I want to run awk on several files. I have the filenames and a path to the files, but I can't seem to connect the two. Here's what I have tried:
files=(a b c)
directory=/my/dir
awk $my_script "$directory/${files[#]}"
It awks the first file and leaves the rest alone. I'd rather not have to add the full path in my array (the values are used in several places). I think I want brace expansion, but it doesn't seem to work with arrays. What else could I do?
Using pattern substitution (# means something like ^ in regexps): ${files[#]/#/$directory/}
for i in /my/dir/[abc]; do
awk $my_script "$i"
done
Or, if you want to actually just pass all of the file names to awk at once:
awk $my_script /my/dir/[abc]
If the file names are not actually single letters:
awk $my_script /my/dir/{file1,file2,file3,...}
Related
I have a large taxonomy file that I need to edit. There is an issue with the file as "Candida" is listed as both Candida and [Candida]. What I want to do is change every case of [Candida] to Candida within the file.
I have tried doing this several ways but never get the output I am after. This is the first few lines of the taxonomy file:
Penicillium;marneffei;NW_002197112.1
Penicillium;marneffei;NW_002197111.1
Penicillium;marneffei;NW_002197110.1
Penicillium;marneffei;NW_002197109.1
Penicillium;marneffei;NW_002197108.1
Using sed gives me this output:
$ sed -i -e 's/[Candida]/Candida/g' Full_HMS_Taxonomy.txt
PeCandidaCandidacCandidallCandidaum;mCandidarCandidaeffeCandida;NW_002197112.1
PeCandidaCandidacCandidallCandidaum;mCandidarCandidaeffeCandida;NW_002197111.1
PeCandidaCandidacCandidallCandidaum;mCandidarCandidaeffeCandida;NW_002197110.1
PeCandidaCandidacCandidallCandidaum;mCandidarCandidaeffeCandida;NW_002197109.1
PeCandidaCandidacCandidallCandidaum;mCandidarCandidaeffeCandida;NW_002197108.1
Using awk gives me this output:
$ awk '{gsub(/[Candida]/,"Candida")}1' Full_HMS_Taxonomy.txt
PeCandidaCandidacCandidallCandidaum;mCandidarCandidaeffeCandida;NW_002197112.1
PeCandidaCandidacCandidallCandidaum;mCandidarCandidaeffeCandida;NW_002197111.1
PeCandidaCandidacCandidallCandidaum;mCandidarCandidaeffeCandida;NW_002197110.1
PeCandidaCandidacCandidallCandidaum;mCandidarCandidaeffeCandida;NW_002197109.1
PeCandidaCandidacCandidallCandidaum;mCandidarCandidaeffeCandida;NW_002197108.1
In both cases it is adding Candida to multiple places and multiple lines, instead of just replacing each instance of [Candida]. Any ideas on what I am doing wrong?
[] are special characters in regexp, so you should escape them like that:
's/\[Candida\]/Candida/g'
Brackets are treated specially by regular expression parsers, matching each character listed inside them. So, [Candida] matches any of the characters inside it (C, a, n...). That's why you get a lot of substitutions.
You need to tell those utilities that you want literal brackets by escaping them with backslashes, e.g. with sed:
sed -i 's/\[Candida\]/Candida/g' Full_HMS_Taxonomy.txt
I was wondering if it was possible to use the sed command to find a range between 2 patterns (in this case, dates) and output these lines in the range to a new file.
Right now, I am just looking at one file and getting lines within my time range of the file FileMoverTransfer.log. However, after a certain time period, these logs are moved to new log files with a suffix such as FileMoverTransfer.log-20180404-xxxxxx.gz. Here is my current code:
sed -n '/^'$start_date'/,/^'$end_date'/p;/^'$end_date'/q' FileMoverTransfer.log >> /public/FileMoverRoot/logs/intervalFMT.log
While this doesn't work, as sed isn't able to look through all of the files in the directory starting with FileMoverTransfer.log?
sed -n '/^'$start_date'/,/^'$end_date'/p;/^'$end_date'/q' FileMoverTransfer.log* >> /public/FileMoverRoot/logs/intervalFMT.log
Any help would be greatly appreciated. Thanks!
The range operator only operates within a single file, so you can't use it if the start is in one file and the end is in another file.
You can use cat to concatenate all the files, and pipe this to sed:
cat FileMoverTransfer.log* | sed -n "/^$start_date/,/^$end_date/p;/^$end_date/q" >> /public/FileMoverRoot/logs/intervalFMT.log
And instead of quoting and unquoting the sed command, you can use double quotes so that the variables will be expanded inside it. This will also prevent problems if the variables contain whitespace.
awk solution
As the OP confirmed that an awk solution would be acceptable, I post it.
(gunzip -c FileMoverTransfer.log-*.gz; cat FileMoverTransfer.log ) \
|awk -v st="$start_date" -v en="$end_date" '$1>=st&&$1<=en{print;next}$1>en{exit}'\
>/public/FileMoverRoot/logs/intervalFMT.log
This solution is functionally almost identical to Barmar’s sed solution, with the difference that his solution, like the OP’s, will print and quit at the first record matching the end date, while mine will print all lines matching the end date and quit at the first record past the end date, without printing it.
Some remarks:
The OP didn't specify the date format. I suppose it is a format compatible with ordinary string order, otherwise some conversion function should be used.
The files FileMoverTransfer.log-*.gz must be named in such a way that their alphabetical ordering corresponds to the chronological order (which is probably the case.)
I suppose that the dates are separated from the rest of the line by whitespace. If they aren’t, you have to supply the -F option to awk. E.g., if the dates are separated by -, you must write awk -F- ...
awk is much faster than sed in this case, because awk simply looks for the separator (whitespace or whatever was supplied with -F) while sed performs a regexp match.
There is no concept of range in my code, only date comparison. The only place where I suppose that the lines are ordered is when I say $1>en{exit}, that is exit when a line is newer than the end date. If you remove that final pattern and its action, the code will run through the whole input, but you could drop the requirement that the files be ordered.
I need to generate filename from three parts, two strings, and one variable.
for f in `cat files.csv`; do echo fastq/$f\_1.fastq.gze; done
files.csv has the following lines:
Sample_11
Sample_12
I need to generate the following:
fastq/Sample_11_1.fastq.gze
fastq/Sample_12_1.fastq.gze
My problem is that I got the below files:
_1.fastq.gze_11
_1.fastq.gze_12
the string after the variable deletes the string before it.
I appreciate any help
Regards
By the way your idiom: for f in cat files.csv should be avoid. Refer: Dangerous Backticks
while read f
do
echo "fastq/${f}/_1.fastq.gze"
done < files.csv
You can make it a one-liner with xargs and printf.
xargs printf 'fastq/%s_1.fastq.gze\n' <files.csv
The function of printf is to apply the first argument (the format string) to each argument in turn.
xargs says to run this command on as many files as it can fit onto the command line (splitting it up into multiple invocations if the input file is too large to fit all the arguments onto a single command line, subject to the ARG_MAX constant in your kernel).
Your best bet, generally, is to wrap the variable name in braces. So, in this case:
echo fastq/${f}_1.fastq.gz
See this answer for some details about the general concept, as well.
Edit: An additional thought looking at the now-provided output makes me think that this isn't a coding problem at all, but rather a conflict between line-endings and the terminal/console program.
Specifically, if the CSV file ends its lines with just a carriage return (ASCII/Unicode 13), the end of Sample_11 might "rewind" the line to the start and overwrite.
In that case, based loosely on this article, I'd recommend replacing cat (if you understandably don't want to re-architect the actual script with something like while) with something that will strip the carriage returns, such as:
for f in $(tr -cd '\011\012\040-\176' < temp.csv)
do
echo fastq/${f}_1.fastq.gze
done
As the cited article explains, Octal 11 is a tab, 12 a line feed, and 40-176 are typeable characters (Unicode will require more thinking). If there aren't any line feeds in the file, for some reason, you probably want to replace that with tr '\015' '\012', which will convert the carriage returns to line feeds.
Of course, at that point, better is to find whatever produces the file and ask them to put reasonable line-endings into their file...
I have several files named scale1.dat, scale2.dat scale3.dat ... up to scale9.dat.
I want to read these files in do loop one by one and with each file I want to do some manipulation (I want to write the 1st column of each scale*.dat file to scale*.txt).
So my question is, is there a way to read files with similar names. Thanks.
The regular syntax for this is
for file in scale*.dat; do
awk '{print $1}' "$file" >"${file%.dat}.txt"
done
The asterisk * matches any text or no text; if you want to constrain to just single non-zero digits, you could say for file in scale[1-9].dat instead.
In Bash, there is a non-standard additional glob syntax scale{1..9}.dat but this is Bash-only, and so will not work in #!/bin/sh scripts. (Your question has both sh and bash so it's not clear which you require. Your comment that the Bash syntax is not working for you suggests that you may need a POSIX portable solution.) Furthermore, Bash has something called extended globbing, which allows for quite elaborate pattern matching. See also http://mywiki.wooledge.org/glob
For a simple task like this, you don't really need the shell at all, though.
awk 'FNR==1 { if (f) close (f); f=FILENAME; sub(/\.dat/, ".txt", f); }
{ print $1 >f }' scale[1-9]*.dat
(Okay, maybe that's slightly intimidating for a first-timer. But the basic point is that you will often find that the commands you want to use will happily work on multiple files, and so you don't need shell loops at all in those cases.)
I don't think so. Similar names or not, you will have to iterate through all your files (perhaps with a for loop) and use a nested loop to iterate through lines or words or whatever you plan to read from those files.
Alternatively, you can copy your files into one (say, scale-all.dat) and read that single file.
Im trying to replace numbers in my textfile by adding one to them. i.e.
sed 's/3/4/g' path.txt
sed 's/2/3/g' path.txt
sed 's/1/2/g' path.txt
Instead of this, Can i automate it, i.e. find a /d and add one to it in the replace.
Something like
sed 's/\([0-8]\)/\1+1/g' path.txt
Also wanted to capture more than one digit i.e. ([0-9])\t([0-9]) and change each one keeping the tab inbetween
Thanks
edited #2
Using the perl example,
I also would like it to work with more digits i.e.
perl -pi~ -e 's/(\d+)\.(\d+)\.(\d+)\.(\d+)/ ($1+1)\.($2+1)\.($3+1)\.($4+1) /ge' output.txt
Any tips on making the above work?
There is no support for arithmetic in sed, but you can easily do this in Perl.
perl -pe 's/(\d+)/ $1+1 /ge'
With the /e option, the replacement expression needs to be valid Perl code. So to handle your final updated example, you need
perl -pi~ -e 's/(\d+)\.(\d+)\.(\d+)\.(\d+)/ $1+1 . "." $2+1 . "." . $3+1 . "." . $4+1 /ge'
where strings are properly quoted and adjacent strings are concatenated together with the . Perl string concatenation operator. (The arithmetic numbers are coerced into strings as well when they are concatenated with a string.)
... Though of course, the first script already does that more elegantly, since with the /g flag it already increments every sequence of digits with one, anywhere in the string.
Triplee's perl solution is the more generic answer, but Michal's sed solution works well for this particular case. However, Michal's sed solution is more easily written:
sed y/12345678/23456789/ path.txt
and is better implemented as
tr 12345678 23456789 < path.txt
This utterly fails to handle 2 digit numbers (as in the edited question).
You can do it with sed but it's not easy, see this thread.
And it's hard with awk too, see this.
I'd rather use perl for this (something like this can be seen in action # ideone):
perl -pe 's/([0-8])/$1+1/e'
(The ideone.com example must have some looping as ideone does not sets -pe by default.)
You can't do addition directly in sed - you could do it in awk by matching numbers using a regex in each line and increasing the value, but it's quite complicated. If do not need to handle arbitrary numbers but a limited set, like only single-digit numbers from 0 to 8, you can just put several replacement commands on a single sed command line by separating them with semicolons:
sed 's/8/9/g ; s/7/8/g; s/6/7/g; s/5/6/g; s/4/5/g; s/3/4/g; s/2/3/g; s/1/2/g; s/0/1/g' path.txt
This might work for you (GNU sed & Bash):
sed 's/[0-9]/$((&+1))/g;s/.*/echo "&"/e' file
This will add one to every individual digit, to increment numbers:
sed 's/[0-9]\+/$((&+1))/g;s/.*/echo "&"/e' file
N.B. This method is fraught with problems and may cause unexpected results.