String split

Split string of variable ${FILE} by delimiter '_'

# filename example
FILE=SRR01234_mapped_ecoli.txt

echo ${FILE%%_*}  # get all before first delimiter '_'
SRR01234

echo ${FILE%_*}   # get all before last delimiter '_'
SRR01234_mapped

echo ${FILE##*_}  # get all after last delimiter '_'
ecoli.txt

echo ${FILE#*_}   # get all after first delimiter '_'
mapped_ecoli.txt


Basename examples

# get filename without path prefix
F=/path/to/sample/SRR01234_mapped_ecoli.txt
FILE=`basename ${F}` 
echo ${FILE}
SRR01234_mapped_ecoli.txt

# get filename without path prefix and without extension
F=/path/to/sample/SRR01234_mapped_ecoli.txt
FILENAME=`basename ${F%%.*}`  # get all before first '.' (remove file ending)
echo ${FILENAME}
SRR01234_mapped_ecoli

# get sample-ID
F=/path/to/sample/SRR01234_mapped_ecoli.txt
SAMPLE=`basename ${F%%_*}`  # get all before '_'
echo ${SAMPLE}
SRR01234

# get speciesname "ecoli"
F=/path/to/sample/SRR01234_mapped_ecoli.txt
FILENAME=`basename ${F%%.*}`  # get all before first '.' (remove file ending)
SPECIES=${FILENAME##*_}  # get all after last delimiter '_'
echo ${SPECIES}
ecoli


Alternative use: cut

# get first word (-f 1) based on delimiter '_'
FILE=SRR01234_mapped_ecoli.txt
SAMPLE=$( cut -d '_' -f 1 - <<< "${FILE}" )
echo ${SAMPLE}
SRR01234