ThingsIdoAllTheTime

Capture a part of a filename

Capture the begining of a filename

Study_Patient_Assay_Date.txt

> echo Study_Patient_Assay_Date.txt | cut -c-13

Study_Patient

Rename Files using Part of Current filename

This can be done multiple ways but I use two commonly depending on the format of the files

1) Files without complete standardization

Patient001_20130102.txt

Patient002_19990203_run2.txt

#Loop through all files in current directory ending with .txt

for line in `ls *.txt`

do

    #Capture the patient name from each file as a variable

    PATIENT_NAME=`echo ${line} | cut -c-10`

    #Rename files

    mv ${line} ${PATIENT_NAME}.txt

    #Message

    echo

    echo "---------------------------------"

    echo "Parsing file: ${line}"

    echo Old Name=${line}

    echo New Name=${PATIENT_NAME}.txt

done

2) Files with standardized endings

Patient001_2013_rc_ir_dm.bam

Patient002_20120118_rc_ir_dm.bam

#Loop through all files in current directory ending with .bam

for line in `ls *.bam`

do

    #Capture the non-standard portion of the filename as a variable, using the unix basename function

    BASE_NAME=`basename ${line} "_rc_ir_dm.bam"`

    #Rename files

    mv ${line} ${BASE_NAME}.bam

    #Message

    echo

    echo "---------------------------------"

    echo "Parsing file: ${line}"

    echo Old Name=${line}

    echo New Name=${BASE_NAME}.bam

done

Replace a portion of a file name with something else (ie. Find X and Replace with Y)

#Loop through all files in current directory ending with .md5

for line in `ls *.md5`

do

#Rename files using move (mv) command

#The substitution function ${line//foo/bar} has two slashes to replace every occurrence of foo with bar

mv $line ${line//KBS5U/KBS5X}

    #Message

    echo

    echo "---------------------------------"

    echo "Parsing file: ${line}"

    echo Old Name=${line}

    echo New Name=${line//KBS5U/KBS5X}

done

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