small bugfixes (#2)

bamdash/__init__.py

@@ -1,3 +1,3 @@
 """interactively visualize coverage and tracks"""
 _program = "bamdash"
-__version__ = "0.1"
+__version__ = "0.1.1"

bamdash/scripts/data.py

@@ -121,14 +121,14 @@ def vcf_to_df(vcf_file, ref):
  variant_dict["reference"].append(rec.ref)
  variant_dict["mutation"].append(rec.alts[0])
  # annotate the point mutation type
- base_exchange = rec.ref + rec.alts[0]
+ base_exchange = f"{rec.ref}{rec.alts[0]}"
  if len(base_exchange) == 2:
  if base_exchange in ["AG", "GA", "CT", "TC"]:
- variant_dict["point mutation type"] = "transition"
+ variant_dict["point mutation type"].append("TRANSITION")
  else:
- variant_dict["point mutation type"] = "transversion"
+ variant_dict["point mutation type"].append("TRANSVERSION")
  else:
- variant_dict["point mutation type"] = "none"
+ variant_dict["point mutation type"].append("NONE")
 
  # get mutation type
  if len(rec.alts[0]) > len(rec.ref):
@@ -289,6 +289,9 @@ def annotate_vcf_df(vcf_df, cds_dict, seq):
  :return: annotated df
  """
 
+ # define the potential identifiers to look for
+ potential_cds_identifiers = ["protein_id", "gene", "locus_tag", "product"]
+
  proteins, as_exchange, as_effect = [], [], []
 
  for variant in vcf_df.iterrows():
@@ -297,22 +300,29 @@ def annotate_vcf_df(vcf_df, cds_dict, seq):
  # check each cds for potential mutations
  for cds in cds_dict:
  # check if a protein identifier is present
- if "protein_id" not in cds_dict[cds]:
+ if not any(identifier in potential_cds_identifiers for identifier in cds_dict[cds]):
  continue
  start, stop = cds_dict[cds]["start"], cds_dict[cds]["stop"]
  # check if pos is in range
  if pos not in range(start, stop):
  continue
  # now we know the protein
- proteins_temp.append(cds_dict[cds]["protein_id"])
+ for identifier in potential_cds_identifiers:
+ if identifier in cds_dict[cds]:
+ proteins_temp.append(cds_dict[cds][identifier])
+ break
  # at the moment only check SNPs
  if mut_type != "SNP":
  as_exchange_temp.append("AMBIG"), as_effect_temp.append(variant[1]["type"])
  continue
  # now we can analyse for a potential as exchange
- strand, seq_mut, codon_start = cds_dict[cds]["strand"], str(seq), int(cds_dict[cds]["codon_start"])
+ if "codon_start" in cds_dict[cds]:
+ codon_start = int(cds_dict[cds]["codon_start"])
+ else:
+ codon_start = 1
+ strand, seq_mut = cds_dict[cds]["strand"], str(seq)
  # mutate the sequence and get the CDS nt seq
- seq_mut = Seq.Seq(seq_mut[:pos] + mut + seq_mut[pos+1:])
+ seq_mut = Seq.Seq(seq_mut[:pos-1] + mut + seq_mut[pos:])
  seq_cds, seq_mut_cds = seq[start+codon_start-2:stop], seq_mut[start+codon_start-2:stop]
  # translate strand depend
  if strand == "+":

bamdash/scripts/plotting.py

@@ -176,7 +176,7 @@ def create_vcf_plot(fig, row, vcf_df):
  if "AF" not in vcf_df:
  fig.update_yaxes(visible=False, row=row, col=1)
  else:
- fig.update_yaxes(title_text="frequency", range=[0, 1], row=row, col=1)
+ fig.update_yaxes(title_text="frequency", range=[0, 1.15], row=row, col=1)
 
 
 def create_track_plot(fig, row, feature_dict, box_size, box_alpha):