本文整理汇总了Python中Helper.retrieveAccessionNumber方法的典型用法代码示例。如果您正苦于以下问题：Python Helper.retrieveAccessionNumber方法的具体用法？Python Helper.retrieveAccessionNumber怎么用？Python Helper.retrieveAccessionNumber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.retrieveAccessionNumber方法的6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: getBasicProteins
# 需要导入模块: import Helper [as 别名]
# 或者: from Helper import retrieveAccessionNumber [as 别名]
def getBasicProteins(self, splittedLine):
temp = []
for i in range(0, len(splittedLine), 2):
p = Protein()
acc = Helper.retrieveAccessionNumber(splittedLine[i])
p.accession = acc
p.orthologGroup = self
temp.append(p)
return temp示例2: filetodb
# 需要导入模块: import Helper [as 别名]
# 或者: from Helper import retrieveAccessionNumber [as 别名]
def filetodb(c, filehandle, tax):
fileAsList = []
accessions = []
for line in filehandle.readlines():
if not line.startswith("#") and not line.startswith("<"): # header usually starts with <
split = line.split("\n")[0].split()
if len(split) == 0:
continue
acc = Helper.retrieveAccessionNumber(split[0])
fileAsList.append(
[
acc,
split[1],
split[2],
split[3],
split[4],
split[5],
split[6],
split[7],
split[8],
split[9],
split[10],
split[11],
split[12],
split[14],
]
)
accessions.append(acc)
lengths = Helper.getSequenceLengthsForAccessionsIds(accessions)
i = c.execute("select count(*) from tsv_storage").fetchone()[0]
for split in fileAsList:
writetodb(
c,
i,
split[0],
tax,
split[1],
split[2],
split[3],
split[4],
split[5],
split[6],
split[7],
split[8],
split[9],
split[10],
split[11],
split[12],
split[13],
int(lengths[split[0]]),
)
i = i + 1示例3: filetodb
# 需要导入模块: import Helper [as 别名]
# 或者: from Helper import retrieveAccessionNumber [as 别名]
def filetodb(c, filehandle):
i = c.execute("select count(*) from fasta_storage").fetchone()[0]
for record in SeqIO.parse(filehandle, "fasta"):
i = i + 1
seqid = Helper.retrieveAccessionNumber(record.id)
writetodb(c, i, record.seq, record.description, seqid)示例4: addSeeds
# 需要导入模块: import Helper [as 别名]
# 或者: from Helper import retrieveAccessionNumber [as 别名]
def addSeeds(self, line):
acc = Helper.retrieveAccessionNumber(line.split()[3])
if acc in self.inparalogsA:
self.seedsA.append(acc)
elif acc in self.inparalogsB:
self.seedsB.append(acc)示例5: open
# 需要导入模块: import Helper [as 别名]
# 或者: from Helper import retrieveAccessionNumber [as 别名]
if ok:
idList = []
inputpath = rcp.get("Filepaths", "tsvpath")
outpath = rcp.get("Filepaths", "idlistpath")
suffix = rcp.get("Fileendings", "idlistsuffix")
inFile = open(inputpath + inputfile + ".tsv", "r")
cutoff = rcp.getint("Options", "domainlengthcutoff")
for line in inFile.readlines():
if not line.startswith("#") and not line.startswith("<"):
splittedLine = line.split()
if len(splittedLine) > 1:
accession = Helper.retrieveAccessionNumber(
splittedLine[0]
) # if error occurs, maybe tsv file has a header
start = int(splittedLine[1])
end = int(splittedLine[2])
hmmtype = splittedLine[7] # hmm type
if accession not in idList and hmmtype in ("Domain", "Family") and end - start >= cutoff:
idList.append(accession)
inFile.close()
outFile = open(outpath + outputfile + str(cutoff) + suffix, "w")
for ac in idList:
outFile.write("%s\n" % ac)
outFile.close()
else:
print __doc__
sys.exit(0)示例6: in
# 需要导入模块: import Helper [as 别名]
# 或者: from Helper import retrieveAccessionNumber [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()