in them (in which case your original approach would not have a chance of working anyway), try this.
printf '%s\n' * | grep -f names.txt | xargs cp -t foldername
The printf is necessary to work around the various issues with ls; passing the list of all the file names to grep in one go produces a list of all the matches, one per line; and passing that to xargs cp performs the copying. (To move instead of copy, use mv instead of cp, obviously; both support the -t option so as to make it convenient to run them under xargs.) The function of xargs is to convert standard input into arguments to the program you run as the argument to xargs.
First off, I'm really bad at shell, as you'll notice :)
Now then, I have the following task: The script gets two arguments (fileName, N). If the number of lines in the file is greater then N, then I need to cut the last N lines, then overwrite the contents of the file with it.
I thought of saving the contents of the file into a variable, then just cat-ing that to the file. However for some reason it's not working.
I have problems with saving the last N lines to a variable.
This is how I tried doing it:
lastNLines=`tail -$2 $1`
cat $lastNLines > $1
Your lastNLines is not a filename. cat takes filenames. You also cannot open the input file for writing, because the shell truncates it before tail can get to it, which is why you need to use a temporary file.
However, if you insist on not using a temporary file, here's a non-portable solution:
tail -n$2 $1 | sponge $1
You may need to install moreutils for sponge.
The arguments cat takes are file names, not the content.
Instead, you can use a temp file, like this:
tail -$2 $1 > $1._tmp
mv $1._tmp $1
To save the content to a variable, you can do what you already included in your question, or:
lastNLines=`cat $1`
(after the mv command, of course)
This should be a no-brainer, but apparently I have no brain today.
I have 50 20-gig logs that contain entries from multiple apps, one of which addes a transaction ID to its log lines. I have 42 transaction IDs I need to review, and I'd like to parse out the appropriate lines into separate files.
To do a single file, the command would be simply,
grep CDBBDEADBEEF2020X02393 server.log* > CDBBDEADBEEF2020X02393.log
that creates a log isolated to that transaction, from all 50 server.logs.
Now, I have a file with 42 txnIDs (shortening to 4 here):
CDBBDEADBEEF2020X02393
CDBBDEADBEEF6548X02302
CDBBDE15644F2020X02354
ABBDEADBEEF21014777811
And I wrote:
#/bin/sh
grep $1 server.\* > $1.log
But that is not working. Changing the shebang to #/bin/bash -xv, gives me this weird output (obviously I'm playing with what the correct escape magic must be):
$ ./xtrakt.sh B7F6E465E006B1F1A
#!/bin/bash -xv
grep - ./server\.\*
' grep - './server.*
: No such file or directory
I have also tried the command line
grep - server.* < txids.txt > $1
But OBVIOUSLY that $1 is pointless and I have no idea how to get a file named per txid using the input redirect form of the command.
Thanks in advance for any ideas. I haven't gone the route of doing a foreach in the shell script, because I want grep to put the original filename in the output lines so I can examine context later if I need to.
Also - it would be great to have the server.* files ordered numerically (server.log.1, server.log.2 NOT server.log.1, server.log.10...)
try this:
while read -r txid
do
grep "$txid" server.* > "$txid.log"
done < txids.txt
and for the file ordering - rename files with one digit to two digit, with leading zeroes, e.g. mv server.log.1 server.log.01.