Sponsored Content
Top Forums Shell Programming and Scripting awk to match file1 and extract specific tag values Post 303028464 by Don Cragun on Tuesday 8th of January 2019 03:22:04 PM
Old 01-08-2019
Hi cmccabe ,
In post #1, you said that the desired output from your two sample input files is:
Code:
AKT1 c.49G>A p.E17K	chr5:112175324 	NOT DETECTED
AKT1 c.155T>G p.L52R	chr7:55242467	NOT DETECTED
APC c.4033G>T p.E1345*	READS=1999	AF=0.248124
EGFR c.2237_2255delAATTAAGAGAAGCAACATCinsT p.E746_S752delinsV	READS=1963	AF=0.0,0.0,0.0,0.139582

Given that there is no record in file2 that contains the file1 field 2 values as a coding value in the single-quoted sub-subfields of field 8 in file2 why were the values show in red in the above output selected as the desired output? (I note that the output produced by the perl script durden_tyler suggested omits that field from the output and you didn't comment on that discrepancy.)

Other than having no idea how the 3rd output field in the first two records of your desired output is supposed to be selected, I think I can come up with an awk script that does what you want just using standard awk features (without the gawk extensions your current code is trying to use).
This User Gave Thanks to Don Cragun For This Post:
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

to extract specific values twice in a file

Hi Friends, I have a file with the following values.. xyz.txt,12345.xml abc.txt,04567.xml cde.txt,12134.xml I would like to extract all the 2nd column values twice as shown in the example like 12345,12345.xml 04567,04567.xml 12134,12134.xml Please advice!! In the formus one of... (7 Replies)
Discussion started by: techmoris
7 Replies

2. Shell Programming and Scripting

AWK: read values from file1; search for values in file2

I have read another post about this issue and am wondering how to adapt it to my own, much simpler, issue. I have a file of user IDs like so: 333333 321321 546465 ...etc I need to take each number and use it to print records wherein the 5th field matches the user ID pulled from the... (2 Replies)
Discussion started by: Bubnoff
2 Replies

3. Shell Programming and Scripting

Extract all content that match exactly only specific word

Input: 21 templeta parent 35718 36554 . - . ID=parent_cluster_50.21.11; Name=Partial%20parent%20for%20training%20set; 21 templeta kids 35718 36554 . - . ID=_52; Parent=parent_cluster_5085.21.11; 21 templeta ... (7 Replies)
Discussion started by: patrick87
7 Replies

4. Shell Programming and Scripting

Get values from different columns from file2 when match values of file1

Hi everyone, I have file1 and file2 comma separated both. file1 is: Header1,Header2,Header3,Header4,Header5,Header6,Header7,Header8,Header9,Header10 Code7,,,,,,,,, Code5,,,,,,,,, Code3,,,,,,,,, Code9,,,,,,,,, Code2,,,,,,,,,file2... (17 Replies)
Discussion started by: cgkmal
17 Replies

5. Shell Programming and Scripting

Extract values from a specific column to the end

Hello friends, I have a text file with many columns (no. columns vary from row to row) separated by space. I need to collect all the values from 18th column to the end from each line and group them as pairs and then numbering like below.. 1. 18th-col-value 19th-col-value 2. 20th-col-value ... (5 Replies)
Discussion started by: prvnrk
5 Replies

6. Shell Programming and Scripting

awk to print string if tag is specific value

In the below awk I am trying to print expName only if another tag planExecuted is true. In addition to the expName I am also printing planShortID. For some reason the word experiment gets printed so I remove it with sed. I have attached the complete index.html as well as included a sample of it... (1 Reply)
Discussion started by: cmccabe
1 Replies

7. Shell Programming and Scripting

Return path of specific tag using awk

The below awk is used with the attached index.html and matches the specific user id in the sub portion with path of /rundb/api/v1/plugin/49/. The command does run but the output is blank. Something changed in the file structure as it used to work. So using the first line in the output: ... (2 Replies)
Discussion started by: cmccabe
2 Replies

8. Shell Programming and Scripting

awk to update specific value in file with match and add +1 to specific digit

I am trying to use awk to match the NM_ in file with $1 of id which is tab-delimited. The NM_ will always be in the line of file that starts with > and be after the second _. When there is a match between each NM_ and id, then the value of $2 in id is substituted or used to update the NM_. Each NM_... (3 Replies)
Discussion started by: cmccabe
3 Replies

9. Shell Programming and Scripting

awk to search field2 in file2 using range of fields file1 and using match to another field in file1

I am trying to use awk to find all the $2 values in file2 which is ~30MB and tab-delimited, that are between $2 and $3 in file1 which is ~2GB and tab-delimited. I have just found out that I need to use $1 and $2 and $3 from file1 and $1 and $2of file2 must match $1 of file1 and be in the range... (6 Replies)
Discussion started by: cmccabe
6 Replies

10. Shell Programming and Scripting

awk to extract tag and add to each line

In the awk below which executes as is, I am trying to add a condition that will extract the text or value after the FR= for the lines in each line of file1 compared to file2. As is the lines between the two files are either a match, Missing in file 1, or Missing in file2, but I can not add the... (1 Reply)
Discussion started by: cmccabe
1 Replies
JOIN(1) 						    BSD General Commands Manual 						   JOIN(1)

NAME
join -- relational database operator SYNOPSIS
join [-a file_number | -v file_number] [-e string] [-j file_number field] [-o list] [-t char] [-1 field] [-2 field] file1 file2 DESCRIPTION
The join utility performs an ``equality join'' on the specified files and writes the result to the standard output. The ``join field'' is the field in each file by which the files are compared. The first field in each line is used by default. There is one line in the output for each pair of lines in file1 and file2 which have identical join fields. Each output line consists of the join field, the remaining fields from file1 and then the remaining fields from file2. The default field separators are tab and space characters. In this case, multiple tabs and spaces count as a single field separator, and leading tabs and spaces are ignored. The default output field separator is a single space character. Many of the options use file and field numbers. Both file numbers and field numbers are 1 based, i.e. the first file on the command line is file number 1 and the first field is field number 1. The following options are available: -a file_number In addition to the default output, produce a line for each unpairable line in file file_number. (The argument to -a must not be preceded by a space; see the COMPATIBILITY section.) -e string Replace empty output fields with string. -o list The -o option specifies the fields that will be output from each file for each line with matching join fields. Each element of list has the form 'file_number.field', where file_number is a file number and field is a field number. The elements of list must be either comma (``,'') or whitespace separated. (The latter requires quoting to protect it from the shell, or, a simpler approach is to use multiple -o options.) -t char Use character char as a field delimiter for both input and output. Every occurrence of char in a line is significant. -v file_number Do not display the default output, but display a line for each unpairable line in file file_number. The options -v 1 and -v 2 may be specified at the same time. -1 field Join on the field'th field of file 1. -2 field Join on the field'th field of file 2. When the default field delimiter characters are used, the files to be joined should be ordered in the collating sequence of sort(1), using the -b option, on the fields on which they are to be joined, otherwise join may not report all field matches. When the field delimiter char- acters are specified by the -t option, the collating sequence should be the same as sort(1) without the -b option. If one of the arguments file1 or file2 is ``-'', the standard input is used. The join utility exits 0 on success, and >0 if an error occurs. COMPATIBILITY
For compatibility with historic versions of join, the following options are available: -a In addition to the default output, produce a line for each unpairable line in both file 1 and file 2. (To distinguish between this and -a file_number, join currently requires that the latter not include any white space.) -j1 field Join on the field'th field of file 1. -j2 field Join on the field'th field of file 2. -j field Join on the field'th field of both file 1 and file 2. -o list ... Historical implementations of join permitted multiple arguments to the -o option. These arguments were of the form ``file_num- ber.field_number'' as described for the current -o option. This has obvious difficulties in the presence of files named ``1.2''. These options are available only so historic shell scripts don't require modification and should not be used. SEE ALSO
awk(1), comm(1), paste(1), sort(1), uniq(1) STANDARDS
The join command is expected to be IEEE Std 1003.2 (``POSIX.2'') compatible. BSD
April 28, 1995 BSD
All times are GMT -4. The time now is 11:47 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy