After analysis of brain scans I ended up with around 1000 .csv files, one for each scan. I've merged them into one in order (by subject ID and date). My problem is, that some subjects had two or more consecutive scans and some had only one. Database now looks like that:
ID, CC_area, CC_perimeter, CC_circularity
024_S_0985, 407.00, 192.15, 0.138530 //first scan of A
024_S_0985, 437.50, 204.80, 0.131074 //second scan of A
024_S_0985, 400.75, 198.80, 0.127420 //third scan of A
024_S_1063, 544.50, 214.34, 0.148939 //first and only scan of B
024_S_1171, 654.75, 240.33, 0.142453 //first scan of C
024_S_1171, 659.50, 242.21, 0.141269 //second scan of C
...
But I want it to look like that:
ID, CC_area, CC_perimeter, CC_circularity, CC_area2, CC_perimeter2, CC_circularity2, CC_area3, CC_perimeter3, CC_circularity3, ..., CC_circularity6
024_S_0985, 407.00, 192.15, 0.138530, 437.50, 204.80, 0.131074, 400.75, 198.80, 0.127420, ... ,
024_S_1063, 544.50, 214.34, 0.148939,,,,,, ...,
024_S_1171, 654.75, 240.33, 0.142453, 659.50, 242.21, 0.141269,,, ... ,
...
What is important, that order of data must not be changed and number of rows for one ID is not known (it varies from 1 to 6). (So first columns of scan 1, then scan 2 etc.). Could you help me, or provide, with solution for that using bash? I am not experienced in programming and I have lost hope, that I could do it myself.
You can combine the line with the same filename (or initial index) using a normal while read loop and then acting on 3 conditions. (1) whether it is the first line following the header; (2) where the current index is equal to the last; and (3) where the current index differs from the last. There are a number of ways to approach this, but a short bash script could look like the following:
#!/bin/bash
fn="${1:-/dev/stdin}" ## accept filename or stdin
[ -r "$fn" ] || { ## validate file is readable
printf "error: file not found: '%s'\n" "$fn"
exit 1
}
declare -i cnt=0 ## flag for 1st iteration
while read -r line; do ## for each line in file
## read header, print & continue
[ ${line//,*/} = ID ] && printf "%s\n" "$line" && continue
line="${line// */}" ## strip //first scan of A....
idx=${line//,*/} ## parse file index from line
line="${line#*, }" ## strip index
if [ $cnt -eq 0 ]; then ## if first line - print
printf "%s, %s" "$idx" "$line"
((cnt++))
elif [ $idx = $lidx ]; then ## if indexes equal, append
printf ", %s" "$line"
else ## else, newline & print
printf "\n%s, %s" "$idx" "$line"
fi
last="$line" ## save last line
lidx=$idx ## save last index
done <"$fn"
printf "\n"
Input
$ cat dat/cmbcsv.dat
ID, CC_area, CC_perimeter, CC_circularity
024_S_0985, 407.00, 192.15, 0.138530 //first scan of A
024_S_0985, 437.50, 204.80, 0.131074 //second scan of A
024_S_0985, 400.75, 198.80, 0.127420 //third scan of A
024_S_1063, 544.50, 214.34, 0.148939 //first and only scan of B
024_S_1171, 654.75, 240.33, 0.142453 //first scan of C
024_S_1171, 659.50, 242.21, 0.141269 //second scan of C
Output
$ bash cmbcsv.sh dat/cmbcsv.dat
ID, CC_area, CC_perimeter, CC_circularity
024_S_0985, 407.00, 192.15, 0.138530, 437.50, 204.80, 0.131074, 400.75, 198.80, 0.127420
024_S_1063, 544.50, 214.34, 0.148939
024_S_1171, 654.75, 240.33, 0.142453, 659.50, 242.21, 0.141269
Note: I didn't know whether you needed all the additional commas or ellipses or if they were just there to show there could be more of the same index (e.g. ,,...,). You can easily add them if need be.
well if you know which scan belongs to which person you can add an extra column like patient name or id, but I guess that's if you have that original info of how much scans per person
Related
I'm trying to create a shell script that will create multiple files (or a batch of files) of a specified amount. When the amount is reached, script stops. When the script is re-executed, the files pick up from the last file created. So if the script creates files 1-10 on first run, then on the next script execution should create 11-20, and so on.
enter code here
#!/bin/bash
NAME=XXXX
valid=true
NUMBER=1
while [ $NUMBER -le 5 ];
do
touch $NAME$NUMBER
((NUMBER++))
echo $NUMBER + "batch created"
if [ $NUMBER == 5 ];
then
break
fi
touch $NAME$NUMBER
((NUMBER+5))
echo "batch complete"
done
Based on my comment above and your description, you can write a script that will create 10 numbered files (by default) each time it is run, starting with the next available number. As mentioned, rather than just use a raw-unpadded number, it's better for general sorting and listing to use zero-padded numbers, e.g. 001, 002, ...
If you just use 1, 2, ... then you end up with odd sorting when you reach each power of 10. Consider the first 12 files numbered 1...12 without padding. a general listing sort would produce:
file1
file11
file12
file2
file3
file4
...
Where 11 and 12 are sorted before 2. Adding leading zeros with printf -v avoids the problem.
Taking that into account, and allowing the user to change the prefix (first part of the file name) by giving it as an argument, and also change the number of new files to create by passing the count as the 2nd argument, you could do something like:
#!/bin/bash
prefix="${1:-file_}" ## beginning of filename
number=1 ## start number to look for
ext="txt" ## file extension to add
newcount="${2:-10}" ## count of new files to create
printf -v num "%03d" "$number" ## create 3-digit start number
fname="$prefix$num.$ext" ## form first filename
while [ -e "$fname" ]; do ## while filename exists
number=$((number + 1)) ## increment number
printf -v num "%03d" "$number" ## form 3-digit number
fname="$prefix$num.$ext" ## form filename
done
while ((newcount--)); do ## loop newcount times
touch "$fname" ## create filename
((! newcount)) && break; ## newcount 0, break (optional)
number=$((number + 1)) ## increment number
printf -v num "%03d" "$number" ## form 3-digit number
fname="$prefix$num.$ext" ## form filename
done
Running the script without arguments will create the first 10 files, file_001.txt - file_010.txt. Run a second time, it would create 10 more files file_011.txt to file_020.txt.
To create a new group of 5 files with the prefix of list_, you would do:
bash scriptname list_ 5
Which would result in the 5 files list_001.txt to list_005.txt. Running again with the same options would create list_006.txt to list_010.txt.
Since the scheme above with 3 digits is limited to 1000 files max (if you include 000), there isn't a big need to get the number from the last file written (bash can count to 1000 quite fast). However, if you used 7-digits, for 10 million files, then you would want to parse the last number with ls -1 | tail -n 1 (or version sort and choose the last file). Something like the following would do:
number=$(ls -1 "$prefix"* | tail -n 1 | grep -o '[1-9][0-9]*')
(note: that is ls -(one) not ls -(ell))
Let me know if that is what you are looking for.
I have read multiple posts about how to exclude lines around a grep match, but none addresses it with finality, most find other ways to sort data, and that does not solve similar issues with different data.
i have a file with a recursive output, a command repeated over and over. i want to trim out the 0 results because it is the only constant value, the result hits are an unknown quantity.
the only unique string i can search by needs to have the 4 lines above it excluded no matter what the content of those lines are, and i have not found any post with info generic enough to fit.
this is a conceptual question, there has to be a simple solution, but if an example is needed:
Path/Path/Path> search
[results]
[results]
2 entries found
Path/Path/Path> search
[result]
1 entry found
Path/Path/Path> search
0 entry found
try this:
# Assumption: The data is in logile.txt
i=0
tac logfile.txt |\
while read -r line; do
if [[ "${line:0:7}" == "0 entry" ]]; then
i=0
continue
else
((i++))
[[ $i -le 4 ]] && continue
fi
echo "$line"
done | tac
output:
Path/Path/Path> search
[results]
[results]
2 entries found
I am trying to create a Bash script that
- prints a random word
- if a number is supplied as the first command line argument then it will select from only words with that many characters.
This is my go at the first section (print a random word):
C=$(sed -n "$RANDOM p" /usr/share/dict/words)
echo $C
I am really stuck with the second section. Can anyone help?
might help someone coming from ryans tutorial
#!/bin/bash
charlen=$1
grep -E "^.{$charlen}$" $PWD/words.txt | shuf -n 1
you have to use a while loop to read every single line of that file and check if the length of a word equals the specified number ( including apostrophes ). In my o.s it is 99171 line ( i.e the file).
#!/usr/bin/env bash
readWords() {
declare -i int="$1"
(( int == 0 )) && {
printf "%s\n" "$int is 0, cant find 0 words"
return 1
}
while read getWords;do
if [[ ${#getWords} -eq $int ]];then
printf "%s\n" "$getWords"
fi
done < /usr/share/dict/words
}
readWords 20
this function takes a single argument. the declare command coerces the argument into an integer, if the argument is a string , it coerces it into a number which is 0 . Since we don't have 0 words if the specified argument ( number ) is 0 ( or a string coerced to 0 ) return from the function.
Read every single line in /usr/share/dict/words, get the length of each line with ${#getWords} ( $# >> gives the length of a string/commandline parameters/array size ) check if it equals the specified argument ( number )
A loop is not required, you can do something like
CH=$1; # how many characters the word must have
WordFile=/usr/share/dict/words; # file to read from
# find how many words that matches that length
TOTW=$(grep -Ec "^.{$CH}$" $WordFile);
# pick a random one, if you expect more than 32767 hits you
# need to do something like ($RANDOM+1)*($RANDOM+1)
RWORD=$(($RANDOM%$TOTW+1));
#show that word
grep -E "^.{$CH}$" $WordFile|sed -n "$RWORD p"
Depending on things you probably need to add checks for things like that $1 is a reasonable number, the file exist, that TOTW is >0 and so on.
This code would achieve what you want:
awk -v n="$1" 'length($0) == n' /usr/share/dict/words > /tmp/wordsHolder
shuf -n 1 /tmp/wordsHolder
Some comments: by using "$RANDOM" (as you did on your original script attempt), one would generate an integer on the range 0 - 32767, which could be more (or less) than the number of words (lines) available, given the desired number of characters on a word -- thus, potential for errors here.
To avoid that, we are using a shuf syntax that will retrieve a (sub)randomly picked word (line) on the file using its entire range (from line 1 - last line of file).
I'm working with a very large text file (4GB) and I want to make a smaller file with only the data I need in it. It is a tab deliminated file and there are row and column headers. I basically want to select a subset of the data that has a given column and/or row name.
colname_1 colname_2 colname_3 colname_4
row_1 1 2 3 5
row_2 4 6 9 1
row_3 2 3 4 2
I'm planning to have a file with a list of the columns I want.
colname_1 colname_3
I'm a newbie to bash scripting and I really don't know how to do this. I saw other examples, but they all new what column number they wanted in advance and I don't. Sorry if this is a repeat question, I tried to search.
I would want the result to be
colname_1 colname_3
row_1 1 3
row_2 2 9
row_3 2 4
Bash works best as "glue" between standard command-line utilities. You can write loops which read each line in a massive file, but it's painfully slow because bash is not optimized for speed. So let's see how to use a few standard utilities -- grep, tr, cut and paste -- to achieve this goal.
For simplicity, let's put the desired column headings into a file, one per line. (You can always convert a tab-separated line of column headings to this format; we're going to do just that with the data file's column headings. But one thing at a time.)
$ printf '%s\n' colname_{1,3} > columns
$ cat columns
colname_1
colname_2
An important feature of the printf command-line utility is that it repeats its format until it runs out of arguments.
Now, we want to know which column in the data file each of these column headings corresponds to. We could try to write this as a loop in awk or even in bash, but if we convert the header line of the data file into a file with one header per line, we can use grep to tell us, by using the -n option (which prefixes the output with the line number of the match).
Since the column headers are tab-separated, we can get turn them into separate lines just by converting tabs to newlines using tr:
$ head -n1 giga.dat | tr '\t' '\n'
colname_1
colname_2
colname_3
colname_4
Note the blank line at the beginning. That's important, because colname_1 actually corresponds to column 2, since the row headers are in column 1.
So let's look up the column names. Here, we will use several grep options:
-F The pattern argument consists of several patterns, one per line, which are interpreted as ordinary strings instead of regexes.
-x The pattern must match the complete line.
-n The output should be prefixed by the line number of the match.
If we have Gnu grep, we could also use -f columns to read the patterns from the file named columns. Or if we're using bash, we could use the bashism "$(<columns)" to insert the contents of the file as a single argument to grep. But for now, we'll stay Posix compliant:
$ head -n1 giga.dat | tr '\t' '\n' | grep -Fxn "$(cat columns)"
2:colname_1
4:colname_3
OK, that's pretty close. We just need to get rid of everything other than the line number; comma-separate the numbers, and put a 1 at the beginning.
$ { echo 1
> grep -Fxn "$(<columns)" < <(head -n1 giga.dat | tr '\t' '\n')
> } | cut -f1 -d: | paste -sd,
1,2,4
cut -f1 Select field 1. The argument could be a comma-separated list, as in cut -f1,2,4.
cut -d: Use : instead of tab as a field separator ("delimiter")
paste -s Concatenate the lines of a single file instead of corresponding lines of several files
paste -d, Use a comma instead of tab as a field separator.
So now we have the argument we need to pass to cut in order to select the desired columns:
$ cut -f"$({ echo 1
> head -n1 giga.dat | tr '\t' '\n' | grep -Fxn -f columns
> } | cut -f1 -d: | paste -sd,)" giga.dat
colname_1 colname_3
row_1 1 3
row_2 4 9
row_3 2 4
You can actually do this by keeping track of the array indexes for the columns that match the column names in your file containing the column list. After you have found the array indexes in the data file for the column names in your column list file, you simply read your data file (beginning at the second line) and output the row_label plus the data for the columns at the array index you determined in matching the column list file to the original columns.
There are probably several ways to approach this and the following assumes the data in each column does not contain any whitespace. The use of arrays presumes bash (or other advanced shell supporting arrays) and not POSIX shell.
The script takes two file names as input. The first is your original data file. The second is your column list file. An approach could be:
#!/bin/bash
declare -a cols ## array holding original columns from original data file
declare -a csel ## array holding columns to select (from file 2)
declare -a cpos ## array holding array indexes of matching columns
cols=( $(head -n 1 "$1") ) ## fill cols from 1st line of data file
csel=( $(< "$2") ) ## read select columns from file 2
## fill column position array
for ((i = 0; i < ${#csel[#]}; i++)); do
for ((j = 0; j < ${#cols[#]}; j++)); do
[ "${csel[i]}" = "${cols[j]}" ] && cpos+=( $j )
done
done
printf " "
for ((i = 0; i < ${#csel[#]}; i++)); do ## output header row
printf " %s" "${csel[i]}"
done
printf "\n" ## output newline
unset cols ## unset cols to reuse in reading lines below
while read -r line; do ## read each data line in data file
cols=( $line ) ## separate into cols array
printf "%s" "${cols[0]}" ## output row label
for ((j = 0; j < ${#cpos[#]}; j++)); do
[ "$j" -eq "0" ] && { ## handle format for first column
printf "%5s" "${cols[$((${cpos[j]}+1))]}"
continue
} ## output remaining columns
printf "%13s" "${cols[$((${cpos[j]}+1))]}"
done
printf "\n"
done < <( tail -n+2 "$1" )
Using your example data as follows:
Data File
$ cat dat/col+data.txt
colname_1 colname_2 colname_3 colname_4
row_1 1 2 3 5
row_2 4 6 9 1
row_3 2 3 4 2
Column Select File
$ cat dat/col.txt
colname_1 colname_3
Example Use/Output
$ bash colnum.sh dat/col+data.txt dat/col.txt
colname_1 colname_3
row_1 1 3
row_2 4 9
row_3 2 4
Give it a try and let me know if you have any questions. Note, bash isn't known for its blinding speed handling large files, but as long as the column list isn't horrendously long, the script should be reasonably fast.
I have a simple search script, where based on user's options it will search in certain column of a file.
The file looks similar to passwd
openvpn:x:990:986:OpenVPN:/etc/openvpn:/sbin/nologin
chrony:x:989:984::/var/lib/chrony:/sbin/nologin
rpcuser:x:29:29:RPC Service User:/var/lib/nfs:/sbin/nologin
nfsnobody:x:65534:65534:Anonymous NFS User:/var/lib/nfs:/sbin/nologin
radvd:x:75:75:radvd user:/:/sbin/nologin
now the function based on user's option will search in different columns of the file. For example
-1 "searchedword" -2 "secondword"
will search in the first column for "searchedword" and in the second column for "secondword"
The function looks like this:
while [ $# -gt 0 ]; do
case "$1" in
-1|--one)
c=1
;;
-2|--two)
c=2
;;
-3|--three)
c=3
;;
...
esac
In the c variable is the number of the column where I want to search.
cat data | if [ "$( cut -f $c -d ':' )" == "$2" ]; then cut -d: -f 1-7 >> result; fi
Now I have something like this, where I try to select the right column and compare it to the second option, which is in this case "searchedword" and then copy the whole column into the result file. But it doesn't work. It doesn't copy anything into the result file.
Does anyone know where is the problem?
Thanks for answers
(At the end of the script I use:
shift
shift
to get the next two options)
I suggest using awk for this task as awk is better tool for processing delimited columns and rows.
Consider this awk command where we pass search column numbers their corresponding search values in 2 different strings cols and vals to awk command:
awk -v cols='1:3' -v vals='rpcuser:29' 'BEGIN {
FS=OFS=":" # set input/output field separator as :
nc = split(cols, c, /:/) # split column # by :
split(vals, v, /:/) # split values by :
}
{
p=1 # initialize p as 1
for(i=1; i<=nc; i++) # iterate the search cols/vals and set p=0
if ($c[i] !~ v[i]) { # if any match fails
p=0
break
} # finally value of p decides if a row is printing or not
} p' file
Output:
rpcuser:x:29:29:RPC Service User:/var/lib/nfs:/sbin/nologin