in reply to Parsing csv without changing dimension of original file

It looks like you added the line: 
  next if $. < 2;

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to the stackoverflow script.

Without access to the data - I'm guessing that this suppresses output of the heading line, and might cause the problem you have seen.

You can avoid speculation about your intent, and get better responses if you show a sample of the original data, and the output you expect.

        ...it is unhealthy to remain near things that are in the process of blowing up.     man page for WARP, by Larry Wall

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Re^2: Parsing csv without changing dimension of original file
by huck (Prior) on Mar 06, 2017 at 20:17 UTC

    Because there is no close $fh;between the two opens next if $. < 2; is meaningless if there are any lines in kegg_pathway_title.txt

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Re^2: Parsing csv without changing dimension of original file
by zillur (Novice) on Mar 06, 2017 at 23:56 UTC

    Thank you very much for your reply. Here is the sample of my original data "kegg_pathway_title.txt":

     PVX_088085    Protein processing in endoplasmic reticulum    
PVX_114095    Protein processing in endoplasmic reticulum    
PVX_123055    Ribosome biogenesis in eukaryotes
PYYM_1032000    -    
PYYM_1120600    -
PCYB_031930    Purine metabolism; Metabolic pathways; DNA replication;
+ Pyrimidine metabolism

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    The orhtogroups_3.csv has 13 columns

    Cparvum    Bmicroti    Tparva    Pberghei    Pchabaudi    Pcynomolgi  
+  Pfalciparum    Pknowlesi    Preichenowi    Pvivax    Pyoelii    Pma
+lariae    Tgondii
OG0000000                PBANKA_0000600, PBANKA_0000701, PBANKA_000080
+1, PBANKA_0001001, PBANKA_0001101, PBANKA_0001201, PBANKA_0001301, PB
+ANKA_0001401, PBANKA_0001501, PBANKA_0006300, PBANKA_0006401, PBANKA_
+0006501, PBANKA_0006600, PBANKA_0006701,
OG0000001                                                PmUG01_000101
+00.1-p1, PmUG01_00010200.1-p1, PmUG01_00010400.1-p1, PmUG01_00010500.
+1-p1, PmUG01_00010600.1-p1, PmUG01_00010700.1-p1, PmUG01_00010800.1-p
+1, PmUG01_00010900.1-p1, PmUG01_00011000.1-p1, PmUG01_00011300.1-p1, 
+PmUG01_00011400.1-p1, PmUG01_00011600.1-p1, PmUG01_00011700.1-p1, PmU
+G01_00012100.1-p1, PmUG01_00012200.1-p1,

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    Expected output: 

        Cparvum    Bmicroti    Tparva    Pberghei    Pchabaudi    Pcynomol
+gi    Pfalciparum    Pknowlesi    Preichenowi    Pvivax    Pyoelii   
+ Pmalariae    Tgondii
OG0000000                -    , -    , -    , -    , -    , -    , -  
+  , -    , -    , -    , -    , -    , -    , -    , -    , -    , - 
+   , -    , -    , -    , -    , -    , -    , -    , -    , -    , -
+    , -    , -    , -    , -    , -    , -    , -    , -    , -    , 
+-    , -    , -    , -    , -    , -    , -    , -    , -    , -    ,
+ -    , -    , -    , -    , -    , -    , -    , -    , -    , -    
+, -    , -    , -    , -    , -    , -    , -    , -    , -    , -   
+ , -    , -    , -    , -    , -    , -    , -    , -    , -    , -  
+  , -    , -    , -    , -    , -    , -    , -    , -    , -    , - 
+   , -    , -    , -    , -    , -    , -    , -    , -    , -    , -
+    , -    , -    , -    , -    , -    , -    , -    , -    , -    , 
+-    , -    , -    , -    , -    , -    , -    , -    , -    , -    ,
+ -    , -    , -    , -    , -    , -    , -    , -    , -    , -    
+, -    , -    
OG0000024    -    , -    , -    , -        -    , -    , -        -   
+ , -    , -        -    , -    , -    , -        -    , -    , -     
+   Protein processing in endoplasmic reticulum    , -    , -    , -  
+  , -        -    , -    , -        -    , -    , -        -    , -  
+  , -        -    , -    , -    , -        -    , -    , -        -  
+  , -    , -    , -        -    , -    , -    , -    , -    , -    , 
+-    , -    , -    , -    , -    , -    , -    , -    , -    
OG0000025    -    , -    , -        -    , -    , -    , -        -   
+ , -    , -    , -        -    , -    , -    , -        -    , -    ,
+ -    , -        Protein processing in endoplasmic reticulum    , Pro
+tein processing in endoplasmic reticulum    , -    , Ribosome biogene
+sis in eukaryotes        -    , -    , -    , -        -    , -    , 
+-    , -        -    , -    , -    , -        -    , Protein processi
+ng in endoplasmic reticulum    , Protein processing in endoplasmic re
+ticulum    , Ribosome biogenesis in eukaryotes        -    , -    , -
+    , -        -    , -    , -    , -        -    , -    , -    , -  
+  , -    , -    , -    
OG0000026

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    I want the column number (13) in orthogroups_3.csv and the parsed results to be same. Best regards Zillur

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      Well there are many many things wrong here

      in your original example page http://stackoverflow.com/questions/11678939/replace-text-based-on-a-dictionary you missed the part where it says "I have a dictionary(dict.txt). It is space separated and it reads like this:. Your kegg_pathway_title.txt instead has a tab after the replace-from field. In a way that is easy to fix, change the Line to 

      my %dict =  map { chomp; split "\t", $_, 2 } <$fh>;

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      Next 

       > grpsTbl <- read.csv("Orthogroups_3.csv", header=T, sep = "\t", row.
+names = 1, stringsAsFactors=F)

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      implies that the fields are separated by a tab (\t). Yes your column headers are separated by a tab, and there are tabs in your other rows, but row OG0000000 only has 5 tab separated fields, three of them being blank due to consecutive tabs, and 
      "PBANKA_0000600, PBANKA_0000701, PBANKA_0000801, PBANKA_0001001, PBANK
+A_0001101, PBANKA_0001201, PBANKA_0001301, PBANKA_0001401, PBANKA_000
+1501, PBANKA_0006300, PBANKA_0006401, PBANKA_0006501, PBANKA_0006600,
+ PBANKA_0006701,"

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      being considered as one field, being number 5. There is a tab however after the OG0000000 at least

      The next line OG0000001 does have 13 tab delimited fields, OG0000001 has a tab after it to put it in its own column, followed by 11 blank fields due to consecutive tabs, and 

      "PmUG01_00010100.1-p1, PmUG01_00010200.1-p1, PmUG01_00010400.1-p1, PmU
+G01_00010500.1-p1, PmUG01_00010600.1-p1, PmUG01_00010700.1-p1, PmUG01
+_00010800.1-p1, PmUG01_00010900.1-p1, PmUG01_00011000.1-p1, PmUG01_00
+011300.1-p1, PmUG01_00011400.1-p1, PmUG01_00011600.1-p1, PmUG01_00011
+700.1-p1, PmUG01_00012100.1-p1, PmUG01_00012200.1-p1,"

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      being considered the contents of the 13th column

      Given the following as your dictionary 

      PVX_088085    Protein processing in endoplasmic reticulum    
PVX_114095    Protein processing in endoplasmic reticulum    
PVX_123055    Ribosome biogenesis in eukaryotes
PYYM_1032000    -    
PYYM_1120600    -
PCYB_031930    Purine metabolism; Metabolic pathways; DNA replication;
+ Pyrimidine metabolism

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      one notices that none of the replace-from fields in it even occur in your sample Orthogroups_3.csv file at all, so your expected output is a myth.

      and besides the tab after the replace-from in your dictionary file, adding this code identifies a major problem 

      for my $k (keys %dict) {
  my $v=$dict{$k}; 
  warn 'for lookup:'.$k.' tab in field:'.$v."\n" if ($v=~"\t"); 
  }

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      result 
      for lookup:PVX_114095 tab in field:Protein processing in endoplasmic r
+eticulum
for lookup:PYYM_1032000 tab in field:-
for lookup:PVX_088085 tab in field:Protein processing in endoplasmic r
+eticulum

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      Those new tabs introduce "extra columns" to the output.

      The code that identifies all these problems is 

       
# This script was excerpted from http://stackoverflow.com/questions/11
+678939/replace-text-based-on-a-dictionary
use strict;
use warnings;
#use Text::CSV;
use Data::Dumper; 
  local $Data::Dumper::Deepcopy=1;
  local $Data::Dumper::Purity=1;
  local $Data::Dumper::Sortkeys=0;
  local $Data::Dumper::Indent=3; 

open my $fh, '<', 'kegg_pathway_title.txt' or die $!;
my %dict =  map { chomp; split "\t", $_, 2 } <$fh>;
warn Dumper \%dict; 
for my $k (keys %dict) {
  my $v=$dict{$k}; 
  warn 'for lookup:'.$k.' tab in field:'.$v."\n" if ($v=~"\t"); 
  }
#my %dict =  map { chomp; split ' ', $_, 2 } <$fh>;
my $re = join '|', keys %dict;
#close $fh;
open $fh, '<', 'Orthogroups_3.csv' or die $!;

while (<$fh>) {
print $. ."\n";
  next if $. < 2;
  my @a0=split("\t",$_); warn Dumper \@a0; 
  s/($re)/$dict{$1}/g;
  print;
}

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      All this leads me to think you dont have much of a clue as to what you are doing and are just trying cookie-cutter examples found on the web. This is a bad thing to do

      Edit: code tabs around the huge fields, but im not sure its any better

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        Thank you very much for your comment. Sorry for the inconvenience. Using "sep=\t" in your first script solved the problem and this give me the exact output as the latest script

        my %dict =  map { chomp; split '\t', $_, 2 } <$fh>;

        I have another problem. In the result, I still have previous text in many cells. Its strange, some cells replaced exactly some not. Either they might not be replaced or replaced by the 1st column of the 'egg_pathway_title.txt'. I was trying to delete those strings but failed. What I have done

        ut -f1 bioDBnet_db2db_KEGG_Title_final.txt > exclude-these.txt

        but failed. I have tried in many ways. Is there any way to upload my files here? Best Regards Zillur

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