Combine count files into one file and keep zero values - bash

I have multiple count files that look like this:
File1.tab
6 10 0
49 0 53
15 0 15
0 0 0
0 0 0
0 0 0
Other file:
File2.tab
3 1 2
29 0 29
4 0 4
0 0 0
0 0 0
0 0 0
I have over 30 files and I want to combine the second column of each file into one big file.
I know this question have already been asked and I found a similar here How to combine column from multiple text files?
I used the answer from previous question for my problem:
paste *.tab | awk '{i=2;while($i); {printf("%d ",$i);i+=3}printf("\n")}'
The problem is that zero values are not printed, I get something like this:
10 1
and I want something like this:
10 1
0 0
0 0
0 0
0 0
0 0
I cheked the printf format specifiers, but none works. How can I solve this problem?

You picked a bad "answer" to build on. Try this:
paste *.tab |
awk '{for (i=2; i<=NF; i+=3) printf "%s%s", (i>2?OFS:""), $i; print ""}'

Related

Splitting a large file containing multiple molecules

I have a file that contains 10,000 molecules. Each molecule is ending with keyword $$$$. I want to split the main files into 10,000 separate files so that each file will have only 1 molecule. Each molecule have different number of lines. I have tried sed on test_file.txt as:
sed '/$$$$/q' test_file.txt > out.txt
input:
$ cat test_file.txt
ashu
vishu
jyoti
$$$$
Jatin
Vishal
Shivani
$$$$
output:
$ cat out.txt
ashu
vishu
jyoti
$$$$
I can loop it through whole main file to create 10,000 separate files but how to delete the last molecule that was just moved to new file from main file. Or please suggest if there is a better method for it, which I believe there is. Thanks.
Edit1:
$ cat short_library.sdf
untitled.cdx
csChFnd80/09142214492D
31 34 0 0 0 0 0 0 0 0999 V2000
8.4660 6.2927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.4660 4.8927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2124 2.0951 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4249 2.7951 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
30 31 1 0 0 0 0
31 26 1 0 0 0 0
M END
> <Mol_ID> (1)
1
> <Formula> (1)
C22H24ClFN4O3
> <URL> (1)
http://www.selleckchem.com/products/Gefitinib.html
$$$$
Dimesna.cdx
csChFnd80/09142214492D
16 13 0 0 0 0 0 0 0 0999 V2000
2.4249 1.4000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
3.6415 2.1024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.8540 1.4024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.4904 1.7512 0.0000 Na 0 3 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
1 14 2 0 0 0 0
M END
> <Mol_ID> (2)
2
> <Formula> (2)
C4H8Na2O6S4
> <URL> (2)
http://www.selleckchem.com/products/Dimesna.html
$$$$
Here's a simple solution with standard awk:
LANG=C awk '
{ mol = (mol == "" ? $0 : mol "\n" $0) }
/^\$\$\$\$\r?$/ {
outFile = "molecule" ++fn ".sdf"
print mol > outFile
close(outFile)
mol = ""
}
' input.sdf
If you have csplit from GNU coreutils:
csplit -s -z -n5 -fmolecule test_file.txt '/^$$$$$/+1' '{*}'
This will do the whole job directly in bash:
molsplit.sh
#!/bin/bash
filenum=0
end=1
while read -r line; do
if [[ $end -eq 1 ]]; then
end=0
filenum=$((filenum + 1))
exec 3>"molecule${filenum}.sdf"
fi
echo "$line" 1>&3
if [[ "$line" = '$$$$' ]]; then
end=1
exec 3>&-
fi
done
Input is read from stdin, though that would be easy enough to change. Something like this:
./molsplit.sh < test_file.txt
ADDENDUM
From subsequent commentary, it seems that the input file being processed has Windows line endings, whereas the processing environment's native line ending format is UNIX-style. In that case, if the line-termination style is to be preserved then we need to modify how the delimiters are recognized. For example, this variation on the above will recognize any line that starts with $$$$ as a molecule delimiter:
#!/bin/bash
filenum=0
end=1
while read -r line; do
if [[ $end -eq 1 ]]; then
end=0
filenum=$((filenum + 1))
exec 3>"molecule${filenum}.sdf"
fi
echo "$line" 1>&3
case $line in
'$$$$'*) end=1; exec 3>&-;;
esac
done
The same statement that sets the current output file name also closes the previous one. close(_)^_ here is same as close(_)^0, which ensures the filename always increments for the next one, even if the close() action resulted in an error.
— if the output file naming scheme allows for leading-edge zeros, then change that bit to close(_)^(_<_), which ALWAYS results in a 1, for any possible string or number, including all forms of zero, the empty string, inf-inities, and nans.
mawk2 'BEGIN { getline __<(_ = "/dev/null")
ORS = RS = "[$][$][$][$][\r]?"(FS = RS)
__*= gsub("[^$\n]+", __, ORS)
} NF {
print > (_ ="mol" (__+=close(_)^_) ".txt") }' test_file.txt
The first part about getline from /dev/null neither sets $0 | NF nor modifies NR | FNR, but it's existence ensures the first time close(_) is called it wouldn't error out.
gcat -n mol12345.txt
1 Shivani
2 jyoti
3 Shivani
4 $$$$
it was reasonably speedy - from 5.60 MB synthetic test file created 187,710 files in 11.652 secs.

Add Columns Values with Shell

I've an input file which looks as below.
pmx . pmnosysrelspeechneighbr -m 1 -r
INFO: The ROP files contain suspected faulty counter values.
They have been discarded but can be kept with pmr/pmx option "k" (pmrk/pmxk) or highlighted with pmx option "s" (pmxs)
Date: 2017-11-04
Object Counter 14:45 15:00 15:15 15:30
UtranCell=UE1069XA0 pmNoSysRelSpeechNeighbr 0 1 0 0
UtranCell=UE1069XA1 pmNoSysRelSpeechNeighbr 0 0 0 0
UtranCell=UE1069XA2 pmNoSysRelSpeechNeighbr 0 0 0 0
UtranCell=UE1069XA3 pmNoSysRelSpeechNeighbr 0 0 2 0
UtranCell=UE1069XB0 pmNoSysRelSpeechNeighbr 0 0 0 0
UtranCell=UE1069XB1 pmNoSysRelSpeechNeighbr 0 0 0 3
UtranCell=UE1069XB2 pmNoSysRelSpeechNeighbr 0 0 0 0
UtranCell=UE1069XB3 pmNoSysRelSpeechNeighbr 0 0 0 0
UtranCell=UE1069XC0 pmNoSysRelSpeechNeighbr 0 0 0 0
UtranCell=UE1069XC1 pmNoSysRelSpeechNeighbr 0 0 0 4
UtranCell=UE1069XC2 pmNoSysRelSpeechNeighbr 0 0 0 0
UtranCell=UE1069XC3 pmNoSysRelSpeechNeighbr 0 0 1 0
UtranCell=UE1164XA0 pmNoSysRelSpeechNeighbr 0 3 0 0
UtranCell=UE1164XA1 pmNoSysRelSpeechNeighbr 0 0 0 0
UtranCell=UE1164XA2 pmNoSysRelSpeechNeighbr 1 0 0 0
Now I want the output as below which is basically sum of the time column (from $3 to $6) values.
Counter 14:45 15:00 15:15 15:30
pmNoSysRelSpeechNeighbr 1 4 3 7
I've been trying with below command. But it's just giving sum of one column values:
pmx . pmnosysrelspeechneighbr -m 1 -r | grep - i ^Object| awk '{sum += $4} END {print $1 , sum}'
Try this out, you will get both header and trailer as sum of individual columns.
BEGIN {
trail="pmNoSysRelSpeechNeighbr";
}
{
if($1=="Object") print $2 OFS $3 OFS $4 OFS $5 OFS $6;
else if($1 ~ /^UtranCell/) {
w+=$3; x+=$4; y+=$5; z+=$6;
}
}
END {
print trail OFS w OFS x OFS y OFS z;
}
You need to sum each of the columns separately:
awk -v g=pmNoSysRelSpeechNeighbr '$0 ~ g { for(i=3;i<=6;i++) sum[i]+=$i }
END { printf g; for(i=3;i<=6;i++) printf OFS sum[i] }' file
but only for lines (records) containing the group (counter) of interest ($0~"pmNoSysRelSpeechNeighbr").
Note you (almost) never need to pipe grep's output to awk, because awk already supports extended regular expressions filtering with /regex/ { action }, or var ~ /regex/ { action }. One exception would be the need for PCRE (grep -P).
As an alternative to awk for simple "command-line statistical operations" on textual files, you could also use GNU datamash.
For example, to sum columns 3 to 6, but group by column 2:
grep 'UtranCell' file | datamash -W -g2 sum 3-6

Find header value for first occurance of "1" instance in column

I have a matrix example:
1 3 5 8 10 12
50 1 1 1 1 1 1
100 0 0 1 1 1 1
150 0 0 1 1 1 1
200 0 0 0 1 1 1
250 0 0 0 0 1 1
300 0 0 0 0 1 1
350 0 0 0 0 0 1
For each row name (50, 100, 150, 200, etc.) I want to know what is the "header" value when the instance "1" first occurs. Based on the example the answer is:
50 1
100 5
150 5
200 8
250 10
300 10
350 12
I am not sure how to play with IFs and WHENs to get my answer from this format. R, Excel, bash, awk, all welcome as solutions.
You can do this using awk as following :
$ awk 'FNR==1{for(i=1; i<=NF; i++){a[i]=$i}; next} {for(i=2; i<=NF; i++){if($i=="1"){print $1, a[i-1]; break}}} ' file
50 1
100 5
150 5
200 8
250 10
300 10
350 12
Explanation :
For header i.e FNR==1 we are populating all values in the array a;
For all next lines we are checking which field equates to 1, if found print the col1 value i.e $1 and the corresponding value in the array a and break the loop.
Awk solution:
awk 'NR==1{ for(i=1;i<=NF;i++) h[i]=$i; next }
{
for(i=2;i<=NF;i++) { if($i==1) { n=h[i-1]; break } }
print $1,(n)?n:"None"; n=""
}' file

Removing duplicate lines with different columns

I have a file which looks like follows:
ENSG00000197111:I12 0
ENSG00000197111:I12 1
ENSG00000197111:I13 0
ENSG00000197111:I18 0
ENSG00000197111:I2 0
ENSG00000197111:I3 0
ENSG00000197111:I4 0
ENSG00000197111:I5 0
ENSG00000197111:I5 1
I have some lines that are duplicated but I cannot remove by sort -u because the second column has different values for them (1 or 0). How do I remove such duplicates by keeping the lines with second column as 1 such that the file will be
ENSG00000197111:I12 1
ENSG00000197111:I13 0
ENSG00000197111:I18 0
ENSG00000197111:I2 0
ENSG00000197111:I3 0
ENSG00000197111:I4 0
ENSG00000197111:I5 1
you can use awk and or operator, if the order isn't mandatory
awk '{d[$1]=d[$1] || $2}END{for(k in d) print k, d[k]}' file
you get
ENSG00000197111:I2 0
ENSG00000197111:I3 0
ENSG00000197111:I4 0
ENSG00000197111:I5 1
ENSG00000197111:I12 1
ENSG00000197111:I13 0
ENSG00000197111:I18 0
Edit, only sort solution
You can use sort with a double pass, example
sort -k1,1 -k2,2r file | sort -u -k1,1
you get,
ENSG00000197111:I12 1
ENSG00000197111:I13 0
ENSG00000197111:I18 0
ENSG00000197111:I2 0
ENSG00000197111:I3 0
ENSG00000197111:I4 0
ENSG00000197111:I5 1

bash script awk with passing variable and if statement

I am writing a bash script using awk with variable passing in AIX powerpc machine.
The code written works fine after I read some questions & answers in this site. :)
Now, I'd like to add if statement in my bash script and I got awk syntax errors.
My requirement (see my script below):
- if awk pattern matching is true, print $0
- else print "transaction: p value not found."
Content of trans.txt
bash-4.2$ cat trans.txt
10291413
8537353
8619033
8619065
8625705
Could someone help me please. Thank you.
content of getDetail.sh
#!/usr/bin/bash
sysDir="/var/syslog-ng/TEST/STS"
syslogFile="DPSTSLog2014-10-22T09.log"
pattern="Latency"
filename=$1
while read f; do
concatPattern="$f.*$pattern"
awk -v p="$concatPattern" '$0 ~ p {print $0}' $sysDir/$syslogFile
done < $filename
run command execution below
./getDetails.sh trans.txt
result
2014-10-22T09:15:53+11:00,10.16.198.50,info,latency,[info] xmlfirewall(ws-TrustValidate): trans(10291413): Latency: 0 0 0 0 14 14 0 14 0 0 0 14 0 0 0 0
2014-10-22T09:15:38+11:00,10.16.198.50,info,latency,[info] xmlfirewall(ws-TrustValidate): trans(8619033): Latency: 0 0 0 0 73 73 0 73 0 0 0 73 0 0 0 0
2014-10-22T09:18:04+11:00,10.16.198.50,info,latency,[info] xmlfirewall(ws-TrustValidate): trans(8625705): Latency: 0 0 0 0 13 13 0 13 0 0 0 13 0 0 0 0
awk -v p="$concatPattern" '
$0 ~ p {print $0; found=1}
END {if (! found) print "transaction: p value not found"}
' $sysDir/$syslogFile

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