egautils.py

import string
import logging

logger = logging.getLogger()


def obj_id(e):
	def filter_alphan(t, additional):
		return ''.join(filter(lambda x: x.lower() in string.ascii_lowercase or x in additional, t))
	try:
		idblock = e.get('@idblock', dict())
		tags = sorted(list(set([idblock[k]  for k in ['alias', 'refname', 'accession'] if k in idblock])))
		return 'unknown' if not tags else filter_alphan('.'.join(tags), '.-_1234567890')
	except Exception as e:
		logger.info('#__could_not_exact_id__:{0}\n'.format(e ))
		return '__cannot_understand_id_block__'


def strategy2schema(s):
	def found(x, alist):
		if x in alist: return True
		else:
			return x.lower() in [e.lower() for e in alist]
			
	if found(s, ["DNase-Hypersensitivity", "ATAC-seq", "NOME-Seq"]): return "chromatin_accessibility"
	elif found(s, ["Bisulfite-Seq"]): return "bisulfite-seq"
	elif found(s, ["MeDIP-Seq"]): return "medip-seq"
	elif found(s, ["MRE-Seq"]): return "mre-seq"
	elif found(s, ["RNA-Seq", "miRNA-Seq"]): return "rna-seq"
	elif found(s, ["WGS"]): return "wgs"
	elif s[0:4].lower() in ['chip', 'hist']: return 'chip-seq'
	else:
		return s.lower()