本文整理匯總了Python中CGAT.Genomics.printPrettyAlignment方法的典型用法代碼示例。如果您正苦於以下問題：Python Genomics.printPrettyAlignment方法的具體用法？Python Genomics.printPrettyAlignment怎麽用？Python Genomics.printPrettyAlignment使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類CGAT.Genomics的用法示例。
在下文中一共展示了Genomics.printPrettyAlignment方法的1個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Python代碼示例。
示例1: main
# 需要導入模塊: from CGAT import Genomics [as 別名]
# 或者: from CGAT.Genomics import printPrettyAlignment [as 別名]
#.........這裏部分代碼省略.........
variants = Variants.mergeVariants(variants)
E.debug("%s: found %i variants after merging in %s:%i..%i" %
(gene_id, len(variants), contig, extended_start, extended_end))
if E.global_options.loglevel >= 10:
print "# merged variants:", variants
# collect coordinate offsets and remove conflicting variants
variants, removed_variants, offsets = Variants.buildOffsets(
variants, contig=contig)
if len(removed_variants) > 0:
E.warn("removed %i conflicting variants" % len(removed_variants))
for v in removed_variants:
E.info("removed variant: %s" % str(v))
E.info("%i variants after filtering" % len(variants))
if len(variants) > 0:
# build variants
indexed_variants = Variants.indexVariants(variants)
# update exon sequences according to variants
variant_exons = buildVariantSequences(indexed_variants, all_exons)
# update intron sequences according to variants
variant_introns = buildVariantSequences(
indexed_variants, all_introns)
if E.global_options.loglevel >= 10:
for key in variant_exons:
print "exon", key
Genomics.printPrettyAlignment(
all_exons[key],
variant_exons[key][0],
variant_exons[key][1],
)
for key in variant_introns:
print "intron", key
Genomics.printPrettyAlignment(
all_introns[key][:30] + all_introns[key][-30:],
variant_introns[key][0][:30] +
variant_introns[key][0][-30:],
variant_introns[key][1][:30] + variant_introns[key][1][-30:])
else:
variant_exons, variant_introns = None, None
for transcript in transcripts:
transcript.sort(key=lambda x: x.start)
transcript_id = transcript[0].transcript_id
alleles = buildAlleles(transcript,
variant_exons,
variant_introns,
all_exons,
all_introns,
offsets,
is_seleno=transcript_id in seleno,
reference_coordinates=False,
)
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