I have a bash that downloads a list and if that list has data in it then a new main directory is created (with the date) with several subdirectories (example1, example2, example3). My question is in that list there are portion of specific file types (.vcf.gz) - identifier towards the end that have an identifier in it that I would like to use a subdirectory. The identifier is also at the beginning of the .bam. The identifiers in this case are IonXpress_001, IonXpress_002, and IonXpress_003). The data in the list (identifiers) will be different each time and the order may also be different but the naming structure within the list file will always be consistent. Is this possible, I am not able to figure it out. That naming structure will always be the same (IonXpress_001 or IonXpress_010)... what will change is the text after the (3digits)_ for the .bam files. In the .vcf.gz files the only thing that will change are the (3digits) so that type may be easiest to use. For example, in the case of TSVC_variants_IonXpress_001.vcf.gz compared to TSVC_variants_IonXpress_002.vcf.gz , only the digits changed while the text remains the same. Thank you 
bash that produces current structure
wget -q --user=xxx --password=xxx --xxxx \
xxxx://www.xxx.com/xxx/xxxxx/xxxx/list
line_no=$(awk '{x++} END {print x}' /home/cmccabe/list) # count new files and store as variable
if [[ -s /home/user/list ]]; then
DATE=`date +%-m-%-d-%Y`
mkdir -p /home/user/Desktop/xxx/xxx/$DATE/{example1,example2,example3} # make new directory and subfolders
current structure
Date is the main directory with each of the examples being a sub-directory within Date.
Date - example1, example2, example3
list
IonXpress_001_R_2016_02_11_11_51_07_user_Proton-34-160210_Lurie_MedExome_Hi-Q_Auto_user_Proton-34-160210_Lurie_MedExome_Hi-Q_84.bam
IonXpress_002_R_2016_02_11_11_51_07_user_Proton-34-160210_Lurie_MedExome_Hi-Q_Auto_user_Proton-34-160210_Lurie_MedExome_Hi-Q_84.bam
IonXpress_003_R_2016_02_11_11_51_07_user_Proton-34-160210_Lurie_MedExome_Hi-Q_Auto_user_Proton-34-160210_Lurie_MedExome_Hi-Q_84.bam
TSVC_variants_IonXpress_001.vcf.gz
TSVC_variants_IonXpress_002.vcf.gz
TSVC_variants_IonXpress_003.vcf.gz
desired output
Date is the main directory with the identifier as a subdirectory within Date and each of the example are subdirectories within the identifier.
`Date - Identifier - example1, example2, example3
2-13-2015 (main directory) - IonXpress_001 (identifier as a sub-directory within 2-13-2015) - example1, example2, example3 (all sub-directories within the identifier).