diff --git a/sbin/assembly-to-json b/sbin/assembly-to-json index 16f05a0..cb5c800 100755 --- a/sbin/assembly-to-json +++ b/sbin/assembly-to-json @@ -1,8 +1,5 @@ #!/usr/bin/env python # -*- coding: utf-8 -*- - -from __future__ import absolute_import, division, print_function, unicode_literals - """convert assembly text file to json eg$ ./sbin/assembly-to-json -p bioutils/_data/assemblies -f pull/GCF_000001405.29.assembly.txt @@ -27,7 +24,7 @@ class AssemblyParser(object): def __init__(self, body): self._body = body.replace("\r","") - + @property def name(self): return re.search("^# Assembly name:\s+(\S+)", self._body, flags=re.MULTILINE).group(1).strip() @@ -42,7 +39,7 @@ class AssemblyParser(object): @property def taxid(self): return re.search("^# Taxid:\s+(\S+)", self._body, flags=re.MULTILINE).group(1).strip() - + @property def genbank_accession(self): try: @@ -148,4 +145,4 @@ if __name__ == "__main__": except Exception as e: logger.error("oopsie on " + assy_id_or_name) logger.exception(e) - + diff --git a/src/bioutils/accessions.py b/src/bioutils/accessions.py index 96d565f..52c0ab1 100644 --- a/src/bioutils/accessions.py +++ b/src/bioutils/accessions.py @@ -25,9 +25,6 @@ The string form may be used as a CURIE, in which case the document in which the CURIE is used must contain a map of ``{namespace : uri}``. """ - -from __future__ import absolute_import, division, print_function, unicode_literals - import re from .exceptions import BioutilsError diff --git a/src/bioutils/coordinates.py b/src/bioutils/coordinates.py index c268214..f0fb69a 100644 --- a/src/bioutils/coordinates.py +++ b/src/bioutils/coordinates.py @@ -32,8 +32,6 @@ *intervals* specified in each of the coordinate systems. """ -from __future__ import absolute_import, division, print_function, unicode_literals - PLUS_STRAND = 1 MINUS_STRAND = -1 diff --git a/src/bioutils/seqfetcher.py b/src/bioutils/seqfetcher.py index 4720b03..a94e294 100644 --- a/src/bioutils/seqfetcher.py +++ b/src/bioutils/seqfetcher.py @@ -2,9 +2,6 @@ """Provides sequence fetching from NCBI and Ensembl. """ - -from __future__ import absolute_import, division, print_function, unicode_literals - import logging import os import random diff --git a/src/bioutils/vmc_digest.py b/src/bioutils/vmc_digest.py index 0af4564..f64cec8 100644 --- a/src/bioutils/vmc_digest.py +++ b/src/bioutils/vmc_digest.py @@ -1,6 +1,4 @@ # -*- coding: utf-8 -*- -from __future__ import unicode_literals - import hashlib from .digest import Digest