def eval(request): assignment = AssignmentInstance.objects.get(pk=request.POST['assignment']) for question in assignment.questions.all(): #Store student answer answer = request.POST[str(question.id)+'choice'] if question.can_edit: question.can_edit=False question.student_answer=answer; question.save() template = question if template.isCopy == True: template = template.original if answer==question.solution: assignment.score += question.value assignment.save() if not template == None: template.numCorrect+=1 template.save() elif not template == None: template.numIncorrect+=1 template.save() if assdone(assignment): assignment.can_edit=False assignment.save() return main(request)
def save(request): assignment = AssignmentInstance.objects.get(pk=request.POST['assignment']) for question in assignment.questions.all(): try: answer = request.POST[str(question.id)+'choice'] question.student_answer=answer; question.save() except: continue return main(request)
def main(): ## this function performs dispatch on the command line that a user proves. Look at the first argument, which specifies he functio nthe user wants pairadise2 to perform, then dispatch to the appropriate module. parser = argparse.ArgumentParser(description='pairadise2') parser.add_argument('command', nargs='*') ## command user wants to run ## multiple modules parser.add_argument( '--gz', help='flag denoting gzipped reads', action='store_true' ) ## gzipped reads (for mapping) or VCF file (for everything else) parser.add_argument( '-e', help="file containing RNA editing positions, downloaded from RADAR" ) #for parser.add_argument( '--rnaedit', help= "flag to check for RNA editing events, must also provide an RNA editing file usng -e parameter", action="store_true") parser.add_argument( '-v', help="VCF genotype directory") ## or vcf file if just providing one parser.add_argument('-g', help="GTF annotation file") parser.add_argument('-o', help="output directory") parser.add_argument( '--nmask', help="flag to N-mask reference genome and align to that", action="store_true") ## personalize parameters parser.add_argument('-r', help="reference fasta file") ## mapping parameters parser.add_argument('-N', help="number of mismatches per read pair") parser.add_argument('-T', help="num threads for STAR alignment") parser.add_argument( '-M', help="max number of multiple alignments in STAR mapping") parser.add_argument( '-s', help="fastq read file(s), comma deliminated if paired end") parser.add_argument( '-r1', help="hap1 reference genome file") #personal genome, if providing own parser.add_argument( '-r2', help="hap2 reference genome file") # personal genome, if providing own parser.add_argument( '-rn', help="N-masked reference genome file") # if providing own parser.add_argument( '--readlength', help= "read length, used to generate genome index (see STAR parameter sjdbOverhang)" ) parser.add_argument( '--genomedir', help= "STAR genome index directory (if user is providing own genome index to use for mapping)" ) parser.add_argument( '--hap', help="only map reads to hap1 and hap2 personal genomes", action="store_true") ## discover/assign parameters parser.add_argument( '-c', help='chromsome') #if not provided, assume run all chromsosomes parser.add_argument('--conflict', help='flag to print conflicting reads', action='store_true') parser.add_argument('-b1', help="haplotype 1 bam file" ) ## alignments to personal genomes, if providing own parser.add_argument('-b2', help="haplotype 2 bam file" ) ## alignments to personal genomes, if providing own parser.add_argument('-br', help="reference alignment bam file") parser.add_argument('--nomerge', help="flag to not merge chromosome bam files", action="store_true") ## splicing parameters parser.add_argument('--hap1Bam', help="provide own hap1 allele specific bam file") parser.add_argument('--hap2Bam', help="provide own hap2 allele specific bam file") parser.add_argument('--asdir', help='directory containing AS events') parser.add_argument('--MXE') parser.add_argument('--SE') parser.add_argument('--RI') parser.add_argument('--A3SS') parser.add_argument('--A5SS') parser.add_argument('--samples', help="sample file for merging") parser.add_argument('--merge', help="merge count files for multiple samples", action="store_true") parser.add_argument('--pos2id', help="flag to change snp pos to snp id in count files", action="store_true") parser.add_argument('--haplotype', help="flag to do hap1 vs hap2", action="store_true") parser.add_argument( '--anchorlength', help="anchor length used for STAR alignment (default=8)") parser.add_argument('--mxeDetail', help="merge mxe detailed read counts", action="store_true") ## assa parameters parser.add_argument( '--sampleDirList', help= "The file contains sample directory.Each directory path a row. Do not include the haplotype bam file." ) parser.add_argument('--ASASOutDir', help="The output folder of ASAS event count result.") # parser.add_argument('--exonreads',help="to include exon reads") args = parser.parse_args() command = args.command if ((args.rnaedit and not args.e) or (args.e and not args.rnaedit)): sys.stderr.write( "pairadise22: if --rnaedit flag is used, you must also provide a file containing RNA editing locations using -e parameter \n" ) sys.exit() if len(command) == 0: sys.stderr.write( 'pairadise2: need a command - personalize, mapping, discover, alleles, splicing, assaevent, statistics\n' ) sys.exit() if (not args.o): sys.stderr.write("pairadise2: -o outDir parameter is required\n") sys.exit() elif command[0] == "personalize": personalize.main(args) elif command[0] == "mapping": mapping.main(args) elif command[0] == "discover": discover.main(args) elif command[0] == "assign": assign.main(args) elif command[0] == "splicing": splicing.main(args) elif command[0] == "asasevent": asasevent.main(args) elif command[0] == "statistics": statistics.main(args) else: sys.stderr.write("pairadise2: I don't recognise the option '" + command[0] + "'\n") sys.exit()
import nuke from assign import addAssign,addAssignAuto,getInfos,main,addAssignManual,getFilePaths nuke.addOnUserCreate(addAssignAuto,nodeClass=('Read')) menu=nuke.menu('Nuke') assignMenu=menu.addMenu('Mo_Tools/assign',icon="M.jpg") assignMenu.addCommand('assign',lambda:main(),icon="assign.png") assignMenu.addCommand('add assign tab to read',lambda:addAssignManual(),icon="addAssign.png") assignMenu.addCommand('Get File Paths only',lambda:getFilePaths(),'alt+d',icon="M.jpg")
def main(): ## this function performs dispatch on the command line that a user proves. Look at the first argument, which specifies he functio nthe user wants rPGA to perform, then dispatch to the appropriate module. parser = argparse.ArgumentParser(description='rPGA') parser.add_argument('command',nargs='*') ## command user wants to run ## multiple modules parser.add_argument('--gz',help='flag denoting gzipped reads',action='store_true') ## gzipped reads (for mapping) or VCF file (for everything else) parser.add_argument('-e',help="file containing RNA editing positions, downloaded from RADAR") #for parser.add_argument('--rnaedit',help="flag to check for RNA editing events, must also provide an RNA editing file usng -e parameter",action="store_true") parser.add_argument('-v',help="VCF genotype directory") ## or vcf file if just providing one parser.add_argument('-g',help="GTF annotation file") parser.add_argument('-o',help="output directory") parser.add_argument('--nmask',help="flag to N-mask reference genome and align to that",action="store_true") ## personalize parameters parser.add_argument('-r',help="reference fasta file") ## mapping parameters parser.add_argument('-N',help="number of mismatches per read pair") parser.add_argument('-T',help="num threads for STAR alignment") parser.add_argument('-M',help="max number of multiple alignments in STAR mapping") parser.add_argument('-s',help="fastq read file(s), comma deliminated if paired end") parser.add_argument('-r1',help="hap1 reference genome file")#personal genome, if providing own parser.add_argument('-r2',help="hap2 reference genome file") # personal genome, if providing own parser.add_argument('-rn',help="N-masked reference genome file") # if providing own parser.add_argument('--readlength',help="read length, used to generate genome index (see STAR parameter sjdbOverhang)") parser.add_argument('--genomedir',help="STAR genome index directory (if user is providing own genome index to use for mapping)") parser.add_argument('--hap',help="only map reads to hap1 and hap2 personal genomes",action="store_true") ## discover/assign parameters parser.add_argument('-c',help='chromsome') #if not provided, assume run all chromsosomes parser.add_argument('--conflict',help='flag to print conflicting reads',action='store_true') parser.add_argument('-b1',help="haplotype 1 bam file") ## alignments to personal genomes, if providing own parser.add_argument('-b2',help="haplotype 2 bam file")## alignments to personal genomes, if providing own parser.add_argument('-br',help="reference alignment bam file") parser.add_argument('--nomerge',help="flag to not merge chromosome bam files",action="store_true") ## splicing parameters parser.add_argument('--hap1Bam', help="provide own hap1 allele specific bam file") parser.add_argument('--hap2Bam', help="provide own hap2 allele specific bam file") parser.add_argument('--asdir',help='directory containing AS events') parser.add_argument('--MXE') parser.add_argument('--SE') parser.add_argument('--RI') parser.add_argument('--A3SS') parser.add_argument('--A5SS') parser.add_argument('--samples',help="sample file for merging") parser.add_argument('--merge',help="merge count files for multiple samples",action="store_true") parser.add_argument('--pos2id',help="flag to change snp pos to snp id in count files",action="store_true") parser.add_argument('--haplotype',help="flag to do hap1 vs hap2", action="store_true") parser.add_argument('--anchorlength', help="anchor length used for STAR alignment (default=8)") parser.add_argument('--mxeDetail',help="merge mxe detailed read counts",action="store_true") # parser.add_argument('--exonreads',help="to include exon reads") args = parser.parse_args() command = args.command if ((args.rnaedit and not args.e) or (args.e and not args.rnaedit)): sys.stderr.write("rPGA2: if --rnaedit flag is used, you must also provide a file containing RNA editing locations using -e parameter \n") sys.exit() if len(command)==0: sys.stderr.write('rPGA2: need a command - personalize, mapping, discover, alleles, splicing\n') sys.exit() if (not args.o): sys.stderr.write("rPGA2: -o outDir parameter is required\n") sys.exit() elif command[0]=="personalize": personalize.main(args) elif command[0]=="mapping": mapping.main(args) elif command[0]=="discover": discover.main(args) elif command[0]=="assign": assign.main(args) elif command[0]=="splicing": splicing.main(args) else: sys.stderr.write("rPGA: I don't recognise the option '" + command[0] +"'\n") sys.exit()