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Request to check:Fetch certain entries

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Top Forums Shell Programming and Scripting Request to check:Fetch certain entries
# 8  
Old 07-23-2012
Request to check
Hi

Thanks for reply.

I did this thing

Quote:
awk 'k>0 {if (a[k] && k==2) {print a[1]": "a[2]": "a[3]; a[1]=a[2]=a[3]="";} a[k]=a[k]?a[k]" "$0:$0; k=0;} /^# Drug_Target_.*_Gene_Name/ {k=3;} /^# Brand_Name/ {k=2;} END {if (a[1]) print a[1]" "a[2]" "a[3];}' drugbank.txt >*drugbank3.txt
but in the output file there is nor generic name now

the output is like this
Quote:
: Refludan: F2
: Erbitux: FCGR2A FCGR2B FCGR2C EGFR FCGR3B C1R C1QA C1QB C1QC FCGR3A C1S FCGR1A
: Pulmozyme: Not Available
: Ontak: IL2RA IL2RB IL2RG
: Enbrel: C1S C1R C1QA C1QB C1QC TNF TNFRSF1B FCGR1A FCGR3A FCGR2A FCGR2B FCGR2C LTA FCGR3B
: Angiomax: F2
: Eligard: GNRHR
: Pegasys: IFNAR2 IFNAR1
: Activase (Genentech Inc): PLG FGA PLAUR SERPINE1
: Geref: GHRHR
: Wellferon (GlaxoSmithKline): IFNAR2 IFNAR1
: Aranesp: EPOR
: Abbokinase: NID1 PLG PLAUR PLAU PLAT SERPINE1 SERPINB2 SERPINA5 LRP2 ST14
: Zoladex: LHCGR GNRHR
: Retavase (Centocor): PLG FGA PLAUR SERPINE1
: Epogen: EPOR
: Calcimar: CALCR
: Alferon (Interferon Sciences Inc.): IFNAR1 IFNAR2
: Neulasta (Amgen Inc.): CSF3R ELANE
: Immunex: CSF2RA IL3RA CSF2RB SDC2 PRG2
: SecreFlo: SCTR
: PEG-Intron (Schering Corp): IFNAR1 IFNAR2
: Elspar (Merck & Co. Inc): Not Available
: Thyrogen (Genzyme Inc): TSHR
: Advate: LRP1 MCFD2 F10 F9 VWF PHYH ASGR2 HSPA5 CALR CANX LMAN1
: Kineret (Amgen Inc): IL1R1
: Neosporin:
: Civacir: C4B C5 FCGR1A FCGR1B FCGR2A FCGR2B FCGR2C FCGR3A FCGR3B C3 C4A
: Eminase (Wulfing Pharma GmbH): PLG FGA PLAUR SERPINE1
: Novolin R (Novo Nordisk): LRP2 IGFBP7 SYTL4 INSR IGF1R RB1 CTSD IDE PCSK2 CPE PCSK1 NOV
: TNKase (Genentech Inc): CANX LRP1 PLG FGA PLAUR SERPINE1 SERPINB2 CLEC3B KRT8 ANXA2 CALR
: Repronex: FSHR LHCGR
: Actimmune: IFNGR1 IFNGR2
: Roferon A (Hoffmann-La Roche Inc): IFNAR1 IFNAR2
: Adiuretin: AVPR2 AVPR1A AVPR1B
: NovoSeven (Novo Nordisk): F10 HPN TFPI GGCX F7 F3
: Neumega: IL11RA
: Kepivance (Amgen Inc): FGFR2 NRP1 FGFR1 FGFR
# 9  
Old 07-23-2012
Hi,

It's in my code that you have to replace " " by ":" and not in your code " " by ": " . . .
So the right code is :
Quote:
awk 'k>0 {if (a[k] && k==2) {print a[1]":"a[2]":"a[3]; a[1]=a[2]=a[3]="";} a[k]=a[k]?a[k]","$0:$0; k=0;} /^# Drug_Target_.*_Gene_Name/ {k=3;} /^# Generic/ {k=1;} /^# Brand_Name/ {k=2;} END {if (a[1]) print a[1]":"a[2]":"a[3];}' drugbank.txt >drugbank3.txt
So now you will have the first field seperator as ":"
and the second fields separator for the drug targets as ","
# 10  
Old 11-14-2012
Changes in code to provide proper result with one additional fiield
Hi all


I am using following code to get results for brand name drug target name and generic name from my attached fiile



Code:
Code:
awk 'k>0 {if (a[k] && k==2) {print a[1]":"a[2]":"a[3]; a[1]=a[2]=a[3]="";} a[k]=a[k]?a[k]","$0:$0; k=0;} /^# Drug_Target_.*_Gene_Name/ {k=3;} /^# Generic/ {k=1;} /^# Brand_Name/ {k=2;} END {if (a[1]) print a[1]":"a[2]":"a[3];}' drugbank.txt >drugbank3.txt

But when I change the code to additional field Drug Type. It is not giving me proper results can anybody guide to make changes in this code to get drug type as well.

---------- Post updated at 10:30 PM ---------- Previous update was at 10:06 PM ----------

Hi

Its working now using the same code completely Smilie dont know why? can any body try on his or her system?Smilie
Last edited by Franklin52; 11-30-2012 at 04:43 AM.. Reason: Code tags
# 11  
Old 11-29-2012
Request to check
Hi all


I am using foloowing code for my above attached file to retrieve mechanis of action and indication alon gwith other details but its nto working properly >Can anybody check anything wrong with this code

Code:
awk 'k>0 {if (a[k] && k==2) {print a[1]":"a[2]":"a[3]":"a[4]":"a[5]":"a]6]; a[1]=a[2]=a[3]=a[4]=a[5]=a[6]"";} a[k]=a[k]?a[k]","$0:$0; k=0;} /^# Drug_Target_.*_Gene_Name/ {k=1;} /^# Generic/ {k=1;} /^# Brand_Name/ {k=2;}  /^# Drug_Type/ {k=3;} /^# Indication/ {k=5;} /^# Mechanism_ Of_ Action / {k=6;} END {if (a[1]) print a[1]":"a[2]":"a[3]":"a[4]":"a[5]":"a[6];}' drugbank.txt >drugbanknew2.txt

My output entries are not right

---------- Post updated at 08:16 PM ---------- Previous update was at 06:04 AM ----------

Please let me know if somebody has suggestions to change the above code as I need it or if somebody didnt understand the questions kindly let me know
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