along with D3E. If not, see <http://www.gnu.org/licenses/>.
'''
from D3EUtil import readData
import sys
inFileName = sys.argv[1]
label1 = sys.argv[2]
label2 = sys.argv[3]
outDir = sys.argv[4]
n = int(sys.argv[5])
inFile = open(inFileName)
data1, data2, ids, lineStatus = readData(inFile,
label1,
label2,
normalise=True)
i = 0
for p1, p2, idx in zip(data1, data2, ids):
if i % n == 0:
ouputFile = open(
outDir + label1 + '_' + label2 + '_' + str(i / n) + '.txt', 'w')
ouputFile.write('GeneID\t' + '\t'.join([label1] * len(data1[0]) +
[label2] * len(data2[0])) +
'\n')
ouputFile.write('\t'.join([idx] + [str(x) for x in p1 + p2]) + '\n')
i = i + 1
D3E is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with D3E. If not, see <http://www.gnu.org/licenses/>.
'''
from D3EUtil import readData
import sys
inFileName = sys.argv[1]
label1 = sys.argv[2]
label2 =sys.argv[3]
outDir = sys.argv[4]
n = int(sys.argv[5])
inFile = open(inFileName)
data1, data2, ids, lineStatus = readData(inFile, label1, label2, normalise = True)
i = 0
for p1, p2, idx in zip(data1, data2, ids):
if i % n == 0:
ouputFile = open( outDir + label1 + '_' + label2 + '_' + str(i/n) + '.txt', 'w' )
ouputFile.write('GeneID\t' + '\t'.join( [label1] * len(data1[0]) + [label2] * len(data2[0]) ) + '\n' )
ouputFile.write('\t'.join ( [idx] + [str(x) for x in p1+p2] ) + '\n')
i = i + 1
action='store_const',
const=True,
dest='verbose',
default=True,
help='verbose')
parser.add_argument('-f',
'--fdr',
action='store',
type=float,
dest='fdr',
default=1,
help='FDR parameter')
args = parser.parse_args()
data1, data2, ids, lineStatus = readData(args.inputFile, args.label1[0],
args.label2[0], args.normalise,
args.removeZeros, args.useSpikeIns,
args.spikeInStart)
if args.verbose:
for status in lineStatus:
logStatus(status)
if args.mode == 0:
args.outputFile.write(
'#GeneID\ta1\tb1\tg1\tGOF1\ta2\tb2\tg2\tGOF2\ts1\tf1\td1\ts2\tf2\td2\tRs\tRf\tRd\tp-value\tmu1\tcv1\tmu2\tcv2\n\n'
)
elif args.mode == 1:
args.outputFile.write(
'#GeneID\ta1\tb1\tg1\tGOF1\ta2\tb2\tg2\tGOF2\ts1\tf1\td1\ts2\tf2\td2\tRs\tRf\tRd\tpSize\tpFreq\tpDuty\tp-value\tmu1\tcv1\tmu2\tcv2\n\n'
)
beta = params.beta
gamma = params.gamma
return BioParams( gamma / beta, alpha, alpha * beta / (alpha + beta) )
inputString = fileinput.input()[0].rstrip('\n')
inputJSON = json.loads(inputString)
inputFile = StringIO.StringIO(inputJSON['input']);
label1 = inputJSON['label1']
label2 = inputJSON['label2']
normalise = int(inputJSON['normalise'])
removeZeros = inputJSON['removeZeros']
useSpikeIns = inputJSON['useSpikeIns']
data1, data2, ids, lineStatus = readData(inputFile, label1, label2, normalise, removeZeros, useSpikeIns)
errors = []
rows = []
cols = []
for status in lineStatus:
if status.code == 1:
errors.append( {'geneId': status.idx, 'message': 'Warning: ' + status.message} )
elif status.code == 2:
errors.append( {'geneId': status.idx, 'message': 'Error: ' + status.message} )
rowKeys = ["geneId"]
rowKeys.extend( ["col" + str(i) for i in range(1,21)] )
(at your option) any later version.
D3E is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with D3E. If not, see <http://www.gnu.org/licenses/>.
'''
import sys
from D3EUtil import readData
inFileName = sys.argv[1]
outFileName = sys.argv[2]
label = sys.argv[3]
inFile = open(inFileName)
outFileName = open(outFileName,'w')
p1, p2, ids, lineStatus = readData(inFile, label, label, normalise=False, removeZeros=False, useSpikeIns = False, verbose = True)
n = len(p1[0]) / 2
outFileName.write('GeneID\t' + '\t'.join( [ label+'_1' ] * n + [label+'_2'] * (len(p1[0])-n) ) + '\n')
for idx, p in zip(ids, p1):
outFileName.write(idx + '\t' + '\t'.join( str(int(x)) for x in p ) + '\n')
You should have received a copy of the GNU General Public License
along with D3E. If not, see <http://www.gnu.org/licenses/>.
'''
import sys
from D3EUtil import readData
inFileName = sys.argv[1]
outFileName = sys.argv[2]
label = sys.argv[3]
inFile = open(inFileName)
outFileName = open(outFileName, 'w')
p1, p2, ids, lineStatus = readData(inFile,
label,
label,
normalise=False,
removeZeros=False,
useSpikeIns=False,
verbose=True)
n = len(p1[0]) / 2
outFileName.write('GeneID\t' + '\t'.join([label + '_1'] * n + [label + '_2'] *
(len(p1[0]) - n)) + '\n')
for idx, p in zip(ids, p1):
outFileName.write(idx + '\t' + '\t'.join(str(int(x)) for x in p) + '\n')