Issue 99

README.md

@@ -57,8 +57,6 @@ Protein sequences (retrieved from GenBank and/or UniProt) from the local CAZyme
 
 Please see the [full documentation at ReadTheDocs](https://cazy-webscraper.readthedocs.io/en/latest/?badge=latest).
 
-**The `bioconda` installation method is not currently supported, but we are working on getting this fixed soon**. For now please install via pypi or from source.
-
 
 ## Table of Contents
 <!-- TOC -->
@@ -599,6 +597,8 @@ Providing the file types **is** case sensitive, but the order the file types are
 cw_get_uniprot_data my_cazyme_db/cazyme_db.db --ec_filter 'EC1.2.3.4,EC2.3.1.-'
 ```
 
+`-F`, `--file_only` - Only add seqs provided via JSON and/or FASTA file. Do not retrieved data from NCBI.
+
 `--families` - List of CAZy (sub)families to scrape.
 
 `--genbank_accessions` - Path to text file containing a list of GenBank accessions to retrieve protein data for. A unique accession per line.
@@ -619,6 +619,10 @@ cw_get_uniprot_data my_cazyme_db/cazyme_db.db --ec_filter 'EC1.2.3.4,EC2.3.1.-'
 
 `--retries`, `-r` - Define the number of times to retry making a connection to CAZy if the connection should fail. Default: 10.
 
+`--seq_dict` - Path to a JSON file, keyed by GenBank accessions and valued by protein sequence. Add seqs in file to the local CAZyme database.
+
+`--seq_file` - Path to a FASTA file, keyed by GenBank accessions and valued by protein sequence. Add seqs in file to the local CAZyme database.
+
 `--sql_echo` - Set SQLite engine echo parameter to True, causing SQLite to print log messages. Default: False.
 
 `--species` - List of species written as Genus Species) to restrict the scraping of CAZymes to. CAZymes will be retrieved for **all** strains of each given species.

cazy_webscraper/__init__.py

@@ -54,7 +54,7 @@
 from cazy_webscraper.sql import sql_orm
 
 
-__version__ = "2.2.3"
+__version__ = "2.2.4"
 
 
 VERSION_INFO = f"cazy_webscraper version: {__version__}"
@@ -127,6 +127,9 @@ def closing_message(job, start_time, args, early_term=False):
     else:
         print(message)
 
+    if early_term:
+        sys.exit(1)
+
 
 def display_citation_info():
     """Display citation inforamtion.