Need to print specific lines of a large txt.gz file, using an index file
Hi all,
I found several examples for printing specific lines of a non-compressed files but could not find any solution for a very large gz file.
My index file (idx.txt) looks like this, and contains 700,000 indices:
1745
1746
7379
13920
13921
16681
16682
...
...
...
54830241
54867703
54867710
I would like to retrieve all these 700,000 lines in my other source file, which is a very large compressed CSV file with 55,000,000 rows and looks like this:
100035243,2,"Chronic obstructive pulmonary disease","SS","LETAIRIS","AMBRISENTAN","","Dyspnoea",NA,73,"F","","","CN"
100035672,1,"Myeloproliferative disorder","PS","JAKAFI","RUXOLITINIB","ORAL","Platelet count increased",20131206,48.501,"F","79.37","KG","OT"
100035914,1,"Multiple sclerosis","PS","GILENYA","FINGOLIMOD HYDROCHLORIDE","ORAL","Lymphocyte count decreased",20130718,47.154,"F","","","OT"
....
What I tried so far:
sed -nf idx.txt <(gzip -dc gzfile.gz) > output.txt
awk 'NR==FNR{i[$0];next}i[FNR]' idx.txt <(gzip -dc gzfile.gz) > output.txt
Both are very slow.
Any thoughts?
IMHO your awk code looks ok to me so there could be 1 way to increase its speed of processing. Though I am not sure(and since your samples are not clear so didn't test also), if your id.txt file's last entry is far lesser than total number of lines in .gz file then you could actually exit from awk code and NO need to read Input_files, try it out once.
awk 'NR==FNR{i[$0]=$0;last=$0;next} i[FNR]{print} FNR!=NR && FNR>last{exit}' idx.txt <(gzip -dc gzfile.gz) > output.txt
So what I am doing is, I am creating a variable named last here whose value should be last line value of ids.txt.Then in 2nd condition I am checking if line number is greater than value of last entry in ids.txt then exit from code.
EDIT: Changed OP's code from i[$0] to i[$0]=$0 in first condition since condition i[FNR] will only work when array i is having values. Changed it after user mentioned in comments.
PS: This will definitely save time only and only in case you have huge difference between last line value of ids.txt and total number of lines present in .gz file. Since I am going with your statement that you have very huge data.
Both sed and awk solutions looks good. Probably, sed one is faster than awk one. And probably they are the faster things you can get. To reduce time... reduce the input file size.
One extra thing you can do is to stop reading after last line printed, so if you know that last line printed will be far away from the end of file, you can avoid a lengthy decompression:
sed -nf idx.txt <(gzip -dc gzfile.gz | head -n "$(sort -nr idx.txt | head -1)") > output.txt
Related
Have a reference file "names.txt" with data as below:
Tom
Jerry
Mickey
Note: there are 20k lines in the file "names.txt"
There is another delimited file with multiple lines for every key from the reference file "names.txt" as below:
Name~~Id~~Marks~~Column4~~Column5
Note: there are about 30 columns in the delimited file:
The delimited file looks like something :
Tom~~123~~50~~C4~~C5
Tom~~111~~45~~C4~~C5
Tom~~321~~33~~C4~~C5
.
.
Jerry~~222~~13~~C4~~C5
Jerry~~888~~98~~C4~~C5
.
.
Need to extract rows from the delimited file for every key from the file "names.txt" having the highest value in the "Marks" column.
So, there will be one row in the output file for every key form the file "names.txt".
Below is the code snipped in unix that I am using which is working perfectly fine but it takes around 2 hours to execute the script.
while read -r line; do
getData `echo ${line// /}`
done < names.txt
function getData
{
name=$1
grep ${name} ${delimited_file} | awk -F"~~" '{if($1==name1 && $3>max){op=$0; max=$3}}END{print op} ' max=0 name1=${name} >> output.txt
}
Is there any way to parallelize this and reduce the execution time. Can only use shell scripting.
Rule of thumb for optimizing bash scripts:
The size of the input shouldn't affect how often a program has to run.
Your script is slow because bash has to run the function 20k times, which involves starting grep and awk. Just starting programs takes a hefty amount of time. Therefore, try an approach where the number of program starts is constant.
Here is an approach:
Process the second file, such that for every name only the line with the maximal mark remains.
Can be done with sort and awk, or sort and uniq -f + Schwartzian transform.
Then keep only those lines whose names appear in names.txt.
Easy with grep -f
sort -t'~' -k1,1 -k5,5nr file2 |
awk -F'~~' '$1!=last{print;last=$1}' |
grep -f <(sed 's/.*/^&~~/' names.txt)
The sed part turns the names into regexes that ensure that only the first field is matched; assuming that names do not contain special symbols like . and *.
Depending on the relation between the first and second file it might be faster to swap those two steps. The result will be the same.
I have some output files (5000 files) of .log which are the results of QM computations. Inside each file there are two special lines indicate the number of electrons and orbitals, like this below as an example (with exact spaces as in output files):
Number of electrons = 9
Number of orbitals = 13
I thought about a script (bash or Fortran), as a solution to this problem, which grep these two lines (at same time) and get the corresponding integer values (9 and 13, for instance), compare them and finds the difference between two values, and finally, list them in a new text file with the corresponding filenames.
I would really appreciate any help given.
Am posting an attempt in GNU Awk, and have tested it in that only.
#!/bin/bash
for file in *.log
do
awk -F'=[[:blank:]]*' '/Number of/{printf "%s%s",$2,(NR%2?" ":RS)}' "$file" | awk 'function abs(v) {return v < 0 ? -v : v} {print abs($1-$2)}' >> output_"$file"
done
The reason I split the AWK logic to two was to reduce the complexity in doing it in single huge command. The first part is for extracting the numbers from your log file in a columnar format and second for getting their absolute value.
I will break-down the AWK logic:-
-F'=[[:blank:]]*' is a mult0 character delimiter logic including = and one or more instances of [[:blank:]] whitespace characters.
'/Number of/{printf "%s%s",$2,(NR%2?" ":RS)}' searches for lines starting with Number of and prints it in a columnar fashion, i.e. as 9 13 from your sample file.
The second part is self-explanatory. I have written a function to get the absolute value from the two returned values and print it.
Each output is saved in a file named output_, for you to process it further.
Run the script from your command line as bash script.sh, where script.sh is the name containing the above lines.
Update:-
In case if you are interested in negative values too i.e. without the absolute function, change the awk statement to
awk -F'=[[:blank:]]*' '/Number of/{printf "%s%s",$2,(NR%2?" ":RS)}' "$file" | awk '{print ($1-$2)}' >> output_"$file"
Bad way to do it (but it will work)-
while read file
do
first=$(awk -F= '/^Number/ {print $2}' "$file" | head -1)
second=$(awk -F= '/^Number/ {print $2}' "$file" | tail -1)
if [ "$first" -gt "$second" ]
then
echo $(("$first" - "$second"))
else
echo $(("$second" - "$first"))
fi > "$file"_answer ;
done < list_of_files
This method picks up the values (in the awk one liner and compares them.
It then subtracts them to give you one value which it saves in the file called "$file"_answer. i.e. the initial file name with '_answer' as a suffix to the name.
You may need to tweak this code to fit your purposes exactly.
I have several large data files (~100MB-1GB of text) and a sorted list of tens of thousands of timestamps that index data points of interest. The timestamp file looks like:
12345
15467
67256
182387
199364
...
And the data file looks like:
Line of text
12345 0.234 0.123 2.321
More text
Some unimportant data
14509 0.987 0.543 3.600
More text
15467 0.678 0.345 4.431
The data in the second file is all in order of timestamp. I want to grep through the second file using the time stamps of the first, printing the timestamp and fourth data item in an output file. I've been using this:
grep -wf time.stamps data.file | awk '{print $1 "\t" $4 }' >> output.file
This is taking on the order of a day to complete for each data file. The problem is that this command searches though the entire data file for every line in time.stamps, but I only need the search to pick up from the last data point. Is there any way to speed up this process?
You can do this entirely in awk …
awk 'NR==FNR{a[$1]++;next}($1 in a){print $1,$4}' timestampfile datafile
JS웃's awk solution is probably the way to go. If join is available and the first field of the irrelevant "data" is not numeric, you could exploit the fact that the files are in the same order and avoid a sorting step. This example uses bash process substitution on linux
join -o2.1,2.4 -1 1 -2 1 key.txt <(awk '$1 ~ /^[[:digit:]]+$/' data.txt)
'grep' has a little used option -f filename which gets the patterns from filename and does the matching. It is likely to beat the awk solution and your timestamps would not have to be sorted.
I am currently working on a script which processes csv files, and one of the things it does is remove and keep note of duplicate lines in the files. My current method to do this is to run uniq once using uniq -d once to display all duplicates, then run uniq again without any options to actually remove the duplicates.
Having said that, I was wondering if it would be possible to perform this same function in one action instead of having to run uniq twice. I've found a bunch of different examples of using awk to remove duplicates out there, but as far as I know I have not been able to find any that both displayed the duplicates and removed them at the same time.
If anyone could offer advice or help for this I would really appreciate it though, thanks!
Here's something to get you started:
awk 'seen[$0]++{print|"cat>&2";next}1' file > tmp && mv tmp file
The above will print any duplicated lines to stderr at the same time as removing them from your input file. If you need more, tell us more....
In general, the size of you input shall be your guide. If you're processing GBs of data, you often have no choice other than relying on sort and uniq, because these tools support external operations.
That said, here's the AWK way:
If you input is sorted, you can keep track of duplicate items in AWK easily by comparing line i to line i-1 with O(1) state: if i == i-1 you have a duplicate.
If your input is not sorted, you have to keep track of all lines, requiring O(c) state, where c is the number of unique lines. You can use a hash table in AWK for this purpose.
This solution does not use awk but it does produce the result you need. In the command below replace sortedfile.txt with your csv file.
cat sortedfile.txt | tee >(uniq -d > duplicates_only.txt) | uniq > unique.txt
tee sends the output of the cat command to uniq -d.
I have a CSV file that I'd like to split up based on a field in the file. Essentially, there can be two brands, GVA and HBVL. I'd like to split the file into a file for each brand before I import it into a database.
Sample of the CSV file
"D509379D5055821451C3695A3752DCCD",'1900-01-01 01:00:00',"M","1740","GVA",'2009-07-01 13:25:00',0
"159A58BE41012787D531C7157F688D86",'1900-01-01 00:00:00',"V","1880","GVA",'2008-06-06 11:21:00',0
"D0BB5C058794BBE4478DDA536D1E4872",'1900-01-01 00:00:00',"M","9270","GVA",'2007-09-18 13:21:00',0
"BCC7096803E5E60E05DC12FB9951E0CF",'1900-01-01 00:00:00',"M","3500","HBVL",'2007-09-18 13:21:00',1
"7F85FCE6F13775A8A3054E3438B81599",'1900-01-01 00:00:00',"M","3970","HBVL",'2007-09-18 13:20:00',0
Part of the problem is the size of the file. It's about 39mb. My original attempt at this looked like this:
while read line ; do
name=`echo $line | sed -n 's/\(.*\)"\(GVA\|HBVL\)",\(.*\)$/\2/ p' | tr [:upper:] [:lower:] `
info=`echo $line | sed -n 's/\(.*\)"\(GVA\|HBVL\)",\(.*\)$/\1\3/ p'`
echo "${info}" >> ${BASEDIR}/${today}/${name}.txt
done < ${file}
After about 2.5 hours, only about 1/2 of the file had been processed. I have another file that could potentially be up to 250 mb in size and I can't imagine how long that would take.
What I'd like to do is pull out the brand out of the line and write the line to a file named after the brand. I can remove the brand, but I don't now how to use it to create a file. I've started in sed, but I'm not above using another language if it's more appropriate.
The original while loop with multiple commands per line is DIRE!
sed -e '/"GVA"/w gva.file' -e '/"HBVL"/w hbvl.file' -n $file
The sed script says:
write lines that match the GVA tag to gva.file
write lines that match the HBVL tag to hbvl.file
and don't print anything else ('-n')
Note that different versions of sed can handle different numbers of auxilliary files. If you need more than, say, twenty output files at once, you may need to look at other technology (but test what the limit is on your machine). If the file is sorted so that all the GVA records appear together followed by all the HBVL records, you could consider using csplit. Alternatively, a scripting language like Perl could handle more. If you exceed the number of file descriptors allowed to your process, it becomes hard to do the splitting in a single pass over the data file.
grep '"GVA"' $file >GVA.txt
grep '"HVBL"' $file >HVBL.txt
# awk -F"," '{o=$5;gsub(/\"/,"",o);print $0 > o}' OFS="," file
# more GVA
"D509379D5055821451C3695A3752DCCD",'1900-01-01 01:00:00',"M","1740","GVA",'2009-07-01 13:25:00',0
"159A58BE41012787D531C7157F688D86",'1900-01-01 00:00:00',"V","1880","GVA",'2008-06-06 11:21:00',0
"D0BB5C058794BBE4478DDA536D1E4872",'1900-01-01 00:00:00',"M","9270","GVA",'2007-09-18 13:21:00',0
# more HBVL
"BCC7096803E5E60E05DC12FB9951E0CF",'1900-01-01 00:00:00',"M","3500","HBVL",'2007-09-18 13:21:00',1
"7F85FCE6F13775A8A3054E3438B81599",'1900-01-01 00:00:00',"M","3970","HBVL",'2007-09-18 13:20:00',0