How to join multiple files?


 
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# 1  
Old 03-23-2010
How to join multiple files?

I am trying to join a few hundred files using join. Is there a way to use while read or something else to automate this. My problem is the following.

Day 1
Code:
City Temp
ABC    20
DEF    30
HIJ     15

Day 2
Code:
City  Temp
ABC    22
DEF    29
KLM     5

Day 3
Code:
City  Temp
 ABC    24
 DEF    27
 KLM     8

And so on for a few hundred days.

I am trying to make a file that looks like this
Code:
ABC  20,22,24
DEF  30,29,27
HIJ   15,,
KLM  ,5,8

My command looks like this:
Code:
join -t',' -j 2 -a1 -a2 -o 0 1.3 2.3 file1.csv file2.csv

where the common identifier is in column 2 (-j2) and the value i want to amend my master file with is always in column 3 (-o 1.3 2.3). I'm trying to avoid running this command over and over again, as the -o option keeps on growing (-o 1.3 1.4 2.3 --> -0 1.3 1.4 1.5 2.3 --> -o 1.3 1.4 1.5 1.6 2.3 --> -o 1.3 1.4 1.5...1.n 2.3, where n=~200)

Is there a way to use while read or something else to make the file?

Your help is much appreciated.

Thanks.

Last edited by zaxxon; 03-24-2010 at 09:33 AM.. Reason: use code tags please, ty
# 2  
Old 03-23-2010
Here's an idea using Perl, assuming that the file contents are in the same order as the file names i.e. file1.csv has data for day 1, file2.csv has data for day 2, and so on...

Code:
$ 
$ 
$ cat file1.csv
Day 1
City Temp
ABC 20
DEF 30
HIJ 15
$ 
$ 
$ cat file2.csv
Day 2
City Temp
ABC 22
DEF 29
KLM 5
$ 
$ 
$ cat file3.csv
Day 3
City Temp
ABC 24
DEF 27
KLM 8
$ 
$ 
$ ls *.csv | sort | cat * | perl -lane '!/Day|City/ and $x{$F[0]}.=",".$F[1]; END{foreach $k (keys %x){print $k,"\t",substr($x{$k},1)}}'
ABC 20,22,24
DEF 30,29,27
HIJ 15
KLM 5,8
$ 
$

Not sure if this is what you wanted. Note that putting all those commas after "HIJ" means that
(a) either the list of cities is hardcoded/known/present in a separate file, or
(b) a separate walk through of all files is done first to get such a list, and then the hash is built

Consider what happens if "HIJ" is absent from files 1 through 199, and present in file # 200. You'd have to have a hash entry with 199 commas on the left.

The city list could also be determined by a single parse of all files, but the program for that would be much more elaborate, I think.

tyler_durden
# 3  
Old 03-24-2010
Thanks, but the problem is that the list of the cities changes from file to file, so they are not in the same order every time. Also this method makes it seem like KLM had temperatures of 5 and 8 on days 1 and 2, when the temps were actually observed on days 2 and 3, which is why I have to have commas in there. The file is a csv, so when i read it into a spreadsheet there will be empty cells at times when a temp was not updated for a particular city.

Thanks for the try though.
# 4  
Old 03-24-2010
Quote:
Originally Posted by theFinn
... but the problem is that the list of the cities changes from file to file, so they are not in the same order every time. Also this method makes it seem like KLM had temperatures of 5 and 8 on days 1 and 2, when the temps were actually observed on days 2 and 3, which is why I have to have commas in there. The file is a csv, so when i read it into a spreadsheet there will be empty cells at times when a temp was not updated for a particular city.
...
I thought so.
Here's a more elaborate program that should take care of those issues. The script comments should be self-explanatory.

Code:
$
$
$ cat file1.csv
Day 1
City Temp
ABC    20
DEF    30
HIJ     15
$
$ cat file2.csv
Day 2
City  Temp
ABC    22
DEF    29
KLM     5
$
$ cat file3.csv
Day 3
City  Temp
 ABC    24
 DEF    27
 KLM     8
$
$ # show the contents of the Perl program
$ cat -n join_temps.pl
     1  #!perl -w
     2
     3  my $ptrn = "file*.csv";  # the pattern of text files that should be globbed
     4  my $maxday = 1;          # variable to store the maximum day number was encountered
     5  my $day;                 # day number in the current csv file that is being processed
     6  my %temps;               # the hash that stores the temp value for the key "cityNNN"
     7  my %cities;              # the hash to store city names
     8
     9  while (glob $ptrn) {
    10    # open the csv file and process it
    11    open(IN, $_) or die "Can't open file $_: $!";
    12    while (<IN>) {
    13      # trim newline and whitespaces
    14      chomp;
    15      s/^\s*//g;
    16      s/\s*$//g;
    17      # capture the day number as a 3 digit number; set $maxday if needed
    18      # otherwise, set the key=>value pair in the hash %temps
    19      # key = City1NNN, value = temperature; NNN = 3 digit day e.g. 001,098,123 etc.
    20      if (/^Day (\d+)/) {$maxday = $1 if $1 > $maxday; $day = sprintf("%03d",$1)}
    21      elsif (!/^City/) {@x = split/[ ]+/; $cities{$x[0]}=1; $temps{$x[0].$day}=$x[1]}
    22    }
    23    close(IN) or die "Can't close file $_: $!";
    24  }
    25
    26  # now start printing the output data in the form: City<=TAB=>temp1,temp2,temp3,...
    27  foreach $k (sort keys %cities){
    28    print $k,"\t";
    29    foreach $i (1..$maxday) {
    30      $n = sprintf("%03d",$i);
    31      $temp = defined $temps{$k.$n} ? $temps{$k.$n} : "";
    32      # you can code this if your Perl version is 5.10 or higher => $temp = $temps{$k.$n} // "";
    33      print $i == 1 ? $temp : ",$temp";
    34    }
    35    print "\n";
    36  }
$
$ # run the Perl program
$ perl join_temps.pl
ABC     20,22,24
DEF     30,29,27
HIJ     15,,
KLM     ,5,8
$
$
$

HTH,
tyler_durden


NB - You may want to change the tab "\t" at line 28 to comma "," for a proper csv file.

Last edited by durden_tyler; 03-24-2010 at 03:05 PM..
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