Page Comparison

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tail -n +2 ~/data/sampleinfo.txt | \
while IFS= read line; do
  jobName=$( echo "$line" | cut -f 1 )
  sampleName=$( echo "$line" | cut -f 3 )
  if [[ "$jobName" == "" ]]; then continue; fi
  echo "Project_${jobName}/${sampleName}.fastq.gz"
done | tee pathnames.txt

A few odds and ends

Arithemetic in bash

Arithmetic in bash is very weird:

echo $(( 50 * 2 + 1 ))

n=0
n=$(( $n + 5 ))
echo $n

And it only returns integer values, after truncation.

echo $(( 4 / 2 ))
echo $(( 5 / 2 ))

echo $(( 24 / 5 ))

As a result, if I need to do anything other than the simplest arithemetic, I use awk:

awk 'BEGIN{print 4/2}'
echo 3 2 | awk '{print ($1+$2)/2}'

You can also use the printf function in awk to control formatting. Just remember that a linefeed ( \n ) has to included in the format string:

echo 3.1415926 | awk '{ printf("%.2f\n", $1) }'

You can even use it to convert a decimal number to hexadecimal using the %x printf format specifier. Note that the convention is to denote hexadecimal numbers with an initial 0x.

echo 65 | awk '{ printf("0x%x\n", $1) }'

Removing file suffixes and prefixes

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