I have this code:
for a in `ls *w.txt`; do perl getSequenceNs.pl $a /home/prenos/medicago/${a:0:1}.NOLE.fas >sequences/${a}_sequence.txt; done
It has been working quite well unless I recognized, that ${a:0:1} extracts first digit from $a and unfortunately there are sometimes two.
So, my variable $a contains:
dsomeletters <-one digit and letters, for example 1.NOLE.fas
ddsomeletters <-two digits and letters, for example 12.NOLE.fas
How can I extract only digits? How should I modify my code (what should I use use instead of ${a:0:1})?
${a//[^0-9]*}
should do what you want. That is actually a bashism, so you might prefer the more portable:
${a%%[^0-9]*}
First, don't parse ls, just the glob will do and properly handle ugly characters. Now then, you can use bash string manipulation a couple ways to get the number:
$ var=123abc456def
$ echo ${var%%[^0-9]*}
123
$ echo ${var//[^0-9]*/}
123
Note that * here is not the usual 0+ repetitions, it is globbing. Both patterns remove from the first character that is not a digit to the end of the string. So your final command should look like this:
for a in *w.txt; do perl getSequenceNs.pl "$a" /home/prenos/medicago/${a%%[^0-9]*}.NOLE.fas >"sequences/${a}_sequence.txt"; done
Are the letter portion of the filename always consistent? If so, you could avoid the problem by using basename:
NAME=`basename $a .NOLE.fas`
Related
I have a large binary file. I want to extract certain strings from it and copy them to a new text file.
For example, in:
D-wM-^?^#^#^#^#^#^#^#^Y^#^#^#^#^#^#^#M-lM-FM-MM-[o#^B^#M-lM-FM MM-[o#^B^#^#^#^#^#E7cacscKLrrok9bwC3Z64NTnZM-^G
I want to take the number '7' (after the #^#^#E) and every character after it stopping at the Z ('ignoring the M-^G).
I want to copy this 7cacscKLrrok9bwC3Z64NTnZ to a new file.
There will be multiple such strings in one file. The end will always be denoted by the M- (which I don't want copied). The start will always be denoted by a 7 (which I do want copied).
Unfortunately, my knowledge of grep, sed, etc, does not extend to this level. Can someone please suggest a viable way to achieve this?
cat -v filename | grep [7][A-Z,a-z] will show all strings with a '7' followed by a letter but that's not much.
Thank you.
I've noticed that my requirements are rather more complicated.
(I've performed the correct - I hope - formatting this time). Thanks to 'tshiono' for his (?) answer to the earlier submission.
I want to check the ending of a string and, if it ends in M-, grep another string that follows it (with junk in between). If the string does not end in M-, then I don't want it copied (let alone any other strings).
So what I would like is:
grep -a -Po "7[[:alnum:]]+(?=M-)" file_name and if the ending is M- then grep -a -Po "5x[[:alnum:]]+(?=\^)" file_name to copy the string that starts with 5x and ends with a ^.
In this example:
D-wM-^?^#^#^#^#^#^#^#^Y^#^#^#^#^#^#^#M-lM-FM-MM-[o#^B^#M-lM-FM MM-[o#^B^#^#^#^#^#E7cacscKLrrok9bwC3Z64NTnZM-^GwM-^?^#^#^#^#^#^#^#^Y^#^#^#^#^#^#^#M-lM-FM-MM-[o#^B^#M-lM5x8w09qewqlkcklwnlkewflewfiewjfoewnflwenfwlkfwelk^89038432nowefe
The outcome would be:
7cacscKLrrok9bwC3Z64NTnZ
5x8w09qewqlkcklwnlkewflewfiewjfoewnflwenfwlkfwelk
However, if the ending is not M- (more precisely, if the ending is ^S), then do not try the second grep and do not record anything at all.
In this example:
D-wM-^?^#^#^#^#^#^#^#^Y^#^#^#^#^#^#^#M-lM-FM-MM-[o#^B^#M-lM-FM MM-[o#^B^#^#^#^#^#E7cacscKLrrok9bwC3Z64NTnZ^SGwM-^?^#^#^#^#^#^#^#^Y^#^#^#^#^#^#^#M-lM-FM-MM-[o#^B^#M-lM5x8w09qewqlkcklwnlkewflewfiewjfoewnflwenfwlkfwelk^89038432nowefe
The outcome would be null (nothing copied) as the 7cacs... string ends in ^S.
Is grep the correct tool? Grep a file and if the condition in the grep command is 'yes' then issue a different grep command but if the condition is 'no' then do nothing.
Thanks again.
I have noticed one addition modification.
Can one add an OR command to the second part? Grep if the second string starts with 5x OR 6x?
In the example below, grep -aPo "7[[:alnum:]]+M-.*?5x[[:alnum:]]+\^" filename | grep -aPo "7[[:alnum:]]+(?=M-)|5x[[:alnum:]]+(?=\^)" will extract the strings starting with 7 and the strings starting with 5x.
How can one change the 5x to 5x or 6x?
D-wM-^?^#^#^#^#^#^#^#^Y^#^#^#^#^#^#^#M-lM-FM-MM-[o#^B^#M-lM-FM MM-[o#^B^#^#^#^#^#E7cacscKLrrok9bwC3Z64NTnZM-^GwM-^?^#^#^#^#^#^#^#^Y^#^#^#^#^#^#^#M-lM-FM-MM-[o#^B^#M-lM5x8w09qewqlkcklwnlkewflewfiewjfoewnflwenfwlkfwelk^89038432nowefe
D-wM-^?^#^#^#^#^#^#^#^Y^#^#^#^#^#^#^#M-lM-FM-MM-[o#^B^#M-lM-FM MM-[o#^B^#^#^#^#^#E7AAAAAscKLrrok9bwC3Z64NTnZM-^GwM-^?^#^#^#^#^#^#^#^Y^#^#^#^#^#^#^#M-lM-FM-MM-[o#^B^#M-lM6x8w09qewqlkcklwnlkewflewfiewjfoewnflwenfwlkfwelk^89038432nowefe
In this example, the desired outcome would be:
7cacscKLrrok9bwC3Z64NTnZ
5x8w09qewqlkcklwnlkewflewfiewjfoewnflwenfwlkfwelk
7AAAAAscKLrrok9bwC3Z64NTnZ
6x8w09qewqlkcklwnlkewflewfiewjfoewnflwenfwlkfwelk
UPDATE MARCH 09:
I need to create a series of complex grep (or perl) commands to extract strings from a series of binary files.
I need two strings from the binary file.
The first string will always start with a 1.
The first string will end with a letter or number. The next letter will always be a lower case k. I do not want this k character.
The difficulty is that the ending k will not always be the first k in the string. It might be the first k but it might not.
After the k, there is a second string. The second string will always start with an A or a B.
The ending of the second string will be in one of two forms:
a) it will end with a space then display the first three characters from the first string in lower case followed by a )
b) it will end with a ^K then display the first three characters from the first string in lower case.
For example:
1pppsx9YPar8Rvs75tJYWZq3eo8PgwbckB4m4zT7Yg042KIDYUE82e893hY ppp)
Should be:
1pppsx9YPar8Rvs75tJYWZq3eo8Pgwbc and B4m4zT7Yg042KIDYUE82e893hY - delete the k and the space then ppp.
For example:
1zzzsx9YPkr8Rvs75tJYWZq3eo8PgwbckA2m4zT7Yg042KIDYUE82e893hY^Kzzz
Should be:
1zzzsx9YPkar8Rvs75tJYWZq3eo8Pgwbc and A4m4zT7Yg042KIDYUE82e893hY - delete the second k and the ^Kzzz.
In the second example, we see that the first k is part of the first string. It is the k before the A that breaks up the first and second strings.
I hope there is a super grep expert who can help! Many thanks!
If your grep supports -P option, would you please try:
grep -a -Po "7[[:alnum:]]+(?=M-)" file
The -a option forces grep to read the input as a text file.
The -P option enables the perl-compatible regex.
The -o option tells grep to print only the matched substring(s).
The pattern (?=M-) is a zero-width lookahead assertion (introduced in
Perl) without including it in the result.
Alternatively you can also say with sed:
sed 's/M-/\n/g' file | sed -n 's/.*\(7[[:alnum:]]\+\).*/\1/p'
The first sed command splits the input file into miltiple lines by
replacing the substring M- with a newline.
It has two benefits: it breaks the lines to allow multiple matches with
sed and excludes the unnecessary portion M- from the input.
The next sed command extracts the desired pattern from the input.
It assumes your sed accepts \n in the replacement, which is
a GNU extension (not POSIX compliant). Otherwise please try (in case you are working on bash):
sed 's/M-/\'$'\n''/g' file | sed -n 's/.*\(7[[:alnum:]]\+\).*/\1/p'
[UPDATE]
(The requirement has been updated by the OP and the followings are solutions according to it.)
Let me assume the string which starts with 7 and ends with M- is always followed
by another (no more and no less than one) string which starts with 5x and ends
with ^ (ascii caret character) with junks in between.
Then would you please try the following:
grep -aPo "7[[:alnum:]]+M-.*?5x[[:alnum:]]+\^" file | grep -aPo "7[[:alnum:]]+(?=M-)|5x[[:alnum:]]+(?=\^)"
It executes the task in two steps (two cascaded greps).
The 1st grep narrows down the input data into the candidate substring
which will include the desired two sequences and junks in between.
The regex .*? in between matches any (ascii or binary) characters
except for a newline character.
The trailing ? enables the shortest match
which avoids the overrun due to the greedy nature of regex. The regex is intended to match junks in between.
The 2nd grep includes two regex's merged with a pipe | meaning logical OR.
Then it extracts two desired sequences.
A potential problem of grep solution is that grep is a line oriented command
and cannot include the newline character in the matched string.
If a newline character is included in the junks in between (I'm not sure about the possibility), the above solution will fail.
As a workaround, perl will provide flexible manipulations with binary data.
perl -0777 -ne '
while (/(7[[:alnum:]]+)M-.*?(5x[[:alnum:]]+)\^/sg) {
printf("%s\n%s\n", $1, $2);
}
' file
The regex is mostly same as that of grep because the -P option of grep means
perl-compatible.
It can capture multiple patterns at once in variables $1 and $2 hence just one regex is enough.
The -0777 option to the perl command tells perl to slurp all data
at once.
The s option at the end the regex makes a dot match a newline character.
The g option enables the global (multiple) match.
[UPDATE2]
In order to make the regex match either 5x or 6x, replace 5x with (5|6)x.
Namely:
grep -aPo "7[[:alnum:]]+M-.*?(5|6)x[[:alnum:]]+\^" file | grep -aPo "7[[:alnum:]]+(?=M-)|(5|6)x[[:alnum:]]+(?=\^)"
As mentioned before, the pipe | means OR. The OR operator has the lowest priority in the evaluation, hence you need to enclose them with parens in this case.
If there is a possibility any other number than 5 or 6 may appear, it will be safer to put [[:digit:]] instead, which matches any one digit betweeen 0 and 9:
grep -aPo "7[[:alnum:]]+M-.*?[[:digit:]]x[[:alnum:]]+\^" file | grep -aPo "7[[:alnum:]]+(?=M-)|[[:digit:]]x[[:alnum:]]+(?=\^)"
[UPDATE3]
(Answering the OP's requirement on March 9th)
Let me start with a perl code which regex will be relatively easier
to explain.
perl -0777 -ne 'while (/(1(.{3}).+)k([AB].*)[\013 ]\2/g){print "$1 $3\n"}' file
Output:
1pppsx9YPar8Rvs75tJYWZq3eo8Pgwbc B4m4zT7Yg042KIDYUE82e893hY
1zzzsx9YPkr8Rvs75tJYWZq3eo8Pgwbc A2m4zT7Yg042KIDYUE82e893hY
[Explanation of regex]
(1(.{3}).+)k([AB].*)[\013 ]\2
( start of the 1st capture group referred by $1 later
1 literal "1"
( start of the 2nd capture group referred by \2 later
.{3} a sequence of the identical three characters such as ppp or zzz
) end of the 2nd capture group
.+ followed by any characters with "greedy" match which may include the 1st "k"
) end of the 1st capture group
k literal "k"
( start of the 3rd capture group referred by $3 later
[AB].* the character "A" or "B" followed by any characters
) end of the 3rd capture group
[\013 ] followed by ^K or a whitespace
\2 followed by the capture group 2 previously assigned
When implementing it with grep, we will encounter a limitation of grep.
Although we want to extract multiple patterns from the input file,
the -e option (which can specify multiple search patterns) does not
work with -P option. Then we need to split the regex into two patterns
such as:
grep -Po "(1(.{3}).+)(?=k([AB].*)[\013 ]\2)" file
grep -Po "(1(.{3}).+)k\K([AB].*)(?=[\013 ]\2)" file
And the result will be:
1pppsx9YPar8Rvs75tJYWZq3eo8Pgwbc
1zzzsx9YPkr8Rvs75tJYWZq3eo8Pgwbc
B4m4zT7Yg042KIDYUE82e893hY
A2m4zT7Yg042KIDYUE82e893hY
Please be noted the order of output is not same as the order of appearance in the original file.
Another option will be to introduce ripgrep or rg which is a fast
and versatile version of grep. You may need to install ripgrep with
sudo apt install ripgrep or using other package handling tool.
An advantage of ripgrep is it supports -r (replace) option in which
you can make use of the backreferences:
rg -N -Po "(1(.{3}).+)k([AB].*)[\013 ]\2" -r '$1 $3' file
The -r '$1 $3' option prints the 1st and the 3rd capture groups and the result will be the same as perl.
In the general case, you can use the strings utility to pluck out ASCII from binary files; then of course you can try to grep that output for patterns that you find interesting.
Many traditional Unix utilities like grep have internal special markers which might get messed up by binary input. For example, the character \xFF was used for internal purposes by some versions of GNU grep so you can't grep for that character even if you can figure out a way to represent it in the shell (Bash supports $'\xff' for example).
A traditional approach would be to run hexdump or a similar utility, and then grep that for patterns. However, more modern scripting languages like Perl and Python make it easy to manipulate arbitrary binary data.
perl -ne 'print if m/\xff\xff/' </dev/urandom
This might work for you (GNU sed):
sed -En '/\n/!{s/M-\^G/\n/;s/7[^\n]*\n/\n&/};/^7[^\n]*/P;D' file
Split each line into zero or more lines that begin with 7 and end just before M-^G and only print such lines.
I have an issue with string manipulation in bash. I have a list of names, each name being composed of two parts, chars and numbers: for example
abcdef01234
I want to cut the last character before the numeric part starts, in this case
f
I think there is a regular expression to help me with this but just can't figure it out. AWK/sed solutions are accepted too. Hope someone can help.
Thank you.
In bash it can be done with parameter expansion with substring removal and string indexes, e.g.,
a=abcdef01234 # your string
tmp=${a%%[0-9]*} # remove all numbers from right
echo ${tmp:(-1)} # output last of remaining chars
Output: f
You can use a regexp like [a-zA-Z]+([a-zA-Z])[0-9]+. If you know how to use sed is pretty easy.
Check https://regex101.com/r/XCkKM5/1
The match will be the letter you want.
^\w+([a-zA-Z])\d+$
As a sed command (on OSX) this will be :
echo "abcdef12345" | sed -E "s#^[a-zA-Z]+([a-zA-Z])[0-9]+\$#\1#"
try following too once.
echo "abcdef01234" | awk '{match($0,/[a-zA-Z]+/);print substr($0,RLENGTH,1)}'
I have a list of names I assume is a file, file. Using grep's PCRE and (positive) lookahead:
$ grep -oP "[a-z](?=[^a-z])" file
f
It prints out the first (lowercase) letter followed by a non-(lowercase)-letter.
I'm trying to extract the last number before a file extension in a bash script. So the format varies but it'll be some combination of numbers and letters, and the last character will always be a digit. I need to pull those digits and store them in a variable.
The format is generally:
sdflkej10_sdlkei450_sdlekr_1.txt
I want to store just the final digit 1 into a variable.
I'll be using this to loop through a large number of files, and the last number will get into double and triple digits.
So for this file:
kej10_sdlkei450_sdlekr_310.txt
I'd need to return 310.
The number of alphanumeric characters and underscores varies with each file, but the number I want always is immediately before the .txt extension and immediately after an underscore.
I tried:
bname=${f%%.*}
number=$(echo $bname | tr -cd '[[:digit:]]')
but this returns all digits.
If I try
number = $(echo $(bname -2) it changes the number it returns.
The problem i'm having is mostly related to the variability, and the fact that I've been asked to do it in bash. Any help would really be appreciated.
regex='([0-9]+)\.[^.]*$'
[[ $file =~ $regex ]] && number=${BASH_REMATCH[1]}
This uses bash's underappreciated =~ regex operator which stores matches in an array named BASH_REMATCH.
You could do this using parameter substitution
var=kej10_sdlkei450_sdlekr_310.txt
var=${var%.*}
var=${var##*_}
echo $var
310
Use a Series of Bash Shell Expansions
While not the most elegant solution, this one uses a sequence of shell parameter expansions to achieve the desired result without having to define a specific extension. For example, this function uses the length and offset expansions to find the digit after removing filename extensions:
extract_digit() {
local basename=${1%%.*}
echo "${basename:$(( ${#basename} - 1 ))}"
}
Capturing Function Output
You can capture the output in a variable with something like:
$ foo=$(extract_digit sdflkej10_sdlkei450_sdlekr_1.txt)
$ echo $foo
1
Sample Output from Function
$ extract_digit sdflkej10_sdlkei450_sdlekr_1.txt
1
$ extract_digit sdflkej10_sdlkei450_sdlekr_9.txt
9
$ extract_digit sdflkej10_sdlkei450_sdlekr_10.txt
0
This should take care of your situation:
INPUT="some6random7numbers_12345_moreletters_789.txt"
SUBSTRING=`expr match "$INPUT" '.*_\([[:digit:]]*\)'`
echo $SUBSTRING
This will output 789
No need of regex here, you can utilize IFS
var="kej10_sdlkei450_sdlekr_310.txt"
v=$(IFS=[_.] read -ra arr <<< "$var" && echo "${arr[#]:(-2):1}")
echo "$v"
310
The overarching problem:
So I have a file name that comes in the form of
JohnSmith14_120325_A10_6.raw
and I want to match it using regex. I have a couple of issues in building a working example but unfortunately my issues won't be solved unless I get the basics.
So I have just recently learned about piping and one of the cool things I learned was that I can do the following.
X=ll_paprika.sc (don't ask)
VAR=`echo $X | cut -p -f 1`
echo $VAR
which gives me paprika.sc
Now when I try to execute the pipe idea in grep, nothing happens.
x=ll_paprika.sc
VAR=`echo $X | grep *.sc`
echo $VAR
Can anyone explain what I am doing wrong?
Second question:
How does one match a single underscore using regex?
Here's what I am ultimately trying to do;
VAR=`echo $X | grep -e "^[a-bA-Z][a-bA-Z0-9]*(_){1}[0-9]*(_){1}[a-bA-Z0-9]*(_){1}[0-9](\.){1}(raw)"
So the basic idea of my pattern here is that the file name must start with a letter
and then it can have any number of letters and numbers following it and it must have an _ delimit a series of numbers and another _ to delimit the next set of numbers and characters and another _ to delimit the next set of numbers and then it must have a single period following by raw. This looks grossly wrong and ugly (because I am not sure about the syntax). So how does one match a file extension? Can someone put up a simple example for something ll_parpika.sc so that I can figure out how to do my own regex?
Thanks.
x=ll_paprika.sc
VAR=`echo $X | grep *.sc`
echo $VAR
The reason this isn't doing what you want is that the grep matches a line and returns it. *.sc does in fact match 11_paprika.sc, so it returns that whole line and sticks it in $VAR.
If you want to just get a part of it, the cut line probably better. There is a grep -o option that returns only the matching portion, but for this you'd basically have to put in the thing you were looking for, at which point why bother?
the file name must start with a letter
`grep -e "^[a-zA-Z]
and then it can have any number
of letters and numbers following it
[a-zA-Z0-9]*
and it must have an _ delimit a
series of numbers and another _ to delimit the next set of numbers and
characters and another _ to delimit the next set of numbers
(_[0-9]+){3}
and then it must have a single period following by raw.
.raw"
For the first, use:
VAR=`echo $X | egrep '\.sc$'`
For the second, you can try this alternative instead:
VAR=`echo $X | egrep '^[[:alpha:]][[:alnum:]]*_[[:digit:]]+_[[:alnum:]]+_[[:digit:]]+\.raw'`
Note that your character classes from your expression differ from the description that follows in that they seem to only be permissive of a-b for lower case characters in some places. This example is permissive of all alphanumeric characters in those places.
I have a file that looks like this:
#"Afghanistan.png",
#"Albania.png",
#"Algeria.png",
#"American_Samoa.png",
I want it to look like this
#"Afghanistan.png",
#"Afghanistan",
#"Albania.png",
#"Albania",
#"Algeria.png",
#"Algeria",
#"American_Samoa.png",
#"American_Samoa",
I thought I could use sed to do this but I can't figure out how to store something in a buffer and then modify it.
Am I even using the right tool?
Thanks
You don't have to get tricky with regular expressions and replacement strings: use sed's p command to print the line intact, then modify the line and let it print implicitly
sed 'p; s/\.png//'
Glenn jackman's response is OK, but it also doubles the rows which do not match the expression.
This one, instead, doubles only the rows which matched the expression:
sed -n 'p; s/\.png//p'
Here, -n stands for "print nothing unless explicitely printed", and the p in s/\.png//p forces the print if substitution was done, but does not force it otherwise
That is pretty easy to do with sed and you not even need to use the hold space (the sed auxiliary buffer). Given the input file below:
$ cat input
#"Afghanistan.png",
#"Albania.png",
#"Algeria.png",
#"American_Samoa.png",
you should use this command:
sed 's/#"\([^.]*\)\.png",/&\
#"\1",/' input
The result:
$ sed 's/#"\([^.]*\)\.png",/&\
#"\1",/' input
#"Afghanistan.png",
#"Afghanistan",
#"Albania.png",
#"Albania",
#"Algeria.png",
#"Algeria",
#"American_Samoa.png",
#"American_Samoa",
This commands is just a replacement command (s///). It matches anything starting with #" followed by non-period chars ([^.]*) and then by .png",. Also, it matches all non-period chars before .png", using the group brackets \( and \), so we can get what was matched by this group. So, this is the to-be-replaced regular expression:
#"\([^.]*\)\.png",
So follows the replacement part of the command. The & command just inserts everything that was matched by #"\([^.]*\)\.png", in the changed content. If it was the only element of the replacement part, nothing would be changed in the output. However, following the & there is a newline character - represented by the backslash \ followed by an actual newline - and in the new line we add the #" string followed by the content of the first group (\1) and then the string ",.
This is just a brief explanation of the command. Hope this helps. Also, note that you can use the \n string to represent newlines in some versions of sed (such as GNU sed). It would render a more concise and readable command:
sed 's/#"\([^.]*\)\.png",/&\n#"\1",/' input
I prefer this over Carles Sala and Glenn Jackman's:
sed '/.png/p;s/.png//'
Could just say it's personal preference.
or one can combine both versions and apply the duplication only on lines matching the required pattern
sed -e '/^#".*\.png",/{p;s/\.png//;}' input