For each file whose name begins with target, create a symbolic link to target whose name begins with newname. The purpose of this script is to make it easy for users to work with files that have long, complex names using symbolic links with short names. The motivation for this script is working with sequencing read files that have long names with flow cell specific references. In the ideal, the links are made to the initial sequencing read files, and all subsequent files in the pipeline can use the short names.

filename - full name of file to which the link should be made

target - A substring of the filename to be replaced

newname - A substring to replace the target. If empty, the target is simply deleted from the name.

If the target file is HI.4183.005.Index_12.450-cont-2_R1.fastq.gz  then

bl_alias.py HI.4183.005.Index_12.450-cont-2_R1.fastq.gz HI.4183.005.Index_12.450 Zm450

will create a link named Zm405-cont-2_R1.fastq.gz, pointing to the target file.

If newname is not provided, the target string will simply be omitted from the name of the link.

bl_alias.py HI.4183.005.Index_12.450-cont-2_R1.fastq.gz HI.4183.005.Index_12.450

would create a link named 450-cont-2_R1.fastq.gz

Dr. Brian Fristensky
Department of Plant Science
University of Manitoba
Winnipeg, MB  Canada R3T 2N2
brian.fristensky@umanitoba.ca
http://home.cc.umanitoba.ca/~frist