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')