awk combine columns from multiple files

Making statements based on opinion; back them up with references or personal experience. 5asdf Why does Mister Mxyzptlk need to have a weakness in the comics? Sorry if it was unclear but files A and B should merge comparing columns (A1, A3, A5) to (B1, B2, B4). last unless $ofc; Data Field For example, if you have two databases SourceDB and DestinationDB, you could create two connection managers named OLEDB_SourceDB and OLEDB_DestinationDB. The paste command can merge lines of multiple files. You could use awk: Relation between transaction data and transaction id. Implement Seek on /dev/stdin file descriptor in Rust. The command displays the line number in the output. Arrays in awk are associative and is a very powerful feature. cnvi0000004 5 166325838 -0.118 0.9883, name Chr Position Log R Ratio B Allele Freq 3asd By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. When NR != FNR it's time to process 2nd input, file1. It has more code, but if you want more complex data treatment, I think it's the better approach. a - Insert Data How do I get the directory where a Bash script is located from within the script itself? if (length(xx_file$name) != length(tot_file$name)){ file1 Thank you. 0819,MTS,MUM ax200 2 3 4. What sort of strategies would a medieval military use against a fantasy giant? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. merging 2 columns from two files in one file. } rev2023.3.3.43278, Not the answer you're looking for? --- #!/bin/sh sed -e 's/#. awk '{print $1"\t"$2}' file # OR awk '$1 = $1' OFS="\t" file 03-14-2012, 11:45 AM #6: David the H. Bash Guru . Is it correct to use "the" before "materials used in making buildings are"? 1) create a dummy field from the desired columns of file A or B. $if[$index]->{F}[3]; 1/2-SBSRNA4 18 $if[$index]->{handle} = undef; # close filehandle I added an extra line to the sample data containing: The output I got from that plus the data in the question looked like this after formatting with tabstops set to 4: Very similar to @sps answer but without the if and using tabs. Is it possible to rotate a window 90 degrees if it has the same length and width? missing_snp <- rbind(missing_snp, missing) How to reload .bash_profile from the command line. I make the (probably incorrect) assumption that you want to pull out field 2 of your datachange this to whatever you really want. Instead, I get only around 11133567. File1_example.txt. 5 166710354 0.2355 0.1529, $ cat file1 2tg name Chr Position Log R Ratio B Allele Freq $if[ $index ]->{ F }[0] = -1; # set default pos value for this file to "unread" Hello Unix gurus, Also, it's pretty easy to use: $ paste left.txt right.txt I am line 1 on the left. cnvi0000004 5 166325838 0.0307 0.9867 I would like to join two files when two columns in each file matches with each other and then produce an output when taking multiple columns. If the goal is just to join columns side by side, it is much simple to use paste command. File2: b.txt p[$1] = p[$1]"\t"llr[$1]; To subscribe to this RSS feed, copy and paste this URL into your RSS reader. file2.csv: you could man gawk check what are NR and FNR. I tried to use bold in it but it doesn't work in code block. "; Not the answer you're looking for? What is the purpose of non-series Shimano components? Hence, I came up with this marginally different version of the code. Dynamic RNA-protein interactions govern the co-transcriptional packaging of RNA polymerase II (RNAPII)-derived transcripts. How to specify the private SSH-key to use when executing shell command on Git? cnvi0000004 5 166325838 -0.118 0.9883 # open all files To find unique values of first column. Example: a ["Jan"]=30 meaning in the array a, "Jan" is an index with value 30. I've already tried several awk command. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. rev2023.3.3.43278. How to reload .bash_profile from the command line. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Did any DOS compatibility layers exist for any UNIX-like systems before DOS started to become outmoded? Add line break to 'git commit -m' from the command line, Euler: A baby on his lap, a cat on his back thats how he wrote his immortal works (origin? Seems that working. Table4|Column3 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Shell: How to call one shell script from another shell script? thought about it, i.e. The problem I'm having is I need to only combine data from the second file in the empty spaces of the first. rev2023.3.3.43278. but i'm getting empty output. But, the records should be (3400*6220 = 21148000). cnvi0000003 5 165772271 0.3361 0 I hope at least that this inspires you all to take advantage of the power of AWK! my $pos = 0; # pos indicates which record we're dealing with This post is already here but want to do this with another way Data_b1 Asking for help, clarification, or responding to other answers. Share your knowledge at the LQ Wiki. How can this new ban on drag possibly be considered constitutional? awk 'FNR==NR{a[$1]=$2 FS $3;next} here we handle the 1st input (file2). I found this question/answer on Google and it appears to be referring to a very specific data set found in another question (How to merge two files using AWK?). It only takes a minute to sign up. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Find centralized, trusted content and collaborate around the technologies you use most. a after all the other columns from file A. I have found several examples here in SO (for example How to merge two files based on the first three columns using awk and How to merge two files using AWK?) when cating you need to ensure the file order is preserved, one way is to explicitly specify the files, extract last column by awk and align using pr, Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. need to merge based on three columns on 6. I want to extract and combine a certain column from a bunch of text files into a single file as shown. d Table5|Column1 Now, let's take a closer look at the awk code above to understand how it works. file2 Learn more about Stack Overflow the company, and our products. Find centralized, trusted content and collaborate around the technologies you use most. So far I've assumed that you want to match line 1 of file 1 with line 1 of file 2, line 2 of file 1 with line 2 of file 2, etc. File: a.txt *//' $1 | awk 'NF > 0 {print $2}' > tmp.$$ sed -e 's/#. for (i in 1:length(files)) { 5 164388439 -0.4241 0.0736 0.2449 5 166710354 0.2355 0.1529, awk 'NR==FNR{ llr[$1]=$4; p[$1]=$2"\t"$3; next } { missing <- data.frame(Position = tot_file[i,]$Position, Log.R.Ratio="NaN") Following awk may help you in same, in case you are not worried about little space which will be created when 3rd field will be nullified. my $ofc = 0; # open filehandle count @sjsam I always recommend people buy the book instead of suggesting they read it for free online as the guy who wrote it deserves to make a few bucks off that plus all the work he's put into providing and maintaining gawk for us and shouldn't be penalized for graciously also providing it online for reference. Can I tell police to wait and call a lawyer when served with a search warrant? it out in one command line is the best solution for me. 2tg cnvi0000001 5 164388439 0.0736 0 2) then use paste to create each pseudo file as dummy comparison field; rest of file. Using Kolmogorov complexity to measure difficulty of problems? By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Is it suspicious or odd to stand by the gate of a GA airport watching the planes? vegan) just to try it, does this inconvenience the caterers and staff? How do/should administrators estimate the cost of producing an online introductory mathematics class? Join 2 files with multiple columns: awk/grep/join. To write numerous files, successively, in the same awk program. awk - compare two files and print all columns from both files. # let's loop the files until all are read thru } a cnvi0000002 5 165771245 0.1811 1 file2 What is the purpose of non-series Shimano components? Here's a way to pre-filter both files that relies . Im trying to join two files depending on multiple matching columns. for (i=1;i<=FNR;++i) Without messing up the elements orders of BOTH files. AA|RR|ESKIM could you be more specific in terms of Input, desired output, how the (and which) columns should be compared? } } else cnvi0000005 5 166710354 0.2355 0, name Chr Position Log R Ratio B Allele Freq How should I go about getting parts for this bike? WE|WW|SUPSS Associate arrays have an index and a corresponding value. #load files to create the "complete list" I need the first column that contain the name of the record 5678,WXYZ,27,MAT,NJ,USA How can I check before my flight that the cloud separation requirements in VFR flight rules are met? else { 3|pqr You want it for 100 files, I mean variable number, not for 4, right? What is the point of Thrower's Bandolier? ax100 20 30 40 Is it possible to rotate a window 90 degrees if it has the same length and width? *, COALES Solution 1: Unless I am missing something in the requirements, what you need to do is get a list of the clients and the dates and then join that to your subqueries. Awk $1 $2 9888,PUN 5 166710354 0.2355 0.1529, awk '{ What is the purpose of non-series Shimano components? plot (y over x). Do roots of these polynomials approach the negative of the Euler-Mascheroni constant? print x[i] Table3|Column2 Not sure if I understood the requirement properly, but this gives the expected output for the given input: From the code in the question, I changed the print statement from. A2LD1 3 How do you ensure that a red herring doesn't violate Chekhov's gun? Ask Ubuntu is a question and answer site for Ubuntu users and developers. How to tell which packages are held back due to phased updates. There are multiple lines in the column containing these words. I didn't bother with any of this, but you might want to. b Why is there a voltage on my HDMI and coaxial cables? 1avq A 172 177 wyfany But changing the awk record directly was definitely the solution. input3 s[$1] = s[$1] " " $4; 5 166710354 0.2355 0.1529 0.1529, #define file path I need the code to work with text files with different numbers of columns, so I can't use something like awk 'BEGIN{FS="\t"} {print $1"\t"$2"-"$3"\t"$4"\t"$5}' file. This is exactly what I need to be able to move forward. if ( $ignore_first_line ) { This will print without the extra ; on unmatched lines. A1BG 3 I have n files (for ex:64 files) with one similar column. It is relatively expressive and easy to understand. Hi all A 123 1 B 234 2 C 345 3 D 456 4 File2_example.txt. 4asdf Follow Up: struct sockaddr storage initialization by network format-string. 1430,Aircel MP,20 File 2 has entries missing for some date time. How to create a new file with required columns from different multiple files in linux? NR: NR command keeps a current count of the number of input records. In this case: Join the file2 and the file1 using the field 1 ( -1 1) of the file2 and the field 2 ( -2 2) of the file1. 5 166325838 0.0403 -0.118 0.0307 I think awk code is more easily understood when formatted using multiple lines for multiple statements. *//' $2 | awk 'NF > 0 {print $2}' | paste tmp.$$ - rm -f tmp.$$ ---. Exemple: File 3 may contain column 1,2,3 from File 1 and column 4 from File 2. The nature of simulating nature: A Q&A with IBM Quantum researcher Dr. Jamie We've added a "Necessary cookies only" option to the cookie consent popup. Making statements based on opinion; back them up with references or personal experience. The nature of simulating nature: A Q&A with IBM Quantum researcher Dr. Jamie We've added a "Necessary cookies only" option to the cookie consent popup, Assignment in braces vs outside braces in awk, Merging columns from 200+ big files into one table, Merging 2 files with based on field match, Read a two-character column as two separate columns, Matching two main columns at the same time between files, and paste supplementary columns into the output file when those main columns match, Awk - Match Values Between Two Files and Create a New File, Compare one column from one file with all columns in another file, How to merge two files with common fields in specific columns. 2345,ABCD,24,SAM,NY,USA use warnings; Is there a single-word adjective for "having exceptionally strong moral principles"? ESKIM|ES How do I copy a folder from remote to local using scp? $cat c_d_s2.xls Merge selected columns from two different files into another file. But it still leaves out one semicolon--or a column--from output lines 1 and 4: An how do I state which columns I want to use for comparing? A1CF 0 Why did Ukraine abstain from the UNHRC vote on China? Theodoros Emmanouilidis Notes & Thoughts. Try this: awk '{sub("#*","");printf "%s ",$0;getline < "file2";sub("#*","");print$0}' file1. Evaluating condition of if statement in awk using a second file, Using file redirects to input a variable search pattern to awk, Use awk to compare file entry as well as condition, Compare two numerical ranges in two distincts files with awk and print ALL lines from file1 and the matching ones from file2. How would "dark matter", subject only to gravity, behave? > > -- > > Sired, squired, hired, RETIRED. 5 165772271 0.4321 0.2955 0.3361 Both of the conditions must be satisfied at the . Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. @{$if[$index]->{F}} = split(/\s/, $if[$index]->{line}); Thanks for contributing an answer to Unix & Linux Stack Exchange! Yes, I want to merge all 100 files. The case where there's an odd number of fields on the line doesn't need special treatment. 5 165772271 0.4321 0.2955 0.3361 How can I check if a program exists from a Bash script? 5 165772271 0.4321 0.2955 0.3361 Connect and share knowledge within a single location that is structured and easy to search. I have several column files like this I have a file1 with 3400 records that are tab separated and I have a file2 with 6220 records. say, FS is space, we build an array(a) up, index is column1, value is column2 " " column3 the FNR==NR and next means, this part of codes work only for file2. How to merge two files based on 2 columns using awk? A2LD1 1 Connect and share knowledge within a single location that is structured and easy to search. I've already tried several awk command. The awk command performs the pattern/action statements once for each record in a file. Right side: line #2 I am line 3 on the left. Awk is primarily geared to processing one file at a time, but you can call getline to read from another file in parallel. Having issues trying to get the columns to format properly. Why did Ukraine abstain from the UNHRC vote on China? My apologies if this has been posted elsewhere, I have had a look at several threads but I am still confused how to use these functions. bash - merging 2 files using 2 common columns and add up the values of the 3rd column, awk - compare files and print lines from both files, If two columns partially match, replace third with awk, How to compare and replace the value at particular location with awk, get specific lines from File1, others from File2 and print them in File3, Awk-compare 2 files using multiple columns and print lines from both files. It concatenates each full line from the first file with the corresponding line from the second file; you can remove unwanted columns before or after. How would "dark matter", subject only to gravity, behave? To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Linux is a registered trademark of Linus Torvalds. awk is the first tool I thought about for the task and one I'm trying to learn, so I'm very interested in answers using it, but any solution with any other tool would be greatly . Lot's of tweaks could be made to this script; for instance, adding trap statements to clean up the temporary file in the event of a signal, adding checks for the appropriate number of arguments to the script, a function for running the sed | awk part of the pipeline, etc. join will do the job provided that the column you want to match is sorted. Relation between transaction data and transaction id, Equation alignment in aligned environment not working properly. You have to provide B file first. one file unit accessing two different files. For example, assuming that your columns are tab-delimited: Here's a way to pre-filter both files that relies on ksh/bash/zsh process substitution. Asking for help, clarification, or responding to other answers. only_files <- dir(path=files_path, pattern = "*.in") Table5|Column4 Data_b4 Is the God of a monotheism necessarily omnipotent? If you don't close the files, eventually you may exceed a system limit on the number of open files in one process. Home: Forums: Tutorials: Articles: Register . and file B I want to compare columns 1,2,4,5 from file 1 with columns 1,2,4,5 from file 2 and then merge matching lines in file 3 with column 3 of file 1 and all columns from files 2. if ( defined ( $if[$index]->{handle} ) ) { # check if the file is open and we can read from it Not the answer you're looking for? If you want to match the contents of a column, that's a completely different matter. Bulk update symbol size units from mm to map units in rule-based symbology, Radial axis transformation in polar kernel density estimate. So, I used it like below: In the above command I took 1st and 2nd column which is same in all files and the 4th columns from all files. (sorry about word wrap) -- Sired, squired, hired, RETIRED. 20130322 05:35 2219 Data Field I have one space delimited file with multiple columns and one tab delimited file with multiple columns (They have the same number of rows). -f file To specify a file that contains awk script. my $str = ""; # build the infoline here Ubuntu and the circle of friends logo are trade marks of Canonical Limited and are used under licence. Linear regulator thermal information missing in datasheet. I am using the following query to group work times and expenses for clients from three tables, one for clients, one for work times and one for expenses: SELECT a. open( $if[ $index ]->{ handle }, "<", $_) or die "Couldn't open file $_: $! @RokhayaBA do your files have DOS-style (CRLF) line endings by any chance? I wanted to see how it could be done with. Full text of the 'Sri Mahalakshmi Dhyanam & Stotram', AC Op-amp integrator with DC Gain Control in LTspice. The closest solution I could get to, is the following Merge files using a common column However, . rev2023.3.3.43278. UNIX is a registered trademark of The Open Group. I'm trying to combine all the second columns ($2) together. Are there tables of wastage rates for different fruit and veg? A while ago I stumbled in a very good solution to handle multiple files at once. END{for(i in p) { For example : 1) awk 'BEGIN{FS=OFS=","}NR==FNR{a[$1$2$4$5]=$3;next} $1$2$4$5 in a{print $0, a[$1$2$4$5]}' file2 file1 > file3 2) awk 'NR==FNR {a[$1$2$4$5] = $3; next} $1$2$4$5 in a' file2 file1 >file3 Buy the book Effective Awk Programming, 4th Edition, by Arnold Robbins. I have 2 files. Create File in Linux. c The nature of simulating nature: A Q&A with IBM Quantum researcher Dr. Jamie We've added a "Necessary cookies only" option to the cookie consent popup. . x[FNR] = sprintf("%s\t%s", x[FNR], $4) The key columns Is the God of a monotheism necessarily omnipotent? File A: (tab-delimited) Share. What is the purpose of this D-shaped ring at the base of the tongue on my hiking boots? Asking for help, clarification, or responding to other answers. #read all file names in the directory and save in a vector The second input file is then put through the same process, but piped through ``paste'' to combine its contents with that of the first file's. a vegan) just to try it, does this inconvenience the caterers and staff? $cat a_b_s1.xls There are different cases when we need to concatenate files by their columns. 3asd Styling contours by colour and by line thickness in QGIS, Doesn't analytically integrate sensibly let alone correctly. Is it possible to create a concave light? 2|jkl Besides, the previous approaches treated the inputs sequentially, so if you needed to do some calculations that depended on data from both files simultaneously you wouldn't be able to do it, and with this approach you can do everything with both files. if ( $if[$index]->{F}[0] < $pos ) { For example: By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2, Combine text from two files, output to another, Combine count files into one file and keep zero values. Data Field I want the 1st and 2nd columns which are the same in all the files and 4th column which is different in all the files. 1/2-SBSRNA4 53 Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? 9664,RAJ Good luck, and I hope this helps out! NF: NF command keeps a count of the number of fields within the current input record. Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2, Using AWK to merge two files based on multiple conditions, Using awk to print all columns from the nth to the last, Swap two columns - awk, sed, python, perl, Using an array in AWK when working with two files, Printing column separated by comma using Awk command line, awk search column from one file, if match print columns from both files, AWK comparing two files and printing individual columns. Browse other questions tagged. 5 166325838 0.0403 -0.118 0.0307 And NR represents it globally, so first line is accepted and the rest are ignored as before. Visit Stack Exchange Tour Start here for quick overview the site Help Center Detailed answers. How can this new ban on drag possibly be considered constitutional? What is the purpose of this D-shaped ring at the base of the tongue on my hiking boots? Each element in FIELD-LIST is either the single character `0' or has the form M.N where the file number, M, is `1' or `2' and N is a positive field number. print "\n"; Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. Making statements based on opinion; back them up with references or personal experience. So, how to make a single file out of all those .tsv files in 100 directories with folder names as column names? I want make a single file with all the information needed from all those tsv files in the 100 directories. file2 } Minimising the environmental effects of my dyson brain, Follow Up: struct sockaddr storage initialization by network format-string. NF. Data_b2 The nature of simulating nature: A Q&A with IBM Quantum researcher Dr. Jamie We've added a "Necessary cookies only" option to the cookie consent popup, Announcement: AI-generated content is now permanently banned on Ask Ubuntu. xx_file <- read.table(files[i], sep="\t", header=TRUE)[c(1,3,4)] }else{ I tried using join file1 and file2 after sorting. (separating the fields with FS i the associative array key string just guards against false matches; if you just concatenate fields you can't distinguish between "abcdef" and "abc""def"). Data_a2 cnvi0000001 5 164388439 0.0736 0 each file using AWK. Which columns in file A must match which ones from file B, and which columns should be printed in the output then? I find the AWK syntax a little bit tough to get the hang of and was hoping someone wouldn't mind breaking the code snippet down for me. ------------ 1234,ABCD,23,JOHN,NJ,USA How to to create a new file with specific columns from files in multiple folders in linux? The files are named GSM1.txt through GSM20.txt. Visit Stack Exchange Tour Start here for quick overview the site Help Center Detailed answers. vegan) just to try it, does this inconvenience the caterers and staff? Connect and share knowledge within a single location that is structured and easy to search. Start here for a quick overview of the site, Detailed answers to any questions you might have, Discuss the workings and policies of this site. Thank you very much. Though you could probably use some UNIX utilities like join or paste, AWK is obviously much more flexible and powerful if your desired output is different, by using if statements, or altering the OFS (which may be more difficult to do depending on the utility; see below) for example, altering the output in a much more expressive way (an important consideration for shell scripters. Connect and share knowledge within a single location that is structured and easy to search. For the Nozomi from Shinagawa to Osaka, say on a Saturday afternoon, would tickets/seats typically be available - or would you need to book? inefficient code: comparing combining different columns from different files awk or perl? Try that when the input file contains a line that starts with, say, At that level of pickiness also OFS should be used instead of "\t", Correct, sorry I missed that one. Why is there a voltage on my HDMI and coaxial cables. if(llr[$1]){ from cnvi0000003 [duplicate]. Relation between transaction data and transaction id. *, COALES Solution 1: Unless I am missing something in the requirements, what you need to do is get a list of the clients and the dates and then join that to your subqueries. To learn more, see our tips on writing great answers. RE|DD|RED| $ cat A3.csv A,B 1,2 $ cat B3.csv A,B 7,9. print p[i] This may look very untidy but should work. } for f0 in path*.m0 Thanks for contributing an answer to Stack Overflow! Here's an example with ellipses () separating the columns: awk 'BEGIN { OFS=""} FNR==NR { a[(FNR"")] = $0; next } { print a[(FNR"")], $0 }' test1 test2. if you need the extra delimiters, change the last print to print $0 OFS OFS, 1) create a dummy field from the desired columns of file A or B, 2) then use paste to create each pseudo file as dummy comparison field; rest of file, 3) sort the output for usability with join, 5) cut the desired columns from the matches join produces.