Matching multiple fields from two files and then some? Post: 302658117

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

AWK Matching Fields and Combining Files

Hello! I am writing a program to run through two large lists of data (~300,000 rows), find where rows in one file match another, and combine them based on matching fields. Due to the large file sizes, I'm guessing AWK will be the most efficient way to do this. Overall, the input and output I'm...

2. Shell Programming and Scripting

comparing two files for matching fields

I am newbie to unix and would please like some help to solve the task below I have two files, file_a.text and file_b.text that I want to evaluate. file_a.text 1698.74 1711.88 6576.25 899.41 3205.63 4187.98 697.35 1551.83 ...

3. Shell Programming and Scripting

How to merge two or more fields from two different files where there is non matching column?

Hi, Please excuse for often requesting queries and making R&D, I am trying to work out a possibility where i have two files field separated by pipe and another file containing only one field where there is no matching columns, Could you please advise how to merge two files. $more...

4. Shell Programming and Scripting

Print matching fields (if they exist) from two text files

Hi everyone, Given two files (test1 and test2) with the following contents: test1: 80263760,I71 80267369,M44 80274628,L77 80276793,I32 80277390,K05 80277391,I06 80279206,I43 80279859,K37 80279866,K35 80279867,J16 80280346,I14and test2: 80263760,PT18 80279867,PT01I need to do some...

5. UNIX for Beginners Questions & Answers

Awk: matching multiple fields between 2 files

Hi, I have 2 tab-delimited input files as follows. file1.tab: green A apple red B apple file2.tab: apple - A;Z Objective: Return $1 of file1 if, . $1 of file2 matches $3 of file1 and, . any single element (separated by ";") in $3 of file2 is present in $2 of file1 In order to...

6. Shell Programming and Scripting

awk to print fields that match using conditions and a default value for non-matching in two files

Trying to use awk to match the contents of each line in file1 with $5 in file2. Both files are tab-delimited and there may be a space or special character in the name being matched in file2, for example in file1 the name is BRCA1 but in file2 the name is BRCA 1 or in file1 name is BCR but in file2...

7. UNIX for Beginners Questions & Answers

Matching fields between two files, repeated records

In two previous posts (here) and (here), I received help from forum members comparing multiple fields across two files and selectively printing portions of each as output based upon would-be matches using awk. I had been fairly comfortable populating awk arrays with fields and using awk's special...

8. Shell Programming and Scripting

Matching two fields in two csv files, create new file and append match

I am trying to parse two csv files and make a match in one column then print the entire file to a new file and append an additional column that gives description from the match to the new file. If a match is not made, I would like to add "NA" to the end of the file Command that Ive been using...

9. Shell Programming and Scripting

Comparing two files by two matching fields

Long time listener first time poster. Hope someone can advise. I have two files, 1000+ lines in each, two fields in each file. After performing a sort, what is the best way to find exact matches where field $1 and $2 in file1 are also present in file2 on the same line, then output only those...

10. UNIX for Beginners Questions & Answers

awk for matching fields between files with repeated records

Hello all, I am having trouble with what should be an easy task, but seem to be missing something fundamental. I have two files, with File 1 consisting of a single field of many thousands of records. I also have File 2 with two fields and many thousands of records. My goal is that when $1 of...

LEARN ABOUT DEBIAN

vcf-isec

VCF-ISEC(1)							   User Commands						       VCF-ISEC(1)

NAME

       vcf-isec - create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files

SYNOPSIS

       vcf-isec [OPTIONS] file1.vcf file2.vcf ...

DESCRIPTION

       About: Create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files.

	      Note that lines from all files can be intermixed together on the output, which can yield unexpected results.

OPTIONS

       -C, --chromosomes <list|file>
	      Process the given chromosomes (comma-separated list or one chromosome per line in a file).

       -c, --complement
	      Output positions present in the first file but missing from the other files.

       -d, --debug
	      Debugging information

       -f, --force
	      Continue even if the script complains about differing columns.

       -o, --one-file-only
	      Print only entries from the left-most file. Without -o, all unique positions will be printed.

       -n, --nfiles [+-=]<int>
	      Output positions present in this many (=), this many or more (+), or this many or fewer (-) files.

       -p, --prefix <path>
	      If present, multiple files will be created with all possible isec combinations. (Suitable for Venn Diagram analysis.)

       -t, --tab <chr:pos:file>
	      Tab-delimited file with indexes of chromosome and position columns. (1-based indexes)

       -w, --win <int>
	      In  repetitive  sequences, the same indel can be called at different positions. Consider records this far apart as matching (be it a
	      SNP or an indel).

       -h, -?, --help
	      This help message.

EXAMPLES

	      bgzip file.vcf; tabix -p vcf file.vcf.gz bgzip file.tab; tabix -s 1 -b 2 -e 2 file.tab.gz

vcf-isec 0.1.5							     July 2011							       VCF-ISEC(1)