print specific strings only Post: 302357449

Sponsored Content

Top Forums Shell Programming and Scripting print specific strings only Post 302357449 by genehunter on Tuesday 29th of September 2009 11:17:12 PM

09-30-2009

Registered User

print specific strings only

Hello,
I have a file like this..

Code:

2    168611167    STK39    STK39    ---    27347    "serine threonine kinase 39 (STE20/SPS1 homolog, yeast)"    YES    SNP_A-2086192    rs16854601    0.001558882
6    13670256    SIRT5 /// RPS4X    SIRT5    ---    23408 /// 6191    "sirtuin (silent mating type information regulation 2 homolog) 5 (S. cerevisiae) /// ribosomal protein S4, X-linked"    YES    SNP_A-8405097    rs16874223    0.00156082
2    105439878    NCK2 /// FHL2    FHL2 /// NCK2    ---    8440 /// 2274    NCK adaptor protein 2 /// four and a half LIM domains 2    ---    SNP_A-2034891    rs41322544    0.001562043
12    80373503    PPFIA2    PPFIA2    ---    8499    "protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2"    YES    SNP_A-8542673    rs17008588    0.001565901
15    41547066    TP53BP1 /// TP53BP1 /// TP53BP1    TP53BP1    ---    7158 /// 7158 /// 7158    tumor protein p53 binding protein 1 /// tumor protein p53 binding protein 1 /// tumor protein p53 binding protein 1    YES    SNP_A-1782700    rs1814538    0.001573326

I need to sort this file ascending on the last column.
Then, I need an output with two columns.
First col. with only the words that start with SNP_A and the the next column with the word found in the right of the column with SNP_A.

e.g output
SNP_A-2086192 rs16854601
SNP_A-8405097 rs16874223
Can you show me howto with awk?

Thanks for reading

genehunter

View Public Profile for genehunter

Find all posts by genehunter

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Remove specific strings from certain fields

I'm working with a set of files where I'm trying to remove a set of characters from specific fields. The files are comma-delimited, and the characters I want to remove include: - open parentheses - ( - close parentheses - ) - space followed by a dollar sign - $ I don't want to remove every...

2. Shell Programming and Scripting

print first few lines, then apply regex on a specific column to print results.

abc.dat tty cpu tin tout us sy wt id 0 0 7 3 19 71 extended device statistics r/s w/s kr/s kw/s wait actv wsvc_t asvc_t %w %b device 0.0 133.2 0.0 682.9 0.0 1.0 0.0 7.2 0 79 c1t0d0 0.2 180.4 0.1 5471.2 3.0 2.8 16.4 15.6 15 52 aaaaaa1-xx I want to skip first 5 line...

3. Shell Programming and Scripting

Print Specific lines when found specific character

Hello all, I have thousand file input like this: file1: $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ $$ | | | |$$ $$ UERT | TTYH | TAFE | FRFG |$$ $$______|______|________|______|$$ $$ | | | |$$ $$ 1 | DISK | TR1311 | 1 |$$ $$ 1 |...

4. UNIX for Dummies Questions & Answers

How to Detect Specific Pattern and Print the Specific String after It?

I'm still beginner and maybe someone can help me. I have this input: the great warrior a, b, c and what i want to know is, with awk, how can i detect the string with 'warrior' string on it and print the a, b, and c seperately, become like this : Warrior Type a b c Im still very...

5. Shell Programming and Scripting

Getting specific strings from output

so i have the following string: ...

6. Shell Programming and Scripting

How to print with awk specific field different from specific character?

Hello, i need help with awk. I have this file: cat number DirB port 67 er_enc_out 0 er_bad_os 0 DirB port 71 er_enc_out 56 er_bad_os 0 DirB port 74 er_enc_out 0 er_bad_os 0 DirB port 75 ...

7. UNIX for Dummies Questions & Answers

Printing lines with specific strings at specific columns

Hi I have a file which is tab-delimited. Now, I'd like to print the lines which have "chr6" string in both first and second columns. Could anybody help?

8. Shell Programming and Scripting

How to print multiple specific column after a specific word?

Hello.... Pls help me (and sorry my english) :) So I have a file (test.txt) with 1 long line.... for example: isgc jsfh udgf osff 8462 error iwzr 653 idchisfb isfbisfb sihfjfeb isfhsi gcz eifh How to print after the "error" word the 2nd 4th 5th and 7th word?? output well be: 653 isfbisfb...

9. UNIX for Dummies Questions & Answers

Delete specific strings in a file

Hi, My file has a numerous sttrings.I want to retain those strings which start with stt and delete entries with >C For eg: my infile is >C4603985...

10. Shell Programming and Scripting

How to extract fields containing specific strings?

Hello I have a log file with thousands of lines like below Sep 21 13:02:52 lnxtst01 kernel: New TCP in: IN=eth0 OUT= MAC=00:1a:4b:50:b7:32:00:08:e3:ff:fc:04:08:00 SRC=10.184.46.4 DST=10.162.139.21 LEN=60 TOS=0x00 PREC=0x00 TTL=59 ID=52961 DF PROTO=TCP SPT=55688 DPT=22 WINDOW=5840 RES=0x00 SYN...

LEARN ABOUT DEBIAN

bp_aacomp

BP_AACOMP(1p)						User Contributed Perl Documentation					     BP_AACOMP(1p)

NAME

       aacomp - amino acid composition of protein sequences

SYNOPSIS

	 aacomp [-f/--format FORMAT] [-h/--help] filename
	 or
	 aacomp [-f/--format FORMAT] < filename
	 or
	 aacomp [-f/--format FORMAT] -i filename

DESCRIPTION

       This scripts prints out the count of amino acids over all protein sequences from the input file.

OPTIONS

       The default sequence format is fasta.

       The sequence input can be provided using any of the three methods:

       unnamed argument
	    aacomp filename

       named argument
	    aacomp -i filename

       standard input
	    aacomp < filename

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason@bioperl.org

HISTORY

       Based on aacomp.c from an old version of EMBOSS

perl v5.14.2							    2012-03-02							     BP_AACOMP(1p)

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Remove specific strings from certain fields

Discussion started by: HLee1981

2. Shell Programming and Scripting

print first few lines, then apply regex on a specific column to print results.

Discussion started by: kchinnam

3. Shell Programming and Scripting

Print Specific lines when found specific character

Discussion started by: attila

4. UNIX for Dummies Questions & Answers

How to Detect Specific Pattern and Print the Specific String after It?

Discussion started by: radynaraya