Login or Register to Ask a Question and Join Our Community


Shell Programming and Scripting

Fetch specific entries

Login to Discuss or Reply to this Discussion in Our Community

 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting Fetch specific entries
# 8  
Old 12-10-2012
Yes, output is not completely correct it has to be according he first row.

It should be 7 columns and second row should not contain inhibitor rather contain agonist.

sorry for that.
# 9  
Old 12-10-2012
Ok, then please provide the correct information to us. Otherwise no one can help you.
# 10  
Old 12-11-2012
Hi

I have corrected the sample output its only 6 columns overall, actually there are many drugs so I was unable to write all of those. But I have corrected sample drug output here in the same way all drug names have to be mentioned.

Code:
P11229    Talsaclidine isomer    DCL000268    Alzheimer's disease   Discontinued  agonist     
 P11229   Sabcomeline hydrochloride    DCL000279    Cardiovascular diseases    Phase IIa    agonist 
P11229    Talsaclidine fumarate    DCL000303    Alzheimer's disease        Discontinued   agonist
P11229    Xanomeline tartrate    DCL000328    Alzheimer's disease    Phase II          agonist

---------- Post updated 12-11-12 at 01:16 AM ---------- Previous update was 12-10-12 at 11:11 PM ----------

Kindly let me know if somebody has any question regarding the above question as I am still skeptic!
Last edited by Priyanka Chopra; 12-11-2012 at 12:33 AM..
# 11  
Old 12-11-2012
Code:
awk -F "\t" '/UniProt/{id=$NF} /Drug\(/{$1=$2="";a[$3 FS $4]=$0;next} {if ($3 FS $4 in a) print id,a[$3 FS $4],$2}' infile

P11229   Pirenzepine DAP000492 Peptic ulcer disease Approved Antagonist
P11229   Glycopyrrolate DAP001116 Anesthetic Approved Antagonist
P11229   Clidinium DAP001117 Abdominal/stomach pain Approved Antagonist
P11229   Dicyclomine DAP001118 Irritable bowel syndrome Approved Antagonist
P11229   Ethopropazine DAP001119 Parkinson's disease Approved Antagonist
P11229   Benztropine DAP001121 Parkinson's disease Approved Antagonist
P11229   Trihexyphenidyl DAP001122 Parkinson's disease Approved Antagonist
P11229   Propantheline DAP001123 Excessive sweating (hyperhidrosis) Approved Antagonist
P11229   Oxyphenonium DAP001124 Spasm Approved Antagonist
P11229   Biperiden DAP001125 Parkinson's disease Approved Antagonist
P11229   Cycrimine DAP001120 Parkinson's disease Approved Binder
P11229   Revatropate DCL000957 Chronic obstructive pulmonary disease Discontinued in Phase I Antagonist
P11229   Talsaclidine isomer DCL000268 Alzheimer's disease Discontinued Agonist
P11229   Sabcomeline hydrochloride DCL000279 Cardiovascular diseases Phase IIa Agonist
P11229   Talsaclidine fumarate DCL000303 Alzheimer's disease Discontinued Agonist
P11229   Xanomeline tartrate DCL000328 Alzheimer's disease Phase II Agonist
P11229   GSK573719 DCL000381 Chronic Obstructive Pulmonary Disease (COPD) Phase II Agonist
P11229   GSK961081 DCL000397 Chronic Obstructive Pulmonary Disease (COPD) Phase II completed Agonist
P11229   GSK1034702 DCL000402 Schizophrenia, Dementia Phase I completed Agonist
P11229   Darotropium DCL000514 COPD Suspended in Phase II in GSK 2009 Report Agonist
P11229   Darotropium + 642444 DCL000515 COPD Phase III Agonist
P11229   GSK961081 DCL000397 Chronic Obstructive Pulmonary Disease (COPD) Phase II completed Multitarget
P11229   Revatropate DCL000957 Chronic obstructive pulmonary disease Discontinued in Phase I Multitarget

# 12  
Old 12-11-2012
Thanks for reply!

It seems working to a certain extent but it's not retrieving the entries without disease names and approved status which are mentioned for example in lower part of the input.

Can u please check.
# 13  
Old 12-11-2012
Try to help you, but your request is hard to understand. Since I have written the frame command for you, if you understand it and do a small adjustment, you should get what you want.
# 14  
Old 12-11-2012
Thanks for reply.

Yes I checked and tried to do but I am not able to pick following data from input which does not include disease or approved name all other things in input which are mentioned in upper part of input are coming properly though.

Code:
TTDS00002	Agonist	77-LH-28-1	DNC000099
TTDS00002	Agonist	AC-260584	DNC000137
TTDS00002	Agonist	AC-42	DNC000138
TTDS00002	Agonist	AF150(S)	DNC000165
TTDS00002	Agonist	AF267B	DNC000166
TTDS00002	Agonist	LY-593039	DNC000910
TTDS00002	Agonist	NGX-267	DNC001012
TTDS00002	Agonist	Sabcomeline	DNC001264
TTDS00002	Agonist	WAY-132983	DNC001510
TTDS00002	Inhibitor	Arecoline	DNC002508
TTDS00002	Inhibitor	Acetic acid 8-aza-bicyclo[3.2.1]oct-6-yl ester	DNC003640
TTDS00002	Inhibitor	Benzoic acid 8-aza-bicyclo[3.2.1]oct-6-yl ester	DNC003654
TTDS00002	Inhibitor	Propionic acid 8-aza-bicyclo[3.2.1]oct-6-yl ester	DNC003659
TTDS00002	Inhibitor	3-Methyl-7-pyrrolidin-1-yl-hept-5-yn-2-one	DNC004147
TTDS00002	Inhibitor	2-Methyl-6-pyrrolidin-1-yl-hex-4-ynal oxime	DNC004159
TTDS00002	Inhibitor	ISOCLOZAPINE	DNC004166
TTDS00002	Inhibitor	SB-202026	DNC004272
TTDS00002	Inhibitor	HIMBACINE	DNC004995
TTDS00002	Inhibitor	RR(17)PZ	DNC005944
TTDS00002	Inhibitor	Bo(15)PZ	DNC005945
TTDS00002	Inhibitor	DIFLUOROBENZTROPINE	DNC005986
TTDS00002	Inhibitor	BI-1356	DNC007901
TTDS00002	Inhibitor	FM1-10	DNC008187
TTDS00002	Inhibitor	FM1-43	DNC008188
TTDS00002	Inhibitor	A-987306	DNC008996
TTDS00002	Inhibitor	GNF-PF-5618	DNC009476
TTDS00002	Inhibitor	CREMASTRINE	DNC009504
TTDS00002	Inhibitor	1,1-diphenyl-2-(3-tropanyl)ethanol	DNC009866
TTDS00002	Inhibitor	R-dimethindene	DNC009877
TTDS00002	Inhibitor	Tiotropium Bromide	DNC009882
TTDS00002	Inhibitor	XANOMELINE	DNC011170
TTDS00002	Inhibitor	4-(4-butylpiperidin-1-yl)-1-o-tolylbutan-1-one	DNC011171
TTDS00002	Inhibitor	1-Methyl-1-(4-pyrrolidin-1-yl-but-2-ynyl)-urea	DNC011427
TTDS00002	Inhibitor	ISOLOXAPINE	DNC011498
TTDS00002	Inhibitor	1'-Benzyl-3-phenyl-[3,4']bipiperidinyl-2,6-dione	DNC011500
TTDS00002	Inhibitor	CARAMIPEN	DNC011755
TTDS00002	Inhibitor	FLUMEZAPINE	DNC011857
TTDS00002	Inhibitor	AMINOBENZTROPINE	DNC011950
TTDS00002	Inhibitor	2-(4-Diethylamino-but-2-ynyl)-isoindole-1,3-dione	DNC012005
TTDS00002	Inhibitor	3-Tetrazol-2-yl-1-aza-bicyclo[2.2.2]octane	DNC012098
TTDS00002	Inhibitor	SULFOARECOLINE	DNC012122
TTDS00002	Inhibitor	6-Dimethylamino-2-methyl-hex-4-ynal oxime	DNC012306
TTDS00002	Inhibitor	7-Pyrrolidin-1-yl-hept-5-yn-2-one	DNC012322
TTDS00002	Inhibitor	7-Dimethylamino-3-methyl-hept-5-yn-2-one	DNC012323
TTDS00002	Inhibitor	7-Pyrrolidin-1-yl-hept-5-yn-2-one oxime	DNC012330
TTDS00002	Inhibitor	7-Dimethylamino-hept-5-yn-2-one	DNC012350
TTDS00002	Inhibitor	7-Dimethylamino-hept-5-yn-2-one oxime	DNC012351
TTDS00002	Inhibitor	N-(4-Dimethylamino-but-2-ynyl)-N-methyl-acetamide	DNC012363
TTDS00002	Inhibitor	ACECLIDINE	DNC012502
TTDS00002	Inhibitor	N-methoxyquinuclidine-3-carboximidoyl fluoride	DNC012588
TTDS00002	Inhibitor	BRL-55473	DNC012594
TTDS00002	Inhibitor	N-methoxyquinuclidine-3-carboximidoyl chloride	DNC012616
TTDS00002	Inhibitor	2,8-Dimethyl-1-oxa-8-aza-spiro[4.5]decan-3-one	DNC012765
TTDS00002	Inhibitor	3alpha-(bis-chloro-phenylmethoxy)tropane	DNC013136
TTDS00002	Inhibitor	3-(3-benzylamino)-piperidin-2-one	DNC013219
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. UNIX for Beginners Questions & Answers

How to fetch specific data from a file.?

Hi , I have a file which contains 2 days logs(here it is 24 and 25) I want to list data only for date 25 fron the file. please suggest me how should i get this. file content mentioned below 17-05-24 Name Succ Fail 00:00:29 ... (5 Replies)
Discussion started by: scriptor
5 Replies

2. Shell Programming and Scripting

Fetch entries with specific pattern

Hi all, I have following sample input file which is a part of big file: ID AINX_HUMAN Reviewed; 499 AA. AC Q16352; B1AQK0; Q9BRC5; DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot. DT 23-JAN-2002, sequence version 2. DT 28-NOV-2012, entry version 123.... (2 Replies)
Discussion started by: kareena
2 Replies

3. Shell Programming and Scripting

Request to check:Fetch certain entries

Hi all. Kindly check it it's urgent!! I have one big file from which which I have to fetch certain data I have attached a small part of this file. from the attached file, I have to fetch and arrange data in 3 columns 1 Generic name 2. Brand names 3. Drug... (10 Replies)
Discussion started by: manigrover
10 Replies

4. Shell Programming and Scripting

Fetch entries in front of specific word till next word

Hi all I have following file which I have to edit for research purpose file:///tmp/moz-screenshot.png body, div, table, thead, tbody, tfoot, tr, th, td, p { font-family: "Liberation Sans"; font-size: x-small; } Drug: KRP-104 QD Drug: Placebo Drug: Metformin|Drug:... (15 Replies)
Discussion started by: Priyanka Chopra
15 Replies

5. Shell Programming and Scripting

Search specific name in a file and fetch specific entries

Hi all, I have 2 files, One file contain data like this FHIT CS CHRM1 PDE3A PDE3B HSP90AA1 PTK2 HTR1A ESR1 PARP1 PLA2G1B These names are mentioned in the second file(Please see attached second file) as (7 Replies)
Discussion started by: manigrover
7 Replies

6. Shell Programming and Scripting

Urgent request to consider:Search specific name in a file and fetch specific entries

Hi all, I have 2 files, One file contain data like this FHIT CS CHRM1 PDE3A PDE3B HSP90AA1 PTK2 HTR1A ESR1 PARP1 PLA2G1B These names are mentioned in the second file(Please see attached second file) as # Drug_Target_X_Gene_Name:(Where X can be any number (1-1000) (1 Reply)
Discussion started by: manigrover
1 Replies

7. Shell Programming and Scripting

How to fetch specific fields

Dear Friends, Please provide some commands to fecth specific filed (data yellow color) from below data.. Input data 2648: 1;20120707;3591|4;20290107;90|5;20290107;3|9;20120705;0|10;20120705;0|16;20290113;15|29;20120705;0 2658: 1;20120722;0|4;20290422;1200|9;20120705;0|10;20120705;0 2646:... (4 Replies)
Discussion started by: suresh3566
4 Replies

8. Shell Programming and Scripting

fetch last line no form file which is match with specific pattern by grep command

Hi i have a file which have a pattern like this Nov 10 session closed Nov 10 Nov 9 08:14:27 EST5EDT 2010 on tty . Nov 10 Oct 19 02:14:21 EST5EDT 2010 on pts/tk . Nov 10 afrtetryytr Nov 10 session closed Nov 10 Nov 10 03:21:04 EST5EDT 2010 Dec 8 Nov 10 05:03:02 EST5EDT 2010 ... (13 Replies)
Discussion started by: Himanshu_soni
13 Replies

9. Shell Programming and Scripting

How to fetch a specific line from file

Hi, I have text file in the following strucher . The files contain hondreds of lines. value1;value2;value3;value4 I would like to get back the line with lowest date (values4 field). In this case its line number 3. groupa;Listener;1;20110120162018 groupb;Database;0;20110201122641... (4 Replies)
Discussion started by: yoavbe
4 Replies

10. Shell Programming and Scripting

To fetch specific words from a file

Hi All, I have a file like this,(This is a sql output file) cat query_file 200000029 12345 10001 0.2 0 I want to fetch the values 200000029,10001,0.2 .I tried using the below code but i could get... (2 Replies)
Discussion started by: girish.raos
2 Replies
Login or Register to Ask a Question