update headers name and make sequence in which lookup to off-target optional

crisprbact/cli.py

@@ -20,18 +20,18 @@ OFF_TARGET_DETAILS = [
     "off_target_feat_start",
     "off_target_feat_end",
     "off_target_feat_strand",
-    "locus_tag",
-    "gene",
-    "note",
-    "product",
-    "protein_id",
+    "off_target_locus_tag",
+    "off_target_gene",
+    "off_target_note",
+    "off_target_product",
+    "off_target_protein_id",
 ]
 HEADER = [
     "target_id",
     "target",
     "PAM position",
     "prediction",
-    "seq_id",
+    "target_seq_id",
     "seed_size",
 ] + OFF_TARGET_DETAILS
 SEED_SIZE = 8
@@ -53,7 +53,7 @@ def predict(config):
 
 @predict.command()
 @click.option("-t", "--target", type=str, required=True)
-@click.option("-g", "--genome", type=click.File("rU"), required=True, help="Genome")
+@click.option("-g", "--genome", type=click.File("rU"), help="Genome")
 @click.option(
     "-gf",
     "--genome-format",
@@ -72,10 +72,12 @@ def from_str(config, target, genome, genome_format, output_file):
     [OUTPUT_FILE] file where the candidate guide RNAs are saved. Default = "stdout"
 
     """
-
     if config.verbose:
         print_parameters(target)
-    genome_fh = SeqIO.parse(genome, genome_format)
+    if genome:
+        genome_fh = SeqIO.parse(genome, genome_format)
+    else:
+        genome_fh = None
     guide_rnas = on_target_predict(target, genome_fh)
 
     click.echo("\t".join(HEADER), file=output_file)
@@ -97,7 +99,7 @@ def from_str(config, target, genome, genome_format, output_file):
 # @click.option(
 #     "-s", "--seed-size", type=click.IntRange(8, 15, clamp=True),
 # )
-@click.option("-g", "--genome", type=click.File("rU"), required=True, help="Genome")
+@click.option("-g", "--genome", type=click.File("rU"), help="Genome")
 @click.option(
     "-gf",
     "--genome-format",
@@ -123,7 +125,10 @@ def from_seq(config, target, seq_format, genome, genome_format, output_file):
     for record in SeqIO.parse(target, seq_format):
         if config.verbose:
             click.secho(" - search guide RNAs for %s " % record.id, fg=fg)
-        genome_fh = SeqIO.parse(genome, genome_format)
+        if genome:
+            genome_fh = SeqIO.parse(genome, genome_format)
+        else:
+            genome_fh = None
         guide_rnas = on_target_predict(str(record.seq), genome_fh)
         # print(guide_rnas)
         write_guide_rnas(guide_rnas, output_file, record.id)
@@ -137,7 +142,7 @@ def print_parameters(target, fg="blue"):
 def write_guide_rnas(guide_rnas, output_file, seq_id="N/A"):
     for guide_rna in guide_rnas:
         row = [
-            str(guide_rna["id"]),
+            str(guide_rna["target_id"]),
             guide_rna["target"],
             str(guide_rna["pam"]),
             str(guide_rna["pred"]),