document analyze fasta commands in hidden-commands.md

rdk · Jul 1, 2021 · 87c86e0 · 87c86e0
1 parent 3a33417
commit 87c86e0
Showing 1 changed file with 18 additions and 3 deletions.
diff --git a/misc/tutorials/hidden-commands.md b/misc/tutorials/hidden-commands.md
@@ -25,9 +25,7 @@ Analyze a dataset with an explicitly specified residue labeling.
 ~~~
 
 
-
-
-## Exporting feature vectors for further analysis
+## Export feature vectors for further analysis
 
 ~~~
 ./prank.sh traineval -t test_data/basic.ds -e test_data/basic.ds \
@@ -36,6 +34,23 @@ Analyze a dataset with an explicitly specified residue labeling.
 ~~~
 
 
+## Export chains to FASTA
+                           
+`fasta-raw` exports residue codes as P2Rank sees them.
+`fasta-mask` will transform any possible non-letter code (such as `_` or `?`) to `X`.
+
+~~~
+# run in P2Rank root directory (distro in repo)
+
+./prank analyze fasta-raw test_data/basic.ds         # dataset
+./prank analyze fasta-raw -f test_data/2W83.pdb      # single file
+./prank analyze fasta-raw test_data/basic.ds 
+
+./prank analyze fasta-masked test_data/basic.ds      # dataset
+./prank analyze fasta-masked -f test_data/2W83.pdb   # single file
+./prank analyze fasta-masked test_data/basic.ds -o out_dir  # specify output directory
+~~~
+
 
 ## More prediction examples