Update docs

fuc/api/common.py

@@ -804,7 +804,12 @@ def parse_variant(variant):
 
 def extract_sequence(fasta, region):
  """
- Extract the region's DNA sequence from the FASTA file.
+ Extract the DNA sequence corresponding to a selected region from a FASTA
+ file.
+
+ The method also allows users to retrieve the reference allele of a
+ variant in a genomic coordinate format, instead of providing a genomic
+ region.
 
  Parameters
  ----------
@@ -817,6 +822,17 @@ def extract_sequence(fasta, region):
  -------
  str
  DNA sequence. Empty string if there is no matching sequence.
+
+ Examples
+ --------
+
+ >>> from fuc import common
+ >>> fasta_file = 'resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta'
+ >>> common.extract_sequence(fasta_file, 'chr1:15000-15005')
+ 'GATCCG'
+ >>> # rs1423852 is chr16-80874864-C-T
+ >>> common.extract_sequence(fasta_file, 'chr16:80874864-80874864')
+ 'C'
  """
  try:
  sequence = pysam.faidx(fasta, region).split('\n')[1]