Update pychip.py

fuc/api/pychip.py

@@ -7,6 +7,8 @@
 import re
 import pandas as pd
 
+from . import common
+
 class AxiomFrame:
  """
  Class for storing Axiom annotation data.
@@ -190,23 +192,73 @@ def from_file(cls, fn):
 
  return cls(df)
 
- def to_vep(self):
+ def to_vep(self, fasta):
  """
  Convert InfiniumFrame to the Ensembl VEP format.
 
  Returns
  -------
  pandas.DataFrame
  Variants in Ensembl VEP format.
+
+ Parameters
+ ----------
+ region : str
+ Region ('chrom:start-end').
  """
+ nucleotides = ['A', 'C', 'G', 'T']
+ n = 15
  df = self.df[(self.df.Chr != 'XY') & (self.df.Chr != '0')]
+ df.MapInfo = df.MapInfo.astype(int)
+ df = df.head(1000)
  def one_row(r):
+ if r.Chr == 'MT':
+ chrom = 'chrM'
+ else:
+ chrom = f'chr{r.Chr}'
  pos = r.MapInfo
  matches = re.findall(r'\[([^\]]+)\]', r.SourceSeq)
  if not matches:
  raise ValueError(f'Something went wrong: {r}')
  a1, a2 = matches[0].split('/')
- data = pd.Series([r.Chr, r.MapInfo, a1, a2])
+ left_seq = r.SourceSeq.split('[')[0]
+ right_seq = r.SourceSeq.split(']')[1]
+ locus = f'{chrom}:{pos}-{pos}'
+ if a1 in nucleotides and a2 in nucleotides: # SNV
+ ref = common.extract_sequence(fasta, locus)
+ if ref == a1:
+ pass
+ elif ref == a2:
+ a1, a2 = a2, a1
+ else:
+ raise ValueError(f'Reference allele not found: {locus}')
+ elif a1 == '-' or a2 == '-':
+ affected = a1 if a2 == '-' else a2
+ c = len(affected)
+ if c == 1:
+ left_query = common.extract_sequence(fasta, f'{chrom}:{pos-n}-{pos-1}')
+ right_query = common.extract_sequence(fasta, f'{chrom}:{pos+1}-{pos+n}')
+ print(locus, left_seq[-n:], left_query, left_seq[-n:] == left_query, 'DEL I')
+ print(locus, right_seq[:n], right_query, right_seq[:n] == right_query, 'DEL I')
+ print()
+ else:
+ left_query = common.extract_sequence(fasta, f'{chrom}:{pos-n}-{pos}') # -1
+ right_query = common.extract_sequence(fasta, f'{chrom}:{pos+c}-{pos+c+n-1}')
+ if left_seq[-n:] == left_query[:-1] and right_seq[:n] == right_query: # DEL I
+ print(locus, left_seq[-n:], left_query[:-1], left_seq[-n:] == left_query[:-1], 'DEL II')
+ print(locus, right_seq[:n], right_query, right_seq[:n] == right_query, 'DEL II')
+ print()
+ else:
+ #left_query = common.extract_sequence(fasta, f'{chrom}:{pos-n}-{pos}')
+ #left_query = left_query[len(affected):] + affected
+ print(locus, left_seq[-n:], left_query, left_seq[-n:] == left_query, 'Other')
+ print(locus, right_seq[:n], right_query, right_seq[:n] == right_query, 'Other')
+ print()
+ else:
+ raise ValueError(f'Unsupported format: {locus}')
+ data = pd.Series([r.Chr, r.MapInfo, r.MapInfo, f'{a1}/{a2}', '+'])
  return data
  df = df.apply(one_row, axis=1)
+ df = df.sort_values(by=[0, 1])
+ df = df.drop_duplicates()
  return df