I have a file called lookupfile.txt with the following info:
path, including filename
Within bash I would like to search through these files in mylookup file.txt for a pattern : myerrorisbeinglookedat. When found, output the lines where found into another recorder file. All the found result can land in the same file.
Please help.
You can write a single grep statement to achieve this:
grep myerrorisbeinglookedat $(< lookupfile.txt) > outfile
Assuming:
the number of entries in lookupfile.txt is small (tens or hundreds)
there are no white spaces or wildcard characters in the file names
Otherwise:
while IFS= read -r file; do
# print the file names separated by a NULL character '\0'
# to be fed into xargs
printf "$file\0"
done < lookupfile.txt | xargs -0 grep myerrorisbeinglookedat > outfile
xargs takes output of the loop, tokenizes them correctly and invokes grep command. xargs batches up the files based on operating system limits in case there are a large number of files.
Related
I have a directory with multiple fasta file named as followed:
BC-1_bin_1_genes.faa
BC-1_bin_2_genes.faa
BC-1_bin_3_genes.faa
BC-1_bin_4_genes.faa
etc. (about 200 individual files)
The fasta header look like this:
>BC-1_k127_3926653_6 # 4457 # 5341 # -1 # ID=2_6;partial=01;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.697
I now want to add the filename to the header since I want to annotate the sequences for each file.I tried the following:
for file in *.faa;
do
sed -i "s/>.*/${file%%.*}/" "$file" ;
done
It worked partially but it removed the ">" from the header which is essential for the fasta file. I tried to modify the "${file%%.*}" part to keep the carrot but it always called me out on bad substitutions.
I also tried this:
awk '/>/{sub(">","&"FILENAME"_");sub(/\.faa/,x)}1' *.faa
This worked in theory but only printed everything on my terminal rather than changing it in the respective files.
Could someone assist with this?
It's not clear whether you want to replace the earlier header, or add to it. Both scenarios are easy to do. Don't replace text you don't want to replace.
for file in ./*.faa;
do
sed -i "s/^>.*/>${file%%.*}/" "$file"
done
will replace the header, but include a leading > in the replacement, effectively preserving it; and
for file in ./*.faa;
do
sed -i "s/^>.*/&${file%%.*}/" "$file"
done
will append the file name at the end of the header (& in the replacement string evaluates to the string we are replacing, again effectively preserving it).
For another variation, try
for file in *.faa;
do
sed -i "/^>/s/\$/ ${file%%.*}/" "$file"
done
which says on lines which match the regex ^>, replace the empty string at the end of the line $ with the file name.
Of course, your Awk script could easily be fixed, too. Standard Awk does not have an option to parallel the -i "in-place" option of sed, but you can easily use a temporary file:
for file in ./*.faa;
do
awk '/>/{ $0 = $0 " " FILENAME);sub(/\.faa/,"")}1' "$file" >"$file.tmp" &&
mv "$file.tmp" "$file"
done
GNU Awk also has an -i inplace extension which you could simply add to the options of your existing script if you have GNU Awk.
Since FASTA files typically contain multiple headers, adding to the header rather than replacing all headers in a file with the same string seems more useful, so I changed your Awk script to do that instead.
For what it's worth, the name of the character ^ is caret (carrot is 🥕). The character > is called greater than or right angle bracket, or right broket or sometimes just wedge.
You just need to detect the pattern to replace and use regex to implement it:
fasta_helper.sh
location=$1
for file in $location/*.faa
do
full_filename=${file##*/}
filename="${full_filename%.*}"
#scape special chars
filename=$(echo $filename | sed 's_/_\\/_g')
echo "adding file name: $filename to: $full_filename"
sed -i -E "s/^[^#]+/>$filename /" $location/$full_filename
done
usage:
Just pass the folder with fasta files:
bash fasta_helper.sh /foo/bar
test:
lectures
Regex: matching up to the first occurrence of a character
Extract filename and extension in Bash
https://unix.stackexchange.com/questions/78625/using-sed-to-find-and-replace-complex-string-preferrably-with-regex
Locating your files
Suggesting to first identify your files with find command or ls command.
find . -type f -name "*.faa" -printf "%f\n"
A find command to print only file with filenames extension .faa. Including sub directories to current directory.
ls -1 "*.faa"
An ls command to print files and directories with extension .faa. In current directory.
Processing your files
Once you have the correct files list, iterate over the list and apply sed command.
for fileName in $(find . -type f -name "*.faa" -printf "%f\n"); do
stripedFileName=${fileName/.*/} # strip extension .faa
sed -i "1s|\$| $stripedFileName|" "fileName" # append value of stripedFileName at end of line 1
done
i have many text files in a directory like 1.txt 2.txt 3.txt 4.txt .......2000.txt and i want to paste them to make a large file.
In this regard i did something like
paste *.txt > largefile.txt
but the above command reads the .txt file randomly, so i need to read the files sequentially and paste as 1.txt 2.txt 3.txt....2000.txt
please suggest a better solution for pasting many files.
Thanks and looking forward to hearing from you.
Sort the file names numerically yourself then.
printf "%s\n" *.txt | sort -n | xargs -d '\n' paste
When dealing with many files, you may hit ulimit -n. On my system ulimit -n is 1024, but this is a soft limit and can be raised with just like ulimit -n 99999.
Without raising the soft limit, go with a temporary file that would accumulate results each "round" of ulimit -n count of files, like:
touch accumulator.txt
... | xargs -d '\n' -n $(($(ulimit -n) - 1)) sh -c '
paste accumulator.txt "$#" > accumulator.txt.sav;
mv accumulator.txt.sav accumulator.txt
' _
cat accumulator.txt
Instead use the wildcard * to enumerate all your files in a directory, if your file names pattern are sequentially ordered, you can manually list all files in order and concatenate to a large file. The output order of * enumeration might look different in different environment, as it not works as you expect.
Below is a simple example
$ for i in `seq 20`;do echo $i > $i.txt;done
# create 20 test files, 1.txt, 2.txt, ..., 20.txt with number 1 to 20 in each file respectively
$ cat {1..20}.txt
# show content of all file in order 1.txt, 2.txt, ..., 20.txt
$ cat {1..20}.txt > 1_20.txt
# concatenate them to a large file named 1_20.txt
In bash or any other shell, glob expansions are done in lexicographical order. When having files numberd, this sadly means that 11.txt < 1.txt < 2.txt. This weird ordering comes from the fact that, lexicographically, 1 < . (<dot>-character (".")).
So here are a couple of ways to operate on your files in order:
rename all your files:
for i in *.txt; do mv "$i" "$(sprintf "%0.5d.txt" ${i%.*}"); done
paste *.txt
use brace-expansion:
Brace expansion is a mechanism that allows for the generation of arbitrary strings. For integers you can use {n..m} to generate all numbers from n to m or {n..m..s} to generate all numbers from n to m in steps of s:
paste {1..2000}.txt
The downside here is that it is possible that a file is missing (eg. 1234.txt). So you can do
shopt -s extglob; paste ?({1..2000}.txt)
The pattern ?(pattern) matches zero or one glob-matches. So this will exclude the missing files but keeps the order.
How to Grep the complete sequences containing a specific motif in a fasta file or txt file with one linux command and write them into another file? Also, I want to include the lines beginning with a ">" before these target sequences.
Example:I have a fasta file of 10000 sequences.
$cat file.fa
>name1
AEDIA
>name2
ALKME
>name3
AAIII
I want to grep sequences containing KME, so I should get:
>name2
ALKME
Attached is the current way I am using based on the answers I got. Maybe others may find it helpful. Thanks to Pierre Lindenbaum, Philipp Bayer, cpad0112 and batMan.
Preprocessing the fasta file first and get each sequence into one line (which is very important)
awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa > file1.fa
Get rid of the first empty line
tail -n +2 file1.fa > file2.fa
Extract the target sequences containing the substring including their names and save it into another file
LC_ALL=C grep -B 1 KME file2.fa > result.txt
Note: Take KME as the target substring as an example
if you have multiline fasta files. First linearize with awk, and use another awk to filter the sequence containing the motif. using grep would be dangerous a sequence name contains a short motif.
awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' input.fa |\
awk -F '\t' '{if(index($2,"KME")!=0) printf("%s\n%s\n",$1,$2);}'
grep -B1 KME file > output_file
-B1 : prints 1 line before the match as well
I would like to use the cat command to concatenate multiple files located in different folders. I have a text file containing the name and location (path) of each file as a long list (e.g. filesLocationNames.txt), and would like to use it as an input for the cat command.
I tried: 'cat filesLocationNames.txt | cat * > output.txt'
but it didn't work.
How about cat filesLocationNames.txt | xargs cat > output.txt
cat will pipe input to output, so piping the names in won't work. You need to supply the filenames as arguments to cat. E.g.:
cat `cat filesLocationNames.txt`
But that has the same problem with spaces in filenames/pathnames...
In TCSH you can try:
cat "'cat filesLocationNames.txt'"
That is doublequote (") backquote (') at the start. (No space between them!) But it will handle spaces in the names...
Also, in TCSH:
foreach FILE ( "`cat filesLocationNames.txt`" )
echo $FILE
end
Will handle spaces in the names...
Only one catch: If filesLocationNames.txt is too long, it will exceed the line buffer and you'll need xargs. How big is it?
Folks,
I have a text file which contains multiple lines with one string per line :
str1
str2
str3
etc..
I would like to read every line of this file and then search for those strings inside multiple files located in a different directory.
I am not quite sure how to proceed.
Thanks very much for your help.
awk 'NR==FNR{a[$0];next} { for (word in a) if ($0 ~ word) print FILENAME, $0 }' fileOfWords /wherever/dir/*
for wrd in $(cut -d, -f1 < testfile.txt); do grep $wrd dir/files* ; done
Use the GNU Grep's --file Option
According to grep(1):
-f FILE, --file=FILE
Obtain patterns from FILE, one per line. The empty file
contains zero patterns, and therefore matches nothing. (-f is
specified by POSIX.)
The -H and -n flags will print the filename and line number of each match. So, assuming you store your patterns in /tmp/foo and want to search all files in /tmp/bar, you could use something like:
# Find regular files with GNU find and grep them all using a pattern
# file.
find /etc -type f -exec grep -Hnf /tmp/foo {} +
while read -r str
do
echo "$str"
grep "$str" /path/to/other/files
done < inputfile