Limit sequence format to fasta or genbank

crisprbact/cli.py

-import click
 from crisprbact import on_target_predict
 from Bio import SeqIO
+import click
 
 
 class Config(object):
@@ -32,7 +32,8 @@ def predict(config):
 @pass_config
 def from_str(config, target, output_file):
     """
-    Outputs candidate guide RNAs for the S. pyogenes dCas9 with predicted on-target activity from a target gene.
+    Outputs candidate guide RNAs for the S. pyogenes dCas9 with predicted on-target
+    activity from a target gene.
 
     [OUTPUT_FILE] file where the precitions are saved. Default = "stdout"
 
@@ -49,12 +50,20 @@ def from_str(config, target, output_file):
 @click.option(
     "-t", "--target", type=click.File("rU"), required=True, help="Sequence file"
 )
-@click.option("-f", "--seq-format", help="Sequence file format", default="fasta")
+@click.option(
+    "-f",
+    "--seq-format",
+    type=click.Choice(["fasta", "fa", "gb", "genbank"]),
+    help="Sequence file format",
+    default="fasta",
+    show_default=True,
+)
 @click.argument("output-file", type=click.File("w"), default="-")
 @pass_config
 def from_seq(config, target, seq_format, output_file):
     """
-    Outputs candidate guide RNAs for the S. pyogenes dCas9 with predicted on-target activity from a target gene.
+    Outputs candidate guide RNAs for the S. pyogenes dCas9 with predicted on-target
+    activity from a target gene.
 
     [OUTPUT_FILE] file where the precitions are saved. Default = "stdout"