Adding find contents to array

Question

I've currently got a script that generates R commands based on the output of find

#!/bin/bash
PATHX="/path/to/my/files"
find "${PATHX}" -maxdepth 1 -type f -name "*.csv" | while read d; do
FN=$(echo -n "${d}" | cut -d/ -f5 | cut -d. -f1)
echo "${FN}<-read.csv(\"${PATHX}/${FN}.csv\",header=TRUE)"
# <snip> etc .etc. etc.
echo "${FN}_2y<-tail(${FN}_log,730)"
done

This works great. But I've got one problem with one R command :

df<-data.frame(list,of,columns,goes,here)

I can't figure out how I can integrate this into the find/while above, namely I need to output a list of ${FN}_2y into the data.frame() function.

So for example, assume my script outputted :

• a_2y
• b_2y
• c_2y

I need to end up with df<-data.frame(a_2y,b_2y,c_2y)

Clarification further to question in comments, I only need one instance of data.frame, right at the very end once the all the csv inputs have been parsed in.

Answer 1

This sort of thing is easier to do in awk or perl than in a shell script (although if you're using a sh like bash which supports arrays, it's a bit easier than if using a sh without arrays. You still have far more complications with quoting and globbing or expansion where you don't want it in a shell script than you do in perl or awk)

For example:

#!/usr/bin/perl

use strict;

my $pathx='/path/to/my/files';

my $dh;
my @frames=();

# get list of .csv files from $pathx
opendir($dh, $pathx) || die "can't open directory '$pathx': $!\n";
my @csvfiles = grep { /\.csv$/ && -f "$pathx/$_" } readdir($dh);
closedir($dh);

foreach my $f (@csvfiles) {
   my @fields=split(/\./,$f);
   my $fn=$fields[@fields-2];   # perl array indices start from 0, not 1.

   printf '%s<-read.csv("%s",header=TRUE)'."\n", $fn, "$pathx/$f";
   # <snip> etc .etc. etc.
   printf '%s_2y<-tail(%s_log,730)'."\n", $fn, $fn;

   push @frames,"${fn}_2y";
}

print "df-<data.frame(", join(',',@frames), ")\n";

NOTE: you can use the File::Find module instead of a simple readdir() if you need directory recursion.

Sample output (with files a.csv, b.csv, and c.csv):

a<-read.csv("/path/to/my/files/a.csv",header=TRUE)
a_2y<-tail(a_log,730)
b<-read.csv("/path/to/my/files/b.csv",header=TRUE)
b_2y<-tail(b_log,730)
c<-read.csv("/path/to/my/files/c.csv",header=TRUE)
c_2y<-tail(c_log,730)
df-<data.frame(a_2y,b_2y,c_2y)

or with awk:

NOTE: awk doesn't have a join() function so I had to write one. awk doesn't have a readdir() function either, so it's easiest to just pipe the output of find into it (write a wrapper sh script to do that if necessary).

#!/usr/bin/awk -f

BEGIN {
  FS="[./]";
  delete A; # has side-effect of defining A as an array
};   

# i isn't an argument to this function, it's a local variable.
# in awk, extra whitespace separates function args from declaration
# of local variable(s)

function join(array,sep,       i) {     
  result=array[1];     # awk array indices start from 1
  for (i=2;i<=length(array);i++) result = result sep array[i];
  return result;
};

# main code block, run on every input line
{
  fn=$(NF-1);
  printf "%s<-read.csv(\"%s\",header=TRUE)\n", fn, $0;
  # <snip> etc .etc. etc.
  printf "%s_2y<-tail(%s_log,730)\n", fn, fn;
  A[length(A)+1] = sprintf("%s_2y",fn);
};

END {
  print "df-<data.frame(" join(",",A) ")";
}

save as, e.g., myscript.awk, make it executable with chmod and run as:

find "${PATHX}" -maxdepth 1 -type f -name "*.csv" | ./myscript.awk

Output is identical to the perl version.

Finally, the same algorithm in bash:

#!/bin/bash

PATHX="/path/to/my/files"

declare -a frames=()
# get list of .csv files and store in array csvfiles.
csvfiles=( $(find "$PATHX" -maxdepth 1 -type f -name '*.csv' ) )

function join() {
  local sep result i
  sep="$1" ; shift
  result="$1" ; shift

  for i in "$@" ; do result="$result$sep$i" ; done
  printf '%s' "$result"
}

for f in "${csvfiles[@]}" ; do
  fn=$(basename "$f" '.csv')

  printf "%s<-read.csv(\"%s\",header=TRUE)\n" $fn $f;
  # <snip> etc .etc. etc.
  printf "%s_2y<-tail(%s_log,730)\n" $fn $fn;

  frames+=( "${fn}_2y" )
done

echo 'df-<data.frame('$( join ',' "${frames[@]}" )')';

This avoids a while read loop which is almost always the worst possible way to process a series of lines in a shell script. Use awk or perl or sed or a for loop around an array - anything to avoid using a while read loop.

Answer 2

You can collect the names into a variable fns and echo this at the end. Since you have a pipe you need to keep the variable in the same subshell as the while/do/done. ${fns:1} is a substring of the variable, dropping the initial extra comma.

#!/bin/bash
PATHX="/path/to/my/files"
find "${PATHX}" -maxdepth 1 -type f -name "*.csv" |
(   fns=
    while read d; do
        FN=$(echo -n "${d}" | cut -d/ -f3 | cut -d. -f1)
        echo "${FN}<-read.csv(\"${PATHX}/${FN}.csv\",header=TRUE)"
        # <snip> etc .etc. etc.
        echo "${FN}_2y<-tail(${FN}_log,730)"
        fns+=",${FN}_2y"
    done
    echo "df<-data.frame(${fns:1})"
)