本文整理汇总了Python中csv.DictReader.get方法的典型用法代码示例。如果您正苦于以下问题：Python DictReader.get方法的具体用法？Python DictReader.get怎么用？Python DictReader.get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csv.DictReader的用法示例。
在下文中一共展示了DictReader.get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: action
# 需要导入模块: from csv import DictReader [as 别名]
# 或者: from csv.DictReader import get [as 别名]
def action(args):
### format format blast data and add additional available information
fieldnames = None if args.has_header else sequtils.BLAST_HEADER_DEFAULT
blast_results = DictReader(args.blast_file, fieldnames = fieldnames)
blast_results = list(blast_results)
sseqids = set(s['sseqid'] for s in blast_results)
qseqids = set(s['qseqid'] for s in blast_results)
# load seq_info and map file
mapfile = DictReader(args.map, fieldnames = ['name', 'specimen'])
mapfile = {m['name']:m['specimen'] for m in mapfile if m['name'] in qseqids}
seq_info = DictReader(args.seq_info)
seq_info = {s['seqname']:s for s in seq_info if s['seqname'] in sseqids}
# pident
def pident(b):
return dict(b, pident = float(b['pident'])) if b['sseqid'] else b
blast_results = (pident(b) for b in blast_results)
# coverage
def cov(b):
if b['sseqid'] and b['qcovs']:
b['coverage'] = float(b['qcovs'])
return b
elif b['sseqid']:
c = coverage(b['qstart'], b['qend'], b['qlen'])
return dict(b, coverage = c)
else:
return b
blast_results = (cov(b) for b in blast_results)
# seq info
def info(b):
return dict(seq_info[b['sseqid']], **b) if b['sseqid'] else b
blast_results = (info(b) for b in blast_results)
# tax info
def tax_info(b):
return dict(args.taxonomy[b['tax_id']], **b) if b['sseqid'] else b
blast_results = (tax_info(b) for b in blast_results)
### output file headers
fieldnames = ['specimen', 'max_percent', 'min_percent', 'max_coverage',
'min_coverage', 'assignment_id', 'assignment']
if args.weights:
weights = DictReader(args.weights, fieldnames = ['name', 'weight'])
weights = {d['name']:d['weight'] for d in weights if d['name'] in qseqids}
fieldnames += ['clusters', 'reads', 'pct_reads']
else:
weights = {}
if args.copy_numbers:
copy_numbers = DictReader(args.copy_numbers)
copy_numbers = {d['tax_id']:float(d['median']) for d in copy_numbers}
fieldnames += ['corrected', 'pct_corrected']
else:
copy_numbers = {}
# TODO: take out target_rank, hi, low and provide in pipeline using csvmod
# TODO: option to include tax_ids (default no)
fieldnames += ['target_rank', 'hi', 'low', 'tax_ids']
### Columns
out = DictWriter(args.out,
extrasaction = 'ignore',
fieldnames = fieldnames)
out.writeheader()
if args.out_detail:
args.out_detail.writeheader()
def blast_hit(hit, args):
return hit['sseqid'] and \
hit[args.target_rank] and \
hit['coverage'] >= args.coverage and \
float(weights.get(hit['qseqid'], 1)) >= args.min_cluster_size and \
hit[args.target_rank] not in args.exclude_by_taxid and \
hit['qseqid'] != hit['sseqid'] and \
int(hit['ambig_count']) <= args.max_ambiguous
### Rows
etc = '[no blast result]' # This row will hold all unmatched
# groups have list position prioritization
groups = [
('> {}%'.format(args.max_identity),
lambda h: blast_hit(h, args) and h['pident'] > args.max_identity),
(None,
lambda h: blast_hit(h, args) and args.max_identity >= h['pident'] > args.min_identity),
('<= {}%'.format(args.min_identity),
lambda h: blast_hit(h, args) and h['pident'] <= args.min_identity),
]
#.........这里部分代码省略.........