本文整理汇总了Python中Helper.extractFromDb方法的典型用法代码示例。如果您正苦于以下问题：Python Helper.extractFromDb方法的具体用法？Python Helper.extractFromDb怎么用？Python Helper.extractFromDb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Helper的用法示例。
在下文中一共展示了Helper.extractFromDb方法的2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: getDomainsForSequences
# 需要导入模块: import Helper [as 别名]
# 或者: from Helper import extractFromDb [as 别名]
def getDomainsForSequences(domains, proteomefile):
handle = open(proteomefile, "rU")
result = ''
accessions = []
for record in handle.readlines():
accessions.append(record.split('\n')[0])
sequences = Helper.extractFromDb(accessions)
for accession in accessions:
seq = sequences[accession]
if accession in domains:
for position in domains[accession]:
start = position[0]
end = position[1]
subseq = seq[start-1:end]
if len(subseq) > 0:
header = ">" + accession + "|" + position[2] + "|start:" + str(start) + "|end:" + str(end) + '\n'
result = result + header + subseq + '\n'
else:
print accession, "was shorter than the location of a domain", len(seq), "[", start, end, "]"
else:
print accession, "does not have assigned domains"
handle.close()
return result示例2: in
# 需要导入模块: import Helper [as 别名]
# 或者: from Helper import extractFromDb [as 别名]
except getopt.error, msg:
print msg
print "for help use --help"
sys.exit(2)
# process options
for o, a in opts:
if o in ("-h", "--help"):
print __doc__
sys.exit(0)
if o in ("-o", "--organism"):
end = rcp.get("Fileendings", "idlistsuffix")
inputfile = idlistpath+a+end
outputfile = outpath+a+"Full"+".fasta"
listin = open(inputfile, 'r')
idlist = []
for line in listin.readlines():
idlist.append(line.split()[0])
listin.close()
result = Helper.extractFromDb(idlist)
outhandle = open(outputfile, 'w')
for key in result:
#changed this after mouse, human and drome 0, 20, 30 and 45 were extracted, before that key was the header
#blastall has problems with ' symbols
outhandle.write('>' + Helper.retrieveAccessionNumber(key) + '\n' + result[key] + '\n')
outhandle.close()
if __name__ == "__main__":
main()