Update README

README.md

@@ -1,26 +1,18 @@
-# [PomBase](/pombase) code for processing domains
+# PomBase code for processing domains from InterProScan
 
-This program processes the `match_complete.xml.gz` from InterPro
-and also runs [TMHMM](https://services.healthtech.dtu.dk/services/TMHMM-2.0/)
-to generate a JSON of domain information.
+This program processes the JSON format output of `InterProScan` to
+generate an simplified JSON file of domain information.
 
-The latest InterPro file is available from: https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/
-
-UniProt IDs for pombe proteins are queried from PostgreSQL.  Those IDs are
-used to filter the InterPro file.
-
-Protein sequences are queried from PostgreSQL and are passed to TMHMM.
-We run TMHMM in a separate thread while the InterPro XML is parsed and
-processed.
+It also runs [TMHMM](https://services.healthtech.dtu.dk/services/TMHMM-2.0/)
+and `segmasker` and includes the results in the JSON output.
 
 ## Running
 
 Run with:
 
-    PATH=$PATH_TO_TMHMM_EXE:$PATH /var/pomcur/bin/pombase-interpro \
-        -p "postgres://<username>:<password>@localhost/<dbname>" \
-        -i <(gzip -d < match_complete.xml.gz) -o pombe_domain_results.json
-
+    PATH=$PATH_TO_TMHMM_EXE:$PATH /var/pomcur/bin/pombase-domain-process \
+        -p pombe_peptide.fa -i interproscan_output.json
+        -o pombe_domain_results.json
 
 ## Status