Retrieving sequences

Complete sequence query

Complete sequence can be retrieved using only the required parameter checksum in fetch_sequence function or Fetcher.sequence class method.

from reference_sequence_fetcher import fetcher
fetcher = Fetcher(<server_base_url>)
print(fetcher.fetch_sequence('<checksum>'))

print(Fetcher.sequence(<server_base_url>, <checksum>))

Sub-sequence query

User can also retrieve sub-sequences using start and end optional parameters

start and end used to retrieve sub-subsequence of specified bytes. Start is 0-start inclusive and end is exclusive.
0 <= start < length of sequence ; 1 <= end <= length of sequence

For ex sequence A is given as ATGCATGCATGC
Length is 12

>>fetcher = Fetcher(<server_base_url>)
>>print(fetcher.fetch_sequence('<checksum>'), start=0, end=5)
>>ATGCA

If a server supports circular chromosomes, the client supports crossing the origin using the start and end parameters

>>fetcher = Fetcher(<server_base_url>)
>>print(fetcher.fetch_sequence('<checksum>'), start=5, end=2)
>>TGCATGCATG

so TGCATGC + ATG is the retrieved sequence.

Note

start and end can be used alone. If only start is given, end is assumed to be equal to length of the sequences. When only end is given start is assumed to be equal to 0.