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oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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Correct Perl errors and English errors #126

Closed Ghepardo closed 2 years ago

Ghepardo commented 2 years ago
  1. Perl errors. The script attempted to remove the last component from the path of each application on which it depends, such as in the line: $repeatmasker=~s/RepeatMasker\n?// unless -d $repeatmasker; However, this command removes the FIRST occurrence of "RepeatMasker" in the string, not the last. This was causing LTR_retriever to fail in our installation (where the path to RepeatMasker is: /home/apps/eb/software/RepeatMasker/4.1.2-p1-foss-2020b/RepeatMasker). I have therefore "anchored" the search expression to the end of the string by adding a "$" to each such expression.

(I do feel the logic here is cumbersome: the script removes the last component from the path of each application, only to add it back later.)

  1. English errors. There were a few occurrences of the phrase "is not exist" in error messages, which is not correct English. I have amended these to "does not exist".
oushujun commented 2 years ago

Thank you for your contributions! @Ghepardo