in reply to Re: probably stupid mistake
in thread probably stupid mistake

oh sorry, well the contents of the first file looks like this (its going to be larger, not that it should matter): 

GRB2
AFF4
GGGB
C7orf42

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and of the second file like these

KEGG_PATHWAY    hsa04722:Neurotrophin signaling pathway    33    0.147
+86271171251902    4,04E+09    GRB2, CAMK2G, NFKB1, MAPKAPK2, MAGED1, 
+KRAS, MAP3K3, MAP3K1, BCL2, RAC1, GAB1, RHOA, CAMK2D, SH2B3, NGFRAP1,
+ SHC1, MAP2K7, FRS2, PIK3R1, IRS2, RELA, YWHAB, YWHAE, TP73, NRAS, MA
+PK1, CRKL, JUN, NTRK2, CALM3, MAPK9, SORT1, RAP1A    575    124    50
+85    2.353.506.311.360.440    6,83E+11    6,83E+11    0.004929324234
+03758
KEGG_PATHWAY    hsa05200:Pathways in cancer    63    0.2822833587239  
+  1,86E+10    FGF18, FGF5, PPARD, FGF9, NFKB1, FGF13, PTEN, CCNE2, AC
+VR1B, MAX, CDKN2B, RHOA, RALB, RALA, FAS, TPR, CHUK, RELA, RXRA, LEF1
+, CDK6, RB1, STK4, DAPK1, JUP, MAPK1, CCDC6, CRKL, HIF1A, NCOA4, JUN,
+ VEGFA, MAPK9, TRAF1, WNT5A, APC2, XIAP, GRB2, IGF1R, KRAS, ITGAV, BC
+L2, RAC1, RUNX1, PIK3R1, APC, CEBPA, COL4A4, FZD8, COL4A1, IL8, VHL, 
+CREBBP, TGFBR2, SMAD2, FZD5, STAT3, NRAS, RASSF5, CDKN1B, ITGA6, RASS
+F1, JAK1    575    328    5085    16.985.949.098.621.400    0.0031423
+34832759053    0.0010485440045103767    0.02269450903600312
KEGG_PATHWAY    hsa04310:Wnt signaling pathway    35    0.156824088179
+94445    4,76E+10    WNT5A, PPARD, APC2, PPP2R5A, CAMK2G, PPP2R5C, PP
+P3R1, RAC1, NFAT5, PPP3CB, RHOA, CAMK2D, FRAT2, PRKACA, CHP, PLCB1, F
+BXW11, APC, FZD8, VANGL1, NLK, VANGL2, CREBBP, LEF1, SMAD2, FZD5, SEN
+P2, SFRP5, SFRP1, CCND2, CSNK1E, JUN, MAPK9, SIAH1, PPP2R5E    575   
+ 151    5085    20.498.128.419.234.000    0.008008272140318184    0.0
+02008108692225119    0.05796850410908494

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Re^3: probably stupid mistake
by toolic (Bishop) on Apr 01, 2011 at 13:58 UTC
    When I run your code using your 2 input files, I get the following output: 
    success
success

    [download]
    You need to describe in much more detail what problem you are having.
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[d/l]
      Yes, Your code works properly for me too.
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      the problem I am having is that although I also want to get success success (or basically instead of printing that to print $fields1 and $line2 if the if statement is true), I am not getting anything at all

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        or to phrase my problem differently, I want a script that reads each word from a file that in each line there is one word and then reads each line from a second file and if the word from the first file is found in the line of the second to print this line. In theory my script should work, it is working for you but not for me and I really do not understand why.

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