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Filter log file entries based on date range
(5 answers)
Closed 5 years ago.
I have the following data located in a .csv file that changes as new data is downloaded.
The syntax of the data is always YYYY-MM-DDTHHMMSS, examples below:
2017-12-08T194949
2017-12-08T194952
2017-12-08T195000
2017-12-08T195007
2017-12-08T195007
2017-12-08T195014
2017-12-08T195016
2017-12-08T195016
2017-12-08T195016
2017-12-08T195016
2017-12-08T195021
2017-12-08T195026
2017-12-08T195029
2017-12-08T195030
2017-12-08T195030
2017-12-08T195034
2017-12-08T195051
2017-12-08T195101
2017-12-08T195105
2017-12-08T195135
2017-12-08T195138
2017-12-08T195140
2017-12-08T195144
2017-12-08T195148
2017-12-08T195154
2017-12-08T195204
2017-12-08T195205
2017-12-08T195219
2017-12-08T195223
2017-12-08T195224
2017-12-08T195225
Currently, I define my datestrings using:
lower_bound=`date -d '1 day ago' "+%Y-%m-%dT%H%M%S"`
upper_bound=`date -d '12 hours ago' "+%Y-%m-%dT%H%M%S"`
Where the amount of minutes I lookback into the file is dependent on the system time. I can set the amount I lookback to be arbitrary.
I think I have gotten close with sed/awk as follows:
sed -n "/$lower_bound/,/$upper_bound/p" data.csv
awk -v a="$lower_bound" -v b="$upper_bound" '/a/{flag=1;next}/b/{flag=0}flag' data.csv
Given those lookback strings, the commands above should print out the range of dates in between the two variables, $lower_bound and $upper_bound. Obviously, I have experimented with different lookback times in the aforementioned variables.
Any ideas to why the range of dates aren't printing? Any help would be greatly appreciated; thank you in advance.
This: /a/ will match the literal "a". This: $0 ~ a will match the string you have stored in variable a, so your command should be:
awk -v a="$lower_bound" -v b="$upper_bound"
'$0 ~ a {flag=1;next} $0 ~ b {flag=0} flag' data.csv
But these awk/sed commands will not give you what you want because only accidentally they could match lines, in case the exact datetime bounds exist in your logs. More probably, the exact lower bound will not exist, so flag will never be set.
If you want to print for that date range then you should make an alphabetical
comparison of these dates, that means $0 > a and $0 < b
awk -v a="$lower_bound" -v b="$upper_bound" '$0 > a && $0 < b' data.csv
Related
I have a tab separated text file, call it input.txt
cat input.txt
Begin Annotation Diff End Begin,End
6436687 >ENST00000422706.5|ENSG00000100342.21|OTTHUMG00000030427.9|-|APOL1-205|APOL1|2901|protein_coding| 50 6436736 6436687,6436736
6436737 >ENST00000426053.5|ENSG00000100342.21|OTTHUMG00000030427.9|-|APOL1-206|APOL1|2808|protein_coding| 48 6436784 6436737,6436784
6436785 >ENST00000319136.8|ENSG00000100342.21|OTTHUMG00000030427.9|OTTHUMT00000075315.5|APOL1-201|APOL1|3000|protein_coding| 51 6436835 6436785,6436835
6436836 >ENST00000422471.5|ENSG00000100342.21|OTTHUMG00000030427.9|OTTHUMT00000319151.1|APOL1-204|APOL1|561|nonsense_mediated_decay| 11 6436846 6436836,6436846
6436847 >ENST00000475519.5|ENSG00000100342.21|OTTHUMG00000030427.9|OTTHUMT00000319153.1|APOL1-212|APOL1|600|retained_intron| 11 6436857 6436847,6436857
6436858 >ENST00000438034.5|ENSG00000100342.21|OTTHUMG00000030427.9|OTTHUMT00000319152.2|APOL1-210|APOL1|566|protein_coding| 11 6436868 6436858,6436868
6436869 >ENST00000439680.5|ENSG00000100342.21|OTTHUMG00000030427.9|OTTHUMT00000319252.1|APOL1-211|APOL1|531|nonsense_mediated_decay| 10 6436878 6436869,6436878
6436879 >ENST00000427990.5|ENSG00000100342.21|OTTHUMG00000030427.9|OTTHUMT00000319154.2|APOL1-207|APOL1|624|protein_coding| 12 6436890 6436879,6436890
6436891 >ENST00000397278.8|ENSG00000100342.21|OTTHUMG00000030427.9|OTTHUMT00000319100.4|APOL1-202|APOL1|2795|protein_coding| 48 6436938 6436891,6436938
6436939 >ENST00000397279.8|ENSG00000100342.21|OTTHUMG00000030427.9|-|APOL1-203|APOL1|1564|protein_coding| 28 6436966 6436939,6436966
6436967 >ENST00000433768.5|ENSG00000100342.21|OTTHUMG00000030427.9|OTTHUMT00000319253.2|APOL1-209|APOL1|541|protein_coding| 11 6436977 6436967,6436977
6436978 >ENST00000431184.1|ENSG00000100342.21|OTTHUMG00000030427.9|OTTHUMT00000319254.1|APOL1-208|APOL1|550|nonsense_mediated_decay| 11 6436988 6436978,6436988
Using the information in input.txt I want to obtain information from a file called Other_File.fa. This file is an annotation file filled with ENST#'s (transcript IDs) and sequences of A's,T's,C's,and G's. I want to store the sequence in a file called Output.log (see example below) and I want to store the command used to retrieve the text in a file called Input.log (see example below).
I have tried to do this using awk and cut so far using a for loop. This is the code I have tried.
for line in `awk -F "\\t" 'NR != 1 {print substr($2,2,17)"#"$5}' input.txt`
do
transcript=`cut -d "#" -f 1 $line`
range=`cut -d "#" -f 2 $line` #Range is the string location in Other_File.fa
echo "Our transcript is ${transcript} and our range is ${range}" >> Input.log
sed -n '${range}' Other_File.fa >> Output.log
done
Here is an example of the 11 lines between ENST00000433768.5 and ENST00000431184.1 in Other_File.fa.
grep -A 11 ENST00000433768.5 Other_File.fa
>ENST00000433768.5|ENSG00000100342.21|OTTHUMG00000030427.9|OTTHUMT00000319253.2|APOL1-209|APOL1|541|protein_coding|
ATCCACACAGCTCAGAACAGCTGGATCTTGCTCAGTCTCTGCCAGGGGAAGATTCCTTGG
AGGAGCACACTGTCTCAACCCCTCTTTTCCTGCTCAAGGAGGAGGCCCTGCAGCGACATG
GAGGGAGCTGCTTTGCTGAGAGTCTCTGTCCTCTGCATCTGGATGAGTGCACTTTTCCTT
GGTGTGGGAGTGAGGGCAGAGGAAGCTGGAGCGAGGGTGCAACAAAACGTTCCAAGTGGG
ACAGATACTGGAGATCCTCAAAGTAAGCCCCTCGGTGACTGGGCTGCTGGCACCATGGAC
CCAGGCCCAGCTGGGTCCAGAGGTGACAGTGGAGAGCCGTGTACCCTGAGACCAGCCTGC
AGAGGACAGAGGCAACATGGAGGTGCCTCAAGGATCAGTGCTGAGGGTCCCGCCCCCATG
CCCCGTCGAAGAACCCCCTCCACTGCCCATCTGAGAGTGCCCAAGACCAGCAGGAGGAAT
CTCCTTTGCATGAGAGCAGTATCTTTATTGAGGATGCCATTAAGTATTTCAAGGAAAAAG
T
>ENST00000431184.1|ENSG00000100342.21|OTTHUMG00000030427.9|OTTHUMT00000319254.1|APOL1-208|APOL1|550|nonsense_mediated_decay|
The range value in input.txt for this transcript is 6436967,6436977. In my file Input.log for this transcript I hope to get
Our transcript is ENST00000433768.5 and our range is 6436967,6436977
And in Output.log for this transcript I hope to get
>ENST00000433768.5|ENSG00000100342.21|OTTHUMG00000030427.9|OTTHUMT00000319253.2|APOL1-209|APOL1|541|protein_coding|
ATCCACACAGCTCAGAACAGCTGGATCTTGCTCAGTCTCTGCCAGGGGAAGATTCCTTGG
AGGAGCACACTGTCTCAACCCCTCTTTTCCTGCTCAAGGAGGAGGCCCTGCAGCGACATG
GAGGGAGCTGCTTTGCTGAGAGTCTCTGTCCTCTGCATCTGGATGAGTGCACTTTTCCTT
GGTGTGGGAGTGAGGGCAGAGGAAGCTGGAGCGAGGGTGCAACAAAACGTTCCAAGTGGG
ACAGATACTGGAGATCCTCAAAGTAAGCCCCTCGGTGACTGGGCTGCTGGCACCATGGAC
CCAGGCCCAGCTGGGTCCAGAGGTGACAGTGGAGAGCCGTGTACCCTGAGACCAGCCTGC
AGAGGACAGAGGCAACATGGAGGTGCCTCAAGGATCAGTGCTGAGGGTCCCGCCCCCATG
CCCCGTCGAAGAACCCCCTCCACTGCCCATCTGAGAGTGCCCAAGACCAGCAGGAGGAAT
CTCCTTTGCATGAGAGCAGTATCTTTATTGAGGATGCCATTAAGTATTTCAAGGAAAAAG
T
But I am getting the following error, and I am unsure as to why or how to fix it.
cut: ENST00000433768.5#6436967,6436977: No such file or directory
cut: ENST00000433768.5#6436967,6436977: No such file or directory
Our transcript is and our range is
My thought was each line from the awk would be read as a string then cut could split the string along the "#" symbol I have added, but it is reading each line as a file and throwing an error when it can't locate the file in my directory.
Thanks.
EDIT2: This is a generic solution which will compare 2 files(input and other_file.fa) and on whichever line whichever range is found it will print them. Eg--> Range numbers are found on 300 line number but range shows you should print from 1 to 20 it will work in that case also. Also note this calls system command which further calls sed command(like you were using range within sed), there are other ways too, like to load whole Input_file into an array or so and then print, but I am going with this one here, fair warning this is not tested with huge size files.
awk -F'[>| ]' '
FNR==NR{
arr[$2]=$NF
next
}
($2 in arr){
split(arr[$2],lineNum,",")
print arr[$2]
start=lineNum[1]
end=lineNum[2]
print "sed -n \047" start","end"p \047 " FILENAME
system("sed -n \047" start","end"p\047 " FILENAME)
start=end=0
}
' file1 FS="[>|]" other_file.fa
EDIT: With OP's edited samples, please try following to print lines based on other file. assumes that the line you find range values, those values will be always after the line on which they found(eg--> 3rd line range values found and range is 4 to 10).
awk -F'[>| ]' '
FNR==NR{
arr[$2]=$NF
next
}
($2 in arr){
split(arr[$2],lineNum," ")
start=lineNum[1]
end=lineNum[2]
}
FNR>=start && FNR<=end{
print
if(FNR==end){
start=end=0
}
}
' file1 FS="[>|]" other_file.fa
You need not to do this with a for loop and then call awk program each time for each line. This could be done in single awk, considering that you have to only print them. Written and tested with your shown samples.
awk -F'[>| ]' 'FNR>1{print "Our transcript is:"$3" and our range is:"$NF}' Input_file
NOTE: This will print for each line of your Input_file values of transcript and range, in case you want to further perform some operation with their values then please do mention.
I have two variables containing tuples of same length generated from a PostgreSQL database and several successful follow on calculations, which I would like to multiply to generate a third variable containing the answer tuple. Each tuple contains 100 numeric records. Variable 1 is called rev_p_client_pa and variable 2 is called lawnp_p_client. I tried the following which gives me a third tuple but the answer rows are not calculated correctly:
rev_p_client_pa data is:
0.018183
0.0202814
0.013676
0.0134083
0.0108168
0.014197
0.0202814
lawn_p_client data is:
52.17
45
30.43
50
40
35
50
The command I used in the script:
awk -v var3="$rev_p_client_pa" 'BEGIN{print var3}' | awk -v var4="$lawnp_p_client" -F ',' '{print $(1)*var4}'
The command gives the following output:
0.948607
1.05808
0.713477
0.699511
0.564312
0.740657
1.05808
However when manually calculated in libreoffice calc i get:
0.94860711
0.912663
0.41616068
0.670415
0.432672
0.496895
1.01407
I used this awk structure to multiply a tuple variable with numeric value variable in a previous calculation and it calculated correctly. Does someone know how the correct awk statement should be written or maybe you have some other ideas that might be useful? Thanks for your help.
Use paste to join the two data sets together, forming a list of pairs, each separated by tab.
Then pipe the result to awk to multiply each pair of numbers, resulting in a list of products.
#!/bin/bash
rev_p_client_pa='0.018183
0.0202814
0.013676
0.0134083
0.0108168
0.014197
0.0202814'
lawn_p_client='52.17
45
30.43
50
40
35
50'
paste <(echo "$rev_p_client_pa") <(echo "$lawn_p_client") | awk '{print $1*$2}'
Output:
0.948607
0.912663
0.416161
0.670415
0.432672
0.496895
1.01407
All awk:
$ awk -v rev_p_client_pa="$rev_p_client_pa" \
-v lawn_p_client="$lawn_p_client" ' # "tuples" in as vars
BEGIN {
split(lawn_p_client,l,/\n/) # split the "tuples" by \n
n=split(rev_p_client_pa,r,/\n/) # get count of the other
for(i=1;i<=n;i++) # loop the elements
print r[i]*l[i] # multiply and output
}'
Output:
0.948607
0.912663
0.416161
0.670415
0.432672
0.496895
1.01407
For our webshop we get from the manufacturers a csv file (automatically updated) with product data.
Some manufacturers use prices without Tax and some within.
I want to change prices with a shell script to add 21% TAX and round it to nearest .95 or .50
For example I get a sheet:
sku|ean|name|type|price_excl_vat|price
EU-123|123123123123|Product name|simple|24.9900
I use this code:
sed -i "1 s/price/price_excl_vat/" inputfile
awk '{FS="|"; OFS="|"; if (NR<=1) {print $0 "|price"} else {print $0 "|" $5*1.21}}' inputfile > outputfile
the output is:
sku|ean|name|type|price_excl_vat|price
EU-123|123123123123|Product name|simple|24.9900|30.2379
How do I round it to the correct price like below ?
sku|ean|name|type|price_excl_vat|price
EU-123|123123123123|Product name|simple|24.9900|29.95
awk to the rescue!
awk 'BEGIN {FS=OFS="|"}
$NF==$NF+0 {a=$NF*1.21;
r=a-int(a);
if (r<0.225) a=a-r-0.05;
else if (r<0.725) a=a-r+0.50;
else a=a-r+0.95;
$(NF+1)=a} 1'
note that in your example the nearest number for 30.2379 will be 30.50 Perhaps you want to round down?
To round down instead of the nearest, and with a variable price column. The new computed value will be appended to the end of the row.
awk 'BEGIN {FS=OFS="|"; k=5}
$k==$k+0 {a=$k*1.21;
r=a-int(a);
if (r<0.50) a=a-r-0.05;
else if (r<0.95) a=a-r+0.50;
else a=a-r+0.95;
$(NF+1)=a} 1'
awk '#define field separator in and out
BEGIN{FS=OFS="|"}
# add/modify a 6th field for price label if missing on header only
NR==1 && NF == 6 { $6 = "price"; print; next}
NR==1 && NF == 5 { $6 = "price"; print; next}
# add price with tva rounded to 0.01 if missing
NF == 5 { $6 = int( $5 * 121 ) / 100 }
# print the line (modified or not, ex empty lines) [7 is just a *not 0*)
7
' inputfile \
> outputfile
self documented
not sure about your sed for header becasue sample show already a header with price so take the one you want
Not knowing what you're program looks like, it makes it difficult to give you more information.
However, both awk and bash have the printf command. This command can be used for rounding floating point numbers. (Yes, Bash is integer arithmetic, but it can pretend a number is a decimal number).
I gave you the link for the C printf command because the one for Bash doesn't include the formatting codes. Read it and weep because the documentation is a bit dense, and if you've never used printf before, it can be quite difficult to understand. Fortunately, an example will bring things to light:
$ foo="23.42532"
$ printf "%2.2f\n", $foo
$ 23.43 #All rounded for you!
The f means it's a floating point number. The % tells you that this is the beginning of a formatting sequence. The 2.2 means you want 2 digits on the left side of the decimal and two digits on the right. If you said %4.2f, it would make sure there's enough room for four digits on the left side of the decimal, and left pad the number with spaces. The \n on the end is the New Line character.
Fortunately, although printf can be hard to understand at first, it's pretty much the same in almost all programming languages. It's in awk, Perl, Python, C, Java, and many more languages. And, if the information you need isn't in printf, try the documentation on sprintf which is like printf, but prints the formatted text into a string.
The best documentation I've seen is in the Perl sprintf documentation because it gives you plenty of examples.
How do I compare current timestamp and a field of a file and print the matched and unmatched data. I have 2 columns in a file (see below)
oac.bat 09:09
klm.txt 9:00
I want to compare the timestamp(2nd column) with current time say suppose(10:00) and print the output as follows.
At 10:00
greater.txt
xyz.txt 10:32
mnp.csv 23:54
Lesser.txt
oac.bat 09:09
klm.txt 9:00
Could anyone help me on this please ?
I used awk $0 > "10:00", which gives me only 2nd column details but I want both the column details and I am taking timestamp from system directly from system with a variable like
d=`date +%H:%M`
With GNU awk you can just use it's builtin time functions:
awk 'BEGIN{now = strftime("%H:%M")} {
split($NF,t,/:/)
cur=sprintf("%02d:%02d",t[1],t[2])
print > ((cur > now ? "greater" : "lesser") ".txt")
}' file
With other awks just set now using -v and date up front, e.g.:
awk -v now="$(date +"%H:%M")" '{
split($NF,t,/:/)
cur = sprintf("%02d:%02d",t[1],t[2])
print > ((cur > now ? "greater" : "lesser") ".txt")
}' file
The above is untested since you didn't provide input/output we could test against.
Pure Bash
The script can be implemented in pure Bash with the help of date command:
# Current Unix timestamp
let cmp_seconds=$(date +%s)
# Read file line by line
while IFS= read -r line; do
let line_seconds=$(date -d "${line##* }" +%s) || continue
(( line_seconds <= cmp_seconds )) && \
outfile=lesser || outfile=greater
# Append the line to the file chosen above
printf "%s\n" "$line" >> "${outfile}.txt"
done < file
In this script, ${line##* } removes the longest match of '* ' (any character followed by a space) pattern from the front of $line thus fetching the last column (the time). The time column is supposed to be in one of the following formats: HH:MM, or H:MM. Actually, date's -d option argument
can be in almost any common format. It can contain month names, time zones, ‘am’ and ‘pm’, ‘yesterday’, etc.
We use the flexibility of this option to convert the time (HH:MM, or H:MM) to Unix timestamp.
The let builtin allows arithmetic to be performed on shell variables. If the last let expression fails, or evaluates to zero, let returns 1 (error code), otherwise 0 (success). Thus, if for some reason the time column is in invalid format, the iteration for such line will be skipped with the help of continue.
Perl
Here is a Perl version I have written just for fun. You may use it instead of the Bash version, if you like.
# For current date
#cmp_seconds=$(date +%s)
# For specific hours and minutes
cmp_seconds=$(date -d '10:05' +%s)
perl -e '
my #t = localtime('$cmp_seconds');
my $minutes = $t[2] * 60 + $t[1];
while (<>) {
/ (\d?\d):(\d\d)$/ or next;
my $fh = ($1 * 60 + $2) > $minutes ? STDOUT : STDERR;
printf $fh "%s", $_;
}' < file >greater.txt 2>lesser.txt
The script computes the number of minutes in the following way:
HH:MM = HH * 60 + MM minutes
If the number of minutes from the file are greater then the number of minutes for the current time, it prints the next line to the standard output, otherwise to standard error. Finally, the standard output is redirected to greater.txt, and the standard error is redirected to lesser.txt.
I have written this script for demonstration of another approach (algorithm), which can be implemented in different languages, including Bash.
I'm trying to write a script to pull the integers out of 4 files that store temperature readings from 4 industrial freezers, this is a hobby script it generates the general readouts I wanted, however when I try to generate a SUM of the temperature readings I get the following printout into the file and my goal is to print the end SUM only not the individual numbers printed out in a vertical format
Any help would be greatly appreciated;here's my code
grep -o "[0.00-9.99]" "/location/$value-1.txt" | awk '{ SUM += $1; print $1} END { print SUM }' >> "/location/$value-1.txt"
here is what I am getting in return
Morningtemp:17.28
Noontemp:17.01
Lowtemp:17.00 Hightemp:18.72
1
7
.
2
8
1
7
.
0
1
1
7
.
0
0
1
8
.
7
2
53
It does generate the SUM I don't need the already listed numbers, just the SUM total
Why not stick with AWK completely? Code:
$ cat > summer.awk
{
while(match($0,/[0-9]+\.[0-9]+/)) # while matches on record
{
sum+=substr($0, RSTART, RLENGTH) # extract matches and sum them
$0=substr($0, RSTART + RLENGTH) # reset to start after previous match
count++ # count matches
}
}
END {
print sum"/"count"="sum/count # print stuff
Data:
$ cat > data.txt
Morningtemp:17.28
Noontemp:17.01
Lowtemp:17.00 Hightemp:18.72
Run:
$ awk -f summer.awk file
70.01/4=17.5025
It might work in the winter too.
The regex in grep -o "[0.00-9.99]" "/location/$value-1.txt" is equivalent to [0-9.], but you're probably looking for numbers in the range 0.00 to 9.99. For that, you need a different regex:
grep -o "[0-9]\.[0-9][0-9]" "/location/$value-1.txt"
That looks for a digit, a dot, and two more digits. It was almost tempting to use [.] in place of \.; it would also work. A plain . would not; that would select entries such as 0X87.
Note that the pattern shown ([0-9]\.[0-9][0-9]) will match 192.16.24.231 twice (2.16 and 4.23). If that's not what you want, you have to be a lot more precise. OTOH, it may not matter in the slightest for the actual data you have. If you'd want it to match 192.16 and 24.231 (or .24 and .231), you have to refine your regex.
Your command structure:
grep … filename | awk '…' >> filename
is living dangerously. In the example, it is 'OK' (but there's a huge grimace on my face as I type 'OK') because the awk script doesn't write anything to the file until grep has read it all. But change the >> to > and you have an empty input, or have awk write material before the grep is complete and suddenly it gets very tricky to determine what happens (it depends, in part, on what awk writes to the end of the file).