Login or Register to Ask a Question and Join Our Community


Shell Programming and Scripting

awk script to parse case with information in two fields of file

Login to Discuss or Reply to this Discussion in Our Community

 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting awk script to parse case with information in two fields of file
# 1  
Old 04-08-2015
awk script to parse case with information in two fields of file
The below awk parser works for most data inputs, but I am having trouble with the last one. The problem is in the below rules steps 1 and 2 come from $2 (NC_000013.10:g.20763686_20763687delinsA) and steps 3 and 4 come from $1 (NM_004004.5:c.34_35delGGinsT).

Code:
Parse Rules:
The header is skipped  and
1. 4 zeros after the NC_  (not always the case) and the digits before the . 
2. g. ### (before underscore)  _### (# after the _)
3. letters after the "del" until the “ins”
4. letters after the "ins"

Desired output: 13     20763686     20763687     GG     T

Code as is so far:
Code:
 awk 'NR>1 {split($2,a,"[_.>]");b=substr(a[4],1,length(a[4]-1));print a[2]+0,b,b,substr(a[4],length(a[4])),a[5]}' OFS="\t" out_position.txt > out_parse.txt

Thank you Smilie.
out_position.zip (265 Bytes) 
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Parse file for fields and specific text

I have a file of ~500,000 entries in the following: file.txt chr1 11868 12227 ENSG00000223972.5 . + HAVANA exon . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type... (17 Replies)
Discussion started by: cmccabe
17 Replies

2. UNIX for Advanced & Expert Users

Script to parse and compare information in two fields of file

Hello, I am working parsing a large input file1(field CFA) I have to compare the the file1 field(CFA byte 88-96) with the content of the file2(It contains only one field) and and insert rows equal in another file. Here is my code and sample input file: ... (7 Replies)
Discussion started by: GERMANOS
7 Replies

3. Shell Programming and Scripting

awk special parse case

I have a special case that awk could be used but I do not have the skill. Trying to create a final output file (indel_parse.txt) that is created from using some information from each of the two files (attached). parse rules: The header is skipped FNR>1 1. 4 zeros after the NC_ (not... (2 Replies)
Discussion started by: cmccabe
2 Replies

4. Shell Programming and Scripting

AWK script to parse a data in a file

Hi Unix gurus.. I have a file which has below data, It has several MQ Queue statistics; QueueName= 'TEST1' CreateDate= '2009-10-30' CreateTime= '13.45.40' QueueType= Predefined QueueDefinitionType= Local QMinDepth= 0 QMaxDepth= 0 QueueName= 'TEST2' CreateDate= '2009-10-30'... (6 Replies)
Discussion started by: dd_psg
6 Replies

5. Shell Programming and Scripting

awk script need to act on same file on matced case

Hello, I have a log file , i want to delete the lines of the log file which is match with 1st and 5th field with different patterns. Once it will meet with that condition it will delete that line from the log . I dont want to create any temp file over there. Successfully able to retrieve the... (1 Reply)
Discussion started by: posix
1 Replies

6. Shell Programming and Scripting

Perl: Parse Hex file into fields

Hi, I want to split/parse certain bits of the hex data into another field. Example: Input data is Word1: 4f72abfd Output: Parse bits (5 to 0) into field word1data1=0x00cd=205 decimal Parse bits (7 to 6) into field word1data2=0x000c=12 decimal etc. Word2: efff3d02 Parse bits (13 to... (1 Reply)
Discussion started by: morrbie
1 Replies

7. Shell Programming and Scripting

how to parse with awk (using different fields), then group by a field?

When parsing multiple fields in a file using AWK, how do you group by one of the fields and parse by delimiters? to clarify If a file had tom | 223-2222-4444 , randofield ivan | 123-2422-4444 , random filed ... | and , are the delimiters ... How would you group by the social security... (4 Replies)
Discussion started by: Josef_Stalin
4 Replies

8. Shell Programming and Scripting

awk script to (un)/concatenate fields in file

Hi everyone, I'm trying to use the "join" function for more than 1 field. Since it's not possible as it is, I want to take my input files and concatenate the joining fields as 1 field (separated by "|"). I wrote 2 awk script to do and undo it (see below). However I'm new to awk and I'm certain I... (5 Replies)
Discussion started by: anthony.cros
5 Replies

9. Shell Programming and Scripting

Trying to Parse Version Information from Text File

I have a file name version.properties with the following data: major.version=14 minor.version=234 I'm trying to write a grep expression to only put "14" to stdout. The following is not working. grep "major.version=(+)" version.properties What am I doing wrong? (6 Replies)
Discussion started by: obfunkhouser
6 Replies

10. Shell Programming and Scripting

To parse through the file and print output using awk or sed script

suppose if u have a file like that Hen ABCCSGSGSGJJJJK 15 Cock ABCCSGGGSGIJJJL 15 * * * * * * : * * * . * * * : Hen CFCDFCSDFCDERTF 30 Cock CHCDFCSDHCDEGFI 30 * . * * * * * * * : * * :* : : . The output shud be where there is : and . It shud... (4 Replies)
Discussion started by: cdfd123
4 Replies
Login or Register to Ask a Question