本文整理汇总了Python中Bio.SeqFeature.SeqFeature.qualifiers['codon_start']方法的典型用法代码示例。如果您正苦于以下问题：Python SeqFeature.qualifiers['codon_start']方法的具体用法？Python SeqFeature.qualifiers['codon_start']怎么用？Python SeqFeature.qualifiers['codon_start']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.qualifiers['codon_start']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: gene2features
# 需要导入模块: from Bio.SeqFeature import SeqFeature [as 别名]
# 或者: from Bio.SeqFeature.SeqFeature import qualifiers['codon_start'] [as 别名]
def gene2features(r, gene, gene2position, gene2product, start, end, gcode, partialyes, verbose):
"""
"""
contig, CDSs, gffstrand, function, frames = gene2position[gene]
if gffstrand in ('1','+'):
strand = +1
else:
strand = -1
CDSs.reverse()
'''#add stop codon if not partial seq
if strand==1 and CDSs[-1][1]+3 <= len(r.seq):
CDSs[-1][1] += 3
elif strand==-1 and CDSs[0][0]-3 > 0:
CDSs[0][0] -= 3'''
cdsloc, mrnaloc = get_locations(CDSs, start, end, strand)
#add gene
geneid = gene #".".join(gene.split('.')[:-1])
#get product
product = "hypothetical protein"
if geneid in gene2product:
product = gene2product[geneid]
if gene.endswith('.t1'):
sf = SeqFeature(FeatureLocation(BeforePosition(start-1),AfterPosition(end)), strand=strand, type='gene', id=geneid)
sf.qualifiers={"locus_tag": geneid, "gene": geneid, "product": product}
r.features.append(sf)
#get mRNA sf
sf = SeqFeature(mrnaloc, type='mRNA', id=gene)
sf.qualifiers={"locus_tag": geneid, "gene": geneid, "product": product} #"protein_id": gene
r.features.append(sf)
#get CDS sf
sf = SeqFeature(cdsloc, type='CDS', id=gene)
#get translation
seq = sf.extract(r.seq)
aa = str(seq.translate(table=gcode))
#solve non-triplets issue
if len(seq) % 3:
if strand==1:
end -= len(seq) % 3
else:
start += len(seq) % 3
##check for partial sequence - no M as first or no * as last aa
partial = 0
#both ends partial
if aa[0]!="M" and aa[-1]!="*":
partial = 1
sf.location = FeatureLocation(BeforePosition(start-1),AfterPosition(end))
#left end partial
elif aa[0]!="M" and strand==1 or aa[-1]!="*" and strand==-1:
partial = 1
sf.location = FeatureLocation(BeforePosition(start-1),end)
#right end partial
elif aa[-1]!="*" and strand==1 or aa[0]!="M" and strand==-1:
partial = 1
sf.location = FeatureLocation(start-1,AfterPosition(end))
#strip stop codon
aa = aa.strip("*")
#replace internal stop codons by X
if "*" in aa:
if verbose:
sys.stderr.write("[Warning] Stop codon(s) in: %s. Skipped!\n" % gene)
return r
#aa = aa.replace("*","X")
sf.qualifiers = {'transl_table': gcode, "locus_tag": geneid, "gene": geneid, "product": product, "translation": aa} #"protein_id": gene,
if function:
sf.qualifiers['note'] = function
#inform about partial entries
if partial:
#skip if not partial are allowed
if not partialyes:
return r
if aa[0]!="M":
sf.qualifiers['codon_start'] = 1
sf.qualifiers['product'] += ", partial cds"
if verbose:
sys.stderr.write("[Warning] Partial sequence: %s\n" % (gene,))
#sys.stderr.write("[Warning] Partial sequence: %s %s\n" % (gene,sf))
#add to features
r.features.append(sf)
return r