How can I give a script that reads input from a file input from stdin?

Question

I am working on a project that uses a script (blastn from NCBI's BLAST+ package) that, as far as I can tell, can only read input from a file. I'd like to be able to pass it a string in stdin and have it treat that as if it's the contents of a query file. I could do that by writing the string to a file then giving this script the name of a file but is there a different way to do it that I could try?

/dev/stdin is also a file

KamilCuk
– KamilCuk

2022-06-29 15:03:35 +00:00
Commented Jun 29, 2022 at 15:03 — KamilCuk
– KamilCuk, Commented Jun 29, 2022 at 15:03
check tldp.org/LDP/abs/html/process-sub.html

Diego Torres Milano
– Diego Torres Milano

2022-06-29 15:31:47 +00:00
Commented Jun 29, 2022 at 15:31 — Diego Torres Milano
– Diego Torres Milano, Commented Jun 29, 2022 at 15:31

glenn jackman · Accepted Answer · 2022-06-29 15:48:24Z

2

2 things come to mind:

many tools (but not all) treat the filename - as "read from stdin"
```
seq 20 | paste - -
```
use a Process Substitution, that looks to the program like a filename
```
rev <( echo "hello world" )
```

answered Jun 29, 2022 at 15:48

glenn jackman

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