def rMap_full(f_in, f_out):
# Database connection parameters
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
gHandler = GeneralHandler(db, cursor)
rHandler = ReagentHandler(db, cursor)
seqHandler = SequenceHandler(db, cursor)
infile = open(f_in, 'r')
outfile = open(f_out, 'w')
for line in infile.readlines():
reagentID = line.strip() # e.g. V123
rID = rHandler.convertReagentToDatabaseID(reagentID)
seqID = rHandler.findDNASequenceKey(rID)
if seqID:
mySeq = seqHandler.findSequenceByID(seqID)
# Construct a Seq object readable by BioPython:
bioSeq = Seq(mySeq)
fSeq = FormattedSeq(bioSeq) # default linear = TRUE
analysis = Analysis(AllEnzymes, fSeq) # linear = true
result = analysis.full()
header = "==============================================\nRestriction analysis for " + reagentID + "\n==============================================\n"
analysis.print_that(title=header+'\n\n')
def rMap_full(f_in, f_out):
# Database connection parameters
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
gHandler = GeneralHandler(db, cursor)
rHandler = ReagentHandler(db, cursor)
seqHandler = SequenceHandler(db, cursor)
infile = open(f_in, 'r')
outfile = open(f_out, 'w')
for line in infile.readlines():
reagentID = line.strip() # e.g. V123
rID = rHandler.convertReagentToDatabaseID(reagentID)
seqID = rHandler.findDNASequenceKey(rID)
if seqID:
mySeq = seqHandler.findSequenceByID(seqID)
# Construct a Seq object readable by BioPython:
bioSeq = Seq(mySeq)
fSeq = FormattedSeq(bioSeq) # default linear = TRUE
analysis = Analysis(AllEnzymes, fSeq) # linear = true
result = analysis.full()
header = "==============================================\nRestriction analysis for " + reagentID + "\n==============================================\n"
analysis.print_that(title=header + '\n\n')
def rMap_specific(f_in, f_out, enz_list):
# Database connection parameters
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
gHandler = GeneralHandler(db, cursor)
rHandler = ReagentHandler(db, cursor)
seqHandler = SequenceHandler(db, cursor)
infile = open(f_in, 'r')
outfile = open(f_out, 'w')
for line in infile.readlines():
reagentID = line.strip() # e.g. V123
rID = rHandler.convertReagentToDatabaseID(reagentID)
seqID = rHandler.findDNASequenceKey(rID)
if seqID:
mySeq = seqHandler.findSequenceByID(seqID)
# Construct a Seq object readable by BioPython:
bioSeq = Seq(mySeq)
fSeq = FormattedSeq(bioSeq, linear=False) # linear = FALSE, we're dealing w/ VECTORS
analysis = Analysis(enz_list, fSeq, linear=False) # linear = FALSE again for VECTORS
result = analysis.full()
outfile.write(reagentID + ": " + '\n')
# calculate bandwidths
allSites = []
for enz in result.keys():
sites = result[enz]
if len(allSites) == 0:
allSites = sites
else:
# concatenate
for s in sites:
allSites.append(s)
allSites.sort()
if len(allSites) > 0:
# calculate distances between sites
bandSizes = []
i = 1
while i < len(allSites):
tmpLen = allSites[i] - allSites[i-1]
bandSizes.append(tmpLen)
i += 1
# last band
tmpLen = len(mySeq) - allSites[i-1] + allSites[0]
bandSizes.append(tmpLen)
bandSizes.sort()
outfile.write(`bandSizes` + '\n')
outfile.write('\n')
infile.close()
outfile.close()
cursor.close()
db.close()
def rMap_specific(f_in, f_out, enz_list):
# Database connection parameters
dbConn = DatabaseConn()
db = dbConn.databaseConnect()
cursor = db.cursor()
gHandler = GeneralHandler(db, cursor)
rHandler = ReagentHandler(db, cursor)
seqHandler = SequenceHandler(db, cursor)
infile = open(f_in, 'r')
outfile = open(f_out, 'w')
for line in infile.readlines():
reagentID = line.strip() # e.g. V123
rID = rHandler.convertReagentToDatabaseID(reagentID)
seqID = rHandler.findDNASequenceKey(rID)
if seqID:
mySeq = seqHandler.findSequenceByID(seqID)
# Construct a Seq object readable by BioPython:
bioSeq = Seq(mySeq)
fSeq = FormattedSeq(
bioSeq,
linear=False) # linear = FALSE, we're dealing w/ VECTORS
analysis = Analysis(
enz_list, fSeq,
linear=False) # linear = FALSE again for VECTORS
result = analysis.full()
outfile.write(reagentID + ": " + '\n')
# calculate bandwidths
allSites = []
for enz in result.keys():
sites = result[enz]
if len(allSites) == 0:
allSites = sites
else:
# concatenate
for s in sites:
allSites.append(s)
allSites.sort()
if len(allSites) > 0:
# calculate distances between sites
bandSizes = []
i = 1
while i < len(allSites):
tmpLen = allSites[i] - allSites[i - 1]
bandSizes.append(tmpLen)
i += 1
# last band
tmpLen = len(mySeq) - allSites[i - 1] + allSites[0]
bandSizes.append(tmpLen)
bandSizes.sort()
outfile.write( ` bandSizes ` + '\n')
outfile.write('\n')
infile.close()
outfile.close()
cursor.close()
db.close()
