本文整理汇总了Python中Bio.SeqFeature.SeqFeature.type方法的典型用法代码示例。如果您正苦于以下问题：Python SeqFeature.type方法的具体用法？Python SeqFeature.type怎么用？Python SeqFeature.type使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Bio.SeqFeature.SeqFeature的用法示例。
在下文中一共展示了SeqFeature.type方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: annotate_dna_reference
# 需要导入模块: from Bio.SeqFeature import SeqFeature [as 别名]
# 或者: from Bio.SeqFeature.SeqFeature import type [as 别名]
def annotate_dna_reference(ref, protein):
'''Annotate DNA reference with the protein secondary structures'''
from Bio.SeqFeature import SeqFeature, FeatureLocation
annotation_table = parse_secondary_structure(protein)
if protein == 'gagpol':
start_protein = ref.annotation['gag'].location.nofuzzy_start
elif protein == 'vpu':
# Uniprot starts one aa downstream of us
start_protein = ref.annotation[protein].location.nofuzzy_start + 3
else:
start_protein = ref.annotation[protein].location.nofuzzy_start
features = []
for _, datum in annotation_table.iterrows():
start_dna = datum['start'] * 3 + start_protein
end_dna = datum['end'] * 3 + start_protein
# Notice ribosomal slippage site
if protein == 'gagpol':
if start_dna >= slippage_site:
start_dna -= 1
if end_dna >= slippage_site:
end_dna -= 1
anno = SeqFeature(FeatureLocation(start_dna, end_dna), strand=+1)
anno.type = datum['feature']
features.append(anno)
return features