implement caller-selectable sequence type for ensembl seqfetcher

[reece]

Implements the ability for seqfetcher callers to specify additional arguments to seqfetcher, and particularly to specify the type of sequence for ensembl transcript sequences. In order to address #75, the default ENST type is "cdna", although this is not the default in Ensembl's rest API. The type may also be set for ENST sequences using the ENST_DEFAULT_TYPE environment variable.

Examples

>>> from bioutils import seqfetcher
>>> import os

# set default type to cds
>>> os.environ["ENST_DEFAULT_TYPE"] = "cds"
>>> s_def = seqfetcher.fetch_seq("ENST00000617537")
>>> s_gen = seqfetcher.fetch_seq("ENST00000617537", type="genomic")
>>> s_cdna = seqfetcher.fetch_seq("ENST00000617537", type="cdna")
>>> s_cds = seqfetcher.fetch_seq("ENST00000617537", type="cds")
>>> len(s_def), len(s_gen), len(s_cdna), len(s_cds)
(1728, 211554, 2385, 1728)
# note that default corresponds to the cds size

# now remove the default type; seqfetcher ENST default type is "cdna"
# warning is emitted when falling back to default
>>> del os.environ["ENST_DEFAULT_TYPE"]
>>> s_def = seqfetcher.fetch_seq("ENST00000617537")
ENST00000617537: Transcript type not specified or set in ENST_DEFAULT_TYPE; assuming cdna
>>> s_gen = seqfetcher.fetch_seq("ENST00000617537", type="genomic")
>>> s_cdna = seqfetcher.fetch_seq("ENST00000617537", type="cdna")
>>> s_cds = seqfetcher.fetch_seq("ENST00000617537", type="cds")
>>> len(s_def), len(s_gen), len(s_cdna), len(s_cds)
(2385, 211554, 2385, 1728)
# note that the default size is that of cdna

Questions

• What do you think of overriding the Ensembl API default (genomic) with cdna?

[reece]

@jsstevenson @davmlaw: Comments please ↑

[jsstevenson]

thanks! looks good, just a minor note about either altering the docstring in _fetch_seq_ensembl or the type argument name

[davmlaw]

I'm happy with default cds. It's what I think of as "transcript" and how RefSeq behaves