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ERV / BLAST scripts
Call the program in the following fashion: ruby find_erv.rb erv path/to/folder/with/xml/files ...or... ruby find_erv.rb ltr path/to/folder/with/xml/files ...and after running, the folder with the XML files should contain .fasta files corresponding to the putative ERVs. From the source code, the files of importance are: find_erv.rb - Main shell script to run from the command line. finderv.rb - Functions to search for putative ERVs / solo LTRs. There are other functions in this file that may be of interest, take a look inside. putative_erv.rb - Class that represents a putative ERV. ltr.rb - Class that represents an LTR (PutativeErv is made up of two LTR classes).
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