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erascheerasche
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Merge pull request #13 from galaxy-genome-annotation/dbxrefs
Add dbxrefs methods
2 parents cdcee82 + 130a701 commit 9899006

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6 files changed

+252
-26
lines changed

6 files changed

+252
-26
lines changed

‎apollo/annotations/__init__.py‎

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Original file line numberDiff line numberDiff line change
@@ -338,6 +338,134 @@ def update_attribute(self, feature_id, attribute_key, old_value, new_value, orga
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data = self._update_data(data, organism, sequence)
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return self.post('deleteAttribute', data)
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def add_dbxref(self, feature_id, db, accession, organism=None, sequence=None):
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"""
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Add a dbxref to a feature
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:type feature_id: str
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:param feature_id: Feature UUID
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:type db: str
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:param db: DB Name (e.g. PMID)
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:type accession: str
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:param accession: Accession Value
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:type organism: str
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:param organism: Organism Common Name
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:type sequence: str
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:param sequence: Sequence Name
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This seems to show two attributes being added, but it behaves like those two are one.
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:rtype: dict
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:return: A standard apollo feature dictionary ({"features": [{...}]})
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"""
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data = {
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'features': [
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{
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'uniquename': feature_id,
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'dbxrefs': [
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{
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'db': db,
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'accession': accession,
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}
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]
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}
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]
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}
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data = self._update_data(data, organism, sequence)
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return self.post('addDbxref', data)
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def delete_dbxref(self, feature_id, db, accession, organism=None, sequence=None):
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"""
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Delete a dbxref from a feature
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:type feature_id: str
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:param feature_id: Feature UUID
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:type db: str
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:param db: DB Name (e.g. PMID)
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:type accession: str
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:param accession: Accession Value
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:type organism: str
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:param organism: Organism Common Name
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:type sequence: str
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:param sequence: Sequence Name
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:rtype: dict
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:return: A standard apollo feature dictionary ({"features": [{...}]})
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"""
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data = {
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'features': [
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{
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'uniquename': feature_id,
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'dbxrefs': [
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{
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'db': db,
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'accession': accession,
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}
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]
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}
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]
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}
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data = self._update_data(data, organism, sequence)
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return self.post('deleteDbxref', data)
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def update_dbxref(self, feature_id, old_db, old_accession, new_db, new_accession, organism=None, sequence=None):
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"""
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Delete a dbxref from a feature
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:type feature_id: str
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:param feature_id: Feature UUID
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:type old_db: str
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:param old_db: Old DB Name (e.g. PMID)
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:type old_accession: str
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:param old_accession: Old accession Value
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:type new_db: str
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:param new_db: New DB Name (e.g. PMID)
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:type new_accession: str
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:param new_accession: New accession Value
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:type organism: str
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:param organism: Organism Common Name
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:type sequence: str
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:param sequence: Sequence Name
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:rtype: dict
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:return: A standard apollo feature dictionary ({"features": [{...}]})
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"""
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data = {
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'features': [
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{
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'uniquename': feature_id,
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'old_dbxrefs': [
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{
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'db': old_db,
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'accession': old_accession,
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}
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],
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'new_dbxrefs': [
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{
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'db': new_db,
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'accession': new_accession,
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}
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]
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}
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]
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}
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data = self._update_data(data, organism, sequence)
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return self.post('deleteDbxref', data)
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def get_features(self, organism=None, sequence=None):
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"""
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Get the features for an organism / sequence

‎arrow/commands/annotations/add_dbxref.py‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,30 @@
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import click
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from arrow.cli import pass_context
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from arrow.decorators import custom_exception, dict_output
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@click.command('add_dbxref')
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@click.argument("feature_id", type=str)
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@click.argument("db", type=str)
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@click.argument("accession", type=str)
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@click.option(
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"--organism",
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help="Organism Common Name",
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type=str
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)
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@click.option(
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"--sequence",
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help="Sequence Name",
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type=str
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)
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@pass_context
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@custom_exception
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@dict_output
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def cli(ctx, feature_id, db, accession, organism="", sequence=""):
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"""Add a dbxref to a feature
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Output:
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A standard apollo feature dictionary ({"features": [{...}]})
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"""
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return ctx.gi.annotations.add_dbxref(feature_id, db, accession, organism=organism, sequence=sequence)

‎arrow/commands/annotations/delete_dbxref.py‎

Lines changed: 30 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,30 @@
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import click
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from arrow.cli import pass_context
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from arrow.decorators import custom_exception, dict_output
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@click.command('delete_dbxref')
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@click.argument("feature_id", type=str)
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@click.argument("db", type=str)
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@click.argument("accession", type=str)
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@click.option(
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"--organism",
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help="Organism Common Name",
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type=str
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)
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@click.option(
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"--sequence",
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help="Sequence Name",
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type=str
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)
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@pass_context
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@custom_exception
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@dict_output
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def cli(ctx, feature_id, db, accession, organism="", sequence=""):
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"""Delete a dbxref from a feature
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Output:
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A standard apollo feature dictionary ({"features": [{...}]})
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"""
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return ctx.gi.annotations.delete_dbxref(feature_id, db, accession, organism=organism, sequence=sequence)

‎arrow/commands/annotations/update_dbxref.py‎

Lines changed: 32 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,32 @@
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import click
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from arrow.cli import pass_context
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from arrow.decorators import custom_exception, dict_output
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@click.command('update_dbxref')
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@click.argument("feature_id", type=str)
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@click.argument("old_db", type=str)
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@click.argument("old_accession", type=str)
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@click.argument("new_db", type=str)
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@click.argument("new_accession", type=str)
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@click.option(
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"--organism",
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help="Organism Common Name",
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type=str
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)
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@click.option(
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"--sequence",
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help="Sequence Name",
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type=str
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)
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@pass_context
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@custom_exception
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@dict_output
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def cli(ctx, feature_id, old_db, old_accession, new_db, new_accession, organism="", sequence=""):
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"""Delete a dbxref from a feature
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Output:
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A standard apollo feature dictionary ({"features": [{...}]})
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"""
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return ctx.gi.annotations.update_dbxref(feature_id, old_db, old_accession, new_db, new_accession, organism=organism, sequence=sequence)

‎arrow/commands/cmd_annotations.py‎

Lines changed: 31 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -1,31 +1,34 @@
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import click
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from arrow.commands.annotations.add_attribute import cli as func0
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from arrow.commands.annotations.add_comment import cli as func1
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from arrow.commands.annotations.add_feature import cli as func2
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from arrow.commands.annotations.add_transcript import cli as func3
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from arrow.commands.annotations.delete_attribute import cli as func4
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from arrow.commands.annotations.delete_feature import cli as func5
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from arrow.commands.annotations.delete_sequence_alteration import cli as func6
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from arrow.commands.annotations.duplicate_transcript import cli as func7
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from arrow.commands.annotations.flip_strand import cli as func8
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from arrow.commands.annotations.get_comments import cli as func9
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from arrow.commands.annotations.get_feature_sequence import cli as func10
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from arrow.commands.annotations.get_features import cli as func11
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from arrow.commands.annotations.get_gff3 import cli as func12
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from arrow.commands.annotations.get_search_tools import cli as func13
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from arrow.commands.annotations.get_sequence_alterations import cli as func14
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from arrow.commands.annotations.merge_exons import cli as func15
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from arrow.commands.annotations.set_boundaries import cli as func16
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from arrow.commands.annotations.set_description import cli as func17
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from arrow.commands.annotations.set_longest_orf import cli as func18
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from arrow.commands.annotations.set_name import cli as func19
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from arrow.commands.annotations.set_readthrough_stop_codon import cli as func20
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from arrow.commands.annotations.set_sequence import cli as func21
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from arrow.commands.annotations.set_status import cli as func22
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from arrow.commands.annotations.set_symbol import cli as func23
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from arrow.commands.annotations.set_translation_end import cli as func24
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from arrow.commands.annotations.set_translation_start import cli as func25
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from arrow.commands.annotations.update_attribute import cli as func26
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from arrow.commands.annotations.add_dbxref import cli as func2
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from arrow.commands.annotations.add_feature import cli as func3
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from arrow.commands.annotations.add_transcript import cli as func4
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from arrow.commands.annotations.delete_attribute import cli as func5
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from arrow.commands.annotations.delete_dbxref import cli as func6
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from arrow.commands.annotations.delete_feature import cli as func7
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from arrow.commands.annotations.delete_sequence_alteration import cli as func8
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from arrow.commands.annotations.duplicate_transcript import cli as func9
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from arrow.commands.annotations.flip_strand import cli as func10
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from arrow.commands.annotations.get_comments import cli as func11
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from arrow.commands.annotations.get_feature_sequence import cli as func12
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from arrow.commands.annotations.get_features import cli as func13
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from arrow.commands.annotations.get_gff3 import cli as func14
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from arrow.commands.annotations.get_search_tools import cli as func15
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from arrow.commands.annotations.get_sequence_alterations import cli as func16
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from arrow.commands.annotations.merge_exons import cli as func17
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from arrow.commands.annotations.set_boundaries import cli as func18
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from arrow.commands.annotations.set_description import cli as func19
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from arrow.commands.annotations.set_longest_orf import cli as func20
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from arrow.commands.annotations.set_name import cli as func21
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from arrow.commands.annotations.set_readthrough_stop_codon import cli as func22
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from arrow.commands.annotations.set_sequence import cli as func23
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from arrow.commands.annotations.set_status import cli as func24
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from arrow.commands.annotations.set_symbol import cli as func25
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from arrow.commands.annotations.set_translation_end import cli as func26
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from arrow.commands.annotations.set_translation_start import cli as func27
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from arrow.commands.annotations.update_attribute import cli as func28
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from arrow.commands.annotations.update_dbxref import cli as func29
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@click.group()
@@ -60,3 +63,6 @@ def cli():
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cli.add_command(func24)
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cli.add_command(func25)
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cli.add_command(func26)
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cli.add_command(func27)
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cli.add_command(func28)
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cli.add_command(func29)

‎scripts‎

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