There are a couple arguments that seem to be hardcoded and don't incorporate what the user specifies (i.e. -bed and -annot arguments).
In line 226, https://github.com/UofLBioinformatics/CSI-UTR/blob/master/CSI-UTR_v1.1.0/bin/CSI-UTR, the annotation file is hardcoded to "./data/annotations/$genome.CSIs.annot.bed" whether or not we specify the flag 'annot' with a path.
In line 255, the bed file is hardocded to './data/locations/$genome.CSIs.bed' even though there is a flag to specify the path to the bed file as an argument. Hence similarly, I can't use a different path for the bed file.
When I specify paths for these arguments, I got an error saying the files are not found. My understanding is that because the paths are hardcoded, the tool will always look at ./data/annotations/ folder for these files.
There are a couple arguments that seem to be hardcoded and don't incorporate what the user specifies (i.e. -bed and -annot arguments).
In line 226, https://github.com/UofLBioinformatics/CSI-UTR/blob/master/CSI-UTR_v1.1.0/bin/CSI-UTR, the annotation file is hardcoded to "./data/annotations/$genome.CSIs.annot.bed" whether or not we specify the flag 'annot' with a path.
In line 255, the bed file is hardocded to './data/locations/$genome.CSIs.bed' even though there is a flag to specify the path to the bed file as an argument. Hence similarly, I can't use a different path for the bed file.
When I specify paths for these arguments, I got an error saying the files are not found. My understanding is that because the paths are hardcoded, the tool will always look at ./data/annotations/ folder for these files.