etvedte
commented
2 weeks ago The path should already exist when you git clone the repo. But prior to executing any GX commands, be sure to build with make first. otherwise it won't work. My guess is that you forgot to do that.
git clone https://github.com/ncbi/fcs-gx.git
cd fcs-gx
ls -l dist/gx
lrwxrwxrwx 1 tvedtees giindex 15 Jun 17 08:50 dist/gx -> ../build/src/gx
./dist/gx get-fasta --help
bash: ./dist/gx: No such file or directory
make
...
...
[100%] Built target gx
./dist/gx get-fasta --help
Fetch fasta from db.
Usage: ./dist/gx get-fasta [OPTIONS]
Options:
-i,--input file [stdin] 3-column TSV of locs, same format as --hardmask in make-db mode.
--gx-db file [db/all.gxi] /dev/shm/path/to/gxdb/ produced by gx make-db.
Should be placed in RAM-disk.
-o,--output file [stdout] Fasta.
-h,--help Print this help message and exit.
Eric
ShenMJ99
I found the README on https://github.com/ncbi/fcs-gx/tree/release which mentions Useful GX subcommands. I am interested in using the get-fasta functionality described there. However, I noticed that the path ./dist/gx, which is supposed to point to ../build/src/gx, does not exist.
The README describes the functionality as follows:
"The sequences used to build the gx database are listed in the file all.seq_info.tsv.gz within the gxdb folder. From there, you can select the sequences of your choice, and then generate the fasta files using the gx get-fasta subcommand: ./dist/gx get-fasta --db /dev/shm/gxdb/all.gxi --input 3col.txt --output out.txt The input file, which is provided by the user, is a tab delimited, 3 column file in the following format, along with the header:
cat 3col.txt
[["GX locs",1,1]]
NC_060925.1 . . To get the fasta for a specific set of coordinates, format your input file with the start and end coordinates in the 2nd and 3rd column, respectively:
[["GX locs",1,1]]
NC_060925.1 1 200"
Could you please provide guidance on how to implement this sub-functionality, considering the discrepancy in the path and how to correctly use the get-fasta command?