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Compare two sample files and find common

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# 8  
Old 11-05-2012
Quote:
Originally Posted by manigrover
Thanks a lot. Can we convert file separated by spaces into column separated file first(second file)
Spacing seems to be the only problem in second file as I tried several options because of spacing nothing is working.
Using my above script it also works if you have spaces in first files.
So don't need to find any workaround for this.
I assume this is the same you want.Smilie
# 9  
Old 11-05-2012
Hi Pamu

actually in my system there is still same outputSmilie

my output is just same as my second file.

Code:
FHIT Adenosine Monotungstate Not Available,T2D Ado-P-Ch2-P-Ps-Ado Not Available,
CHRM1 Trospium Sanctura T2D Oxyphenonium Antrenyl T2D
PDE3B 5r-6-4-2-3-Iodobenzyl-3-Oxocyclohex-1-En-1-YlAminoPhenyl-5-Methyl-4,5-Dihydropyridazin-32h-One Not Available,T1D Hg9a-9, Nonanoyl-N-Hydroxyethylglucamide Not Available,
HSP90AA19-Butyl-8-2,5-Dimethoxy-Benzyl-9h-Purin-6-Ylamine Not Available,T2D 8-2-Chloro-3,4,5-Trimethoxy-Benzyl-2-Fluoro-9-Pent-4-Ylnyl-9h-Purin-6-Ylamine Not Available,T2D
ESR1 Chlorotrianisene Anisene,BD Conjugated Estrogens Conestoral,BD
INS M-Cresol Not Available,
FAH Acetoacetic Acid Not Available,BD 4-Hydroxy-Methyl-Phosphinoyl-3-Oxo-Butanoic Acid Not Available,
LPL Tyloxapol Alevaire,
ADAM17 3S-1-4-BUT-2-YN-1-YLOXYPHENYLSULFONYLPYRROLIDINE-3-THIOL Not Available T2D 3-4-but-2-yn-1-yloxyphenylsulfonylpropane-1-thiol Not Available T2D
GUCY1A2 Nitric Oxide INOmax,RA Isosorbide Mononitrate Conpin,
B4GALT1 6-Aminohexyl-Uridine-C1,5'-Diphosphate Not Available,
LCK 4-2-Acetylamino-2-3-Carbamoyl-2-Cyclohexylmethoxy-6,7,8,9-Tetrahydro-5h-Benzocyclohepten-5ylcarbamoyl-Ethyl-2-Phosphono-Phenyl-Phosphonic Acid Not Available,T1D 4-2-Acetylamino-2-1-3-Carbamoyl-4-Cyclohexylmethoxy-Phenyl-Ethylcarbamoyl-Ethyl-2-Phosphono-Phenoxy-Acetic Acid Not Available,T1D
GMDS Guanosine-5'-Diphosphate-Rhamnose Not Available,
LCT D-Gluconhydroximo-1,5-Lactam Not Available T2D Gluconolactone Not Available T2D
CALM1 3''-Beta-Chloroethyl-2'',4''-Dioxo-3, 5''-Spiro-Oxazolidino-4-Deacetoxy-Vinblastine Not Available T2D Prenylamine Bismethin,
RET 4-BROMO-2-FLUORO-N-4E-6-METHOXY-7-1-METHYLPIPERIDIN-4-YLMETHOXYQUINAZOLIN-41H-YLIDENEANILINE Not Available,
CYP1A2 2-PHENYL-4H-BENZOHCHROMEN-4-ONE Not Available,
PPARA Clofibrate Amotril,CD Gemfibrozil Bolutol,
TGFBR1 4-3-Pyridin-2-Yl-1h-Pyrazol-4-YlQuinoline Not Available,T2D Naphthyridine Inhibitor Not Available,T2D
PPARD 11E-OCTADEC-11-ENOIC ACID Not Available T2D 2S-2-3-2-fluoro-4-trifluoromethylphenylcarbonylaminomethyl-4-methoxybenzylbutanoic acid Not Available T2D
CSNK1G3 2Z-4-AMINO-2-4-METHOXYPHENYLIMINO-2,3-DIHYDRO-1,3-THIAZOL-5-YL4-METHOXYPHENYLMETHANONE Not Available T2D 4-AMINO-2-3-CHLOROANILINO-1,3-THIAZOL-5-YL4-FLUOROPHENYLMETHANONE Not Available,

Today is surely not a good day for me!
# 10  
Old 11-05-2012
I checked basically it seems there are irregular spaces between columns in second file. Thats seems to be the main issue......Smilie
# 11  
Old 11-05-2012
Quote:
Originally Posted by manigrover
actually in my system there is still same outputSmilie
Today is surely not a good day for me!
Using your sample files

Code:
$ awk 'NR==FNR{X[$0]=$0;next}{s=$1;$1="";for(i in X){if($0 ~ i){gsub(i,i" (matched)",$0)}};$0=s""$0}1' file1 file2
FHIT Adenosine (matched) Monotungstate Not Available,T2D Ado-P-Ch2-P-Ps-Ado Not Available,
CHRM1 Trospium (matched) Sanctura T2D Oxyphenonium (matched) Antrenyl T2D
PDE3B 5r-6-4-2-3-Iodobenzyl-3-Oxocyclohex-1-En-1-YlAminoPhenyl-5-Methyl-4,5-Dihydropyridazin-32h-One Not Available,T1D Hg9a-9, Nonanoyl-N-Hydroxyethylglucamide Not Available,
HSP90AA19-Butyl-8-2,5-Dimethoxy-Benzyl-9h-Purin-6-Ylamine Not Available,T2D 8-2-Chloro-3,4,5-Trimethoxy-Benzyl-2-Fluoro-9-Pent-4-Ylnyl-9h-Purin-6-Ylamine Not Available,T2D
ESR1 Chlorotrianisene (matched) Anisene,BD Conjugated Estrogens (matched) Conestoral,BD
INS M-Cresol Not Available,
FAH Acetoacetic Acid Not Available,BD 4-Hydroxy-Methyl-Phosphinoyl-3-Oxo-Butanoic Acid Not Available,
LPL Tyloxapol (matched) Alevaire,
ADAM17 3S-1-4-BUT-2-YN-1-YLOXYPHENYLSULFONYLPYRROLIDINE-3-THIOL Not Available T2D 3-4-but-2-yn-1-yloxyphenylsulfonylpropane-1-thiol Not Available T2D
GUCY1A2 Nitric Oxide (matched) INOmax,RA Isosorbide Mononitrate (matched) Conpin,
B4GALT1 6-Aminohexyl-Uridine-C1,5'-Diphosphate Not Available,
LCK 4-2-Acetylamino-2-3-Carbamoyl-2-Cyclohexylmethoxy-6,7,8,9-Tetrahydro-5h-Benzocyclohepten-5ylcarbamoyl-Ethyl-2-Phosphono-Phenyl-Phosphonic Acid Not Available,T1D 4-2-Acetylamino-2-1-3-Carbamoyl-4-Cyclohexylmethoxy-Phenyl-Ethylcarbamoyl-Ethyl-2-Phosphono-Phenoxy-Acetic Acid Not Available,T1D
GMDS Guanosine-5'-Diphosphate-Rhamnose Not Available,
LCT D-Gluconhydroximo-1,5-Lactam Not Available T2D Gluconolactone Not Available T2D
CALM1 3''-Beta-Chloroethyl-2'',4''-Dioxo-3, 5''-Spiro-Oxazolidino-4-Deacetoxy-Vinblastine (matched) Not Available T2D Prenylamine Bismethin,
RET 4-BROMO-2-FLUORO-N-4E-6-METHOXY-7-1-METHYLPIPERIDIN-4-YLMETHOXYQUINAZOLIN-41H-YLIDENEANILINE Not Available,
CYP1A2 2-PHENYL-4H-BENZOHCHROMEN-4-ONE Not Available,
PPARA Clofibrate (matched) Amotril,CD Gemfibrozil (matched) Bolutol,
TGFBR1 4-3-Pyridin-2-Yl-1h-Pyrazol-4-YlQuinoline Not Available,T2D Naphthyridine Inhibitor Not Available,T2D
PPARD 11E-OCTADEC-11-ENOIC ACID Not Available T2D 2S-2-3-2-fluoro-4-trifluoromethylphenylcarbonylaminomethyl-4-methoxybenzylbutanoic acid Not Available T2D
CSNK1G3 2Z-4-AMINO-2-4-METHOXYPHENYLIMINO-2,3-DIHYDRO-1,3-THIAZOL-5-YL4-METHOXYPHENYLMETHANONE Not Available T2D 4-AMINO-2-3-CHLOROANILINO-1,3-THIAZOL-5-YL4-FLUOROPHENYLMETHANONE Not Available,
NR3C1 Flunisolide (matched) Aerobid T2D Diflorasone (matched) Florone T2D
CTSD 1h-Benoximidazole-2-Carboxylic Acid Not Available T2D N-Aminoethylmorpholine Not Available T2D
TLL2 Carbobenzoxy-Pro-Lys-Phe-YPo2-Ala-Pro-Ome Not Available,
TYR Monobenzone (matched) AgeRite Alba,
HSD11B1 3,3-dimethylpiperidin-1-yl6-3-fluoro-4-methylphenylpyridin-2-ylmethanone Not Available,RA 5S-2-1S-1-4-fluorophenylethylamino-5-1-hydroxy-1-methylethyl-5-methyl-1,3-thiazol-45H-one Not Available,RA
C5 Eculizumab (matched) Soliris,
FGF1 Sucrose Octasulfate Not Available T2D Naphthalene Trisulfonate Not Available T2D
SORD Cp-166572, 2-Hydroxymethyl-4-4-N,N-Dimethylaminosulfonyl-1-Piperazino-Pyrimidine Not Available,
EGFR Gefitinib (matched) Iressa,T2D Panitumumab (matched) Vectibix,T2D
EPHB4 N-5-chloro-1,3-benzodioxol-4-yl-6-methoxy-7-3-piperidin-1-ylpropoxyquinazolin-4-amine Not Available T2D N'-5-CHLORO-1,3-BENZODIOXOL-4-YL-N-3,4,5- TRIMETHOXYPHENYLPYRIMIDINE-2,4-DIAMINE Not Available T2D
TPR N-1s-4-Bis2-ChloroethylAmino-1-Methylbutyl-N-6-Chloro-2-Methoxy-9-AcridinylAmine Not Available T2D Trypanothione Not Available,
CCL5 Heparin (matched) Disaccharide I-S Not Available,T1D Heparin (matched) Disaccharide Iii-S Not Available,

Here i can see many matched patterns.

Don't know what's wrong going with your machine..Smilie

Quote:
Originally Posted by Priyanka Chopra
I checked basically it seems there are irregular spaces between columns in second file. Thats seems to be the main issue......Smilie
@Priyanka,
Spaces in second file doesn't matter much while substituting single word. like Adenosin,
But it may fail if we are trying to substitute word with spaces like good man(first file) with good man(second file).
so here it will fail.
Last edited by pamu; 11-05-2012 at 08:18 AM..
# 12  
Old 11-05-2012
Hi Pamu

Thanks for reply. Although I tried in different machines at my place and still it's not working.

But I found that Adenosine monotungstatate is not present in first file but still it shows matched becasue adenosine is present which will be wrong in my case as I have to match whole word present in first file with whole word in second file columns.

Let me know if you come across any solution.
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