CODEWITHSUNDEEP
bashfile-copying
user5481267
user5481267

Reputation: 141

How to copy files in Bash that have more than 1 line

I am trying to copy files from one directory (defined as $inDir below) to another (defined as $outDir below) if they 1) exist and 2) have more than 1 line in the file (this is to avoid copying files that are empty text files). I am able to do the first part using the below code but am struggling to know how to do the latter part. I'm gussing maybe using awk and NR somehow but I'm not very good with coding in Bash so any help would be appreciated. I'd like this to be incorporated into the below if possible, so that it can be done in one step.

for i in $inDir/NVDI_500m_mean_distance_*_40PCs; do
    batch_name_dir=$i;
    batch_name=$(basename $i);
    if [ ! -f $outDir/${batch_name}.plink.gz ]; then
            echo 'Copying' $batch_name;
            find $batch_name_dir -name ${batch_name}.plink.gz -exec cp {} $outDir/${batch_name}.plink.gz \;
    else
            echo $batch_name 'already exists'
    fi
done

Upvotes: 0

Views: 769

Answers (2)

Nathan TM
Nathan TM

Reputation: 143

You can use wc -l to check how many lines are in a file and awk to strip only the number from the result.

lines=$(wc -l $YOUR_FILE_NAME | awk '{print $1}')

if [ $lines -gt 0 ]; then 
    //copy the file 
fi

Edit: I have corrected LINES to lines according to the comments below.

Upvotes: 1

krysopath
krysopath

Reputation: 344

I propose this:

for f in "$(find $indir -type f -name 'NVDI_500m_mean_distance_*_40PC' -not -empty)"; 
do 
  cp "$f" /some/targetdir; 
done

find is faster than wc to check for zero size.

I consider it more readable, than the other solution, subjectivly.

However, the for-loop is not necessary, since:

find "$indir" -type f -name 'NVDI_500m_mean_distance_*_40PC' -not -empty |\
    xargs -I % cp % /some/targetdir/%

Always "quote" path strings, since most shell utils break when there are unescaped shell chars or white spaces in the string. There are rarely good reasons to use unquoted strings.

Upvotes: 0

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