How to use outputdir method in avocado

Best Python code snippet using avocado_python

gen_meta.py

Source:gen_meta.py

1from binding import *2from classes.Extension import *3def metaExtensionToString(extension):4    return '{ GLextension::%s, "%s" }' % (extensionBID(extension), extension.name)5def metaStringToExtension(extension):6    return '{ "%s", GLextension::%s }' % (extension.name, extensionBID(extension))7def genMetaStringsByExtension(extensions, outputdir, outputfile):8    status(outputdir + outputfile)9    with open(outputdir + outputfile, 'w') as file:10        file.write(template(outputfile) % (",\n" + tab).join(11            [ metaExtensionToString(e) for e in extensions ]))12def genMetaExtensionsByString(extensions, outputdir, outputfile):    13    status(outputdir + outputfile)14    with open(outputdir + outputfile, 'w') as file:15        file.write(template(outputfile) % (",\n" + tab).join(16            [ metaStringToExtension(e) for e in extensions ]))17def metaEnumToString(enum, type):18    # t = (enum.groupString if type == "GLbitfield" else type)19    return ('{ ' + type + '::%s, "%s" }') % (enumBID(enum), enum.name)20def metaStringToEnum(enum, type):21    # t = (enum.groupString if type == "GLbitfield" else type)22    return ('{ "%s", ' + type + '::%s }') % (enum.name, enumBID(enum))23def metaStringToBitfieldGroupMap(group):24    return "extern const std::unordered_map<std::string, gl::%s> Meta_%sByString;" % (group.name, group.name)25def metaBitfieldGroupToStringMap(group):26    return "extern const std::unordered_map<gl::%s, std::string> Meta_StringsBy%s;" % (group.name, group.name)27def metaStringsByBitfieldGroup(group):28    return """const std::unordered_map<%s, std::string> Meta_StringsBy%s 29{30#ifdef STRINGS_BY_GL31    %s32#endif33};34    """ % (group.name, group.name, ",\n\t".join([ metaEnumToString(e, group.name) for e in sorted(group.enums) ]))35def genMetaMaps(enums, outputdir, outputfile, bitfGroups):36    status(outputdir + outputfile)37    with open(outputdir + outputfile, 'w') as file:38        file.write(template(outputfile) % ("\n".join([ metaBitfieldGroupToStringMap(g) for g in bitfGroups ])))39def genMetaStringsByEnum(enums, outputdir, outputfile, type):40    status(outputdir + outputfile)41    pureEnums = [ e for e in enums if e.type == type ]42    d = sorted([ es[0] for v, es in groupEnumsByValue(pureEnums).items() ])43    44    with open(outputdir + outputfile, 'w') as file:45        file.write(template(outputfile) % ((",\n" + tab).join(46            [ metaEnumToString(e, type) for e in d ])))    47def genMetaStringsByBitfield(bitfGroups, outputdir, outputfile):48    status(outputdir + outputfile)49    d = sorted([ metaStringsByBitfieldGroup(g) for g in bitfGroups ])50    51    with open(outputdir + outputfile, 'w') as file:52        file.write(template(outputfile) % "\n".join(d))53def genMetaBitfieldByString(bitfGroups, outputdir, outputfile):54    55    status(outputdir + outputfile)56    map = [ (",\n"+tab).join([ '{ "%s", static_cast<GLbitfield>(%s::%s) }' % (e.name, g.name, e.name) 57        for e in sorted(g.enums) ]) for g in sorted(bitfGroups) ]58    with open(outputdir + outputfile, 'w') as file:59        file.write(template(outputfile) % ((",\n" + tab).join(map)))60def genMetaEnumsByString(enums, outputdir, outputfile, type):61    status(outputdir + outputfile)62    pureEnums = [ e for e in enums if e.type == type ]63    with open(outputdir + outputfile, 'w') as file:64        file.write(template(outputfile) % ((",\n" + tab).join(65            [ metaStringToEnum(e, type) for e in pureEnums ])))66def groupEnumsByValue(enums):67    d = dict()68    for e in enums:69        v = int(e.value, 0)70        if not v in d:71            d[v] = []72        d[v].append(e)73    74    for key in d.keys():75        d[key] = sortEnumsBySuffix(d[key])76        77    return d78def sortEnumsBySuffix(enums):79    return sorted(enums, key = lambda e : enumSuffixPriority(e.name))80def enumSuffixPriority(name):81    index = name.rfind("_")82    if index < 0:83        return -184    ext = name[index + 1:]85    if ext not in Extension.suffixes:86        return -187    88    return Extension.suffixes.index(ext)89def extensionVersionPair(extension):90    return "{ GLextension::%s, { %s, %s } }" % (91        extensionBID(extension), extension.incore.major, extension.incore.minor)92def genReqVersionsByExtension(extensions, outputdir, outputfile):93    status(outputdir + outputfile)94    inCoreExts = [ e for e in extensions if e.incore ]95    sortedExts = sorted(inCoreExts, key = lambda e : e.incore)96    with open(outputdir + outputfile, 'w') as file:97        file.write(template(outputfile) % (",\n" + tab).join(98            [ extensionVersionPair(e) for e in sortedExts if e.incore ]))99def extensionRequiredFunctions(extension):100    return "{ GLextension::%s, { %s } }" % (extensionBID(extension), ", ".join(101        [ '"%s"' % f.name for f in extension.reqCommands ]))102def functionRequiredByExtensions(function, extensions):103    return '{ "%s", { %s } }' % (function.name, ", ".join(104        [ "GLextension::" + extensionBID(e) for e in extensions ]))105def genFunctionStringsByExtension(extensions, outputdir, outputfile):                106    status(outputdir + outputfile)107    with open(outputdir + outputfile, 'w') as file:        108        file.write(template(outputfile) % ((",\n" + tab).join(109            [ extensionRequiredFunctions(e) for e in extensions if len(e.reqCommands) > 0 ])))110def genExtensionsByFunctionString(extensions, outputdir, outputfile):    111    status(outputdir + outputfile)112    extensionsByCommands = dict()113    for e in extensions:114        for c in e.reqCommands:115            if not c in extensionsByCommands:116                extensionsByCommands[c] = set()117            extensionsByCommands[c].add(e)118    with open(outputdir + outputfile, 'w') as file:        119        file.write(template(outputfile) % ((",\n" + tab).join(...

packageRelease.py

Source:packageRelease.py

1import os2import sys3import shutil4import re5global gCompiler6global gPlatform7def copyIgnore( path, names ):8    result = []9    if re.search( "__AppTemplates", path ) != None:10        return result11    for name in names:12        if name == 'vc2013' and gCompiler != 'vc2013':13            result.append( name )14        if name == 'vc2015_winrt' and gCompiler != 'vc2013':15            result.append( name )16        elif name == 'vc2015' and gCompiler != 'vc2015':17            result.append( name )18        elif name == 'ios' and gCompiler != 'xcode':19            result.append( name )20        elif name == 'ios-sim' and gCompiler != 'xcode':21            result.append( name )22        elif name == 'macosx' and gCompiler != 'xcode':23            result.append( name )24        elif name == 'xcode' and gCompiler != 'xcode':25            result.append( name )26        elif name == 'xcode_ios' and gCompiler != 'xcode':27            result.append( name )28        elif name == 'msw' and gCompiler == 'xcode':29            result.append( name )30        elif name == 'msw-uwp' and gCompiler == 'xcode':31            result.append( name )32        elif gPlatform == 'mac' and name == 'TinderBox-Win':33            result.append( name )34        elif gPlatform == 'msw' and name == 'TinderBox-Mac':35            result.append( name )36        elif name == 'Readme.md':37            result.append( name )38        elif name == 'scripts':39            result.append( name )40        elif name == 'linux' and re.search( "lib", path ) != None:41            result.append( name )42        elif name == 'android':43            result.append( name )44        elif name == 'androidstudio':45            result.append( name )46        elif re.search( "libboost.*-vc120.*", name ) != None and gCompiler != 'vc2013':47            result.append( name )48        elif re.search( "^.git.*", name ) != None:49            result.append( name )50    return result51def printUsage():52    print "Run from the root of the repository (having run vcvars):"53    print "python tools/packageRelease.py (version number) (xcode|vc2013|vc2015)"54def processExport( outputName, compilerName, version ):55    print "creating a clean clone of cinder"56    baseDir = os.getcwd()57    fileUrl = "file://" + baseDir58    fileUrl.replace( os.sep, "/" )59    os.system( "git clone --recursive --depth 1 -b master " + fileUrl + " .." + os.sep + "cinder_temp" )60    os.chdir( baseDir + os.sep + ".." + os.sep + "cinder_temp" )61    outputDir = baseDir + os.sep + ".." + os.sep + "cinder_" + version + "_" + outputName + os.sep62    print "performing selective copy to " + outputDir63    shutil.copytree( ".", outputDir, ignore=copyIgnore )64    print "removing test"65    shutil.rmtree( outputDir + "test" )66    return outputDir67    68def cleanupMswLibDir( dir ):69    for f in os.listdir( dir ):70        if os.path.splitext( f ) == ".idb":71            os.remove( os.path.join(dir, f) )72    73if len(sys.argv) != 3:74    printUsage()75elif sys.argv[2] == 'xcode':76    gCompiler = 'xcode'77    gPlatform = 'mac'78    outputDir = processExport( "mac", "xcode", sys.argv[1] )79    os.chdir( outputDir + "proj/xcode" )80    os.system( "./fullbuild.sh" )81    shutil.rmtree( outputDir + "proj/xcode/build" )82    # strip debug symbols83    os.chdir( outputDir + "lib/ios/Debug" )84    os.system( "strip -S -r libcinder.a" )85    os.chdir( outputDir + "lib/ios/Release" )86    os.system( "strip -S -r libcinder.a" )87    os.chdir( outputDir + "lib/ios-sim/Debug" )88    os.system( "strip -S -r libcinder.a" )89    os.chdir( outputDir + "lib/ios-sim/Release" )90    os.system( "strip -S -r libcinder.a" )91    os.chdir( outputDir + "lib/macosx/Debug" )92    os.system( "strip -S -r libcinder.a" )93    os.chdir( outputDir + "lib/macosx/Release" )94    os.system( "strip -S -r libcinder.a" )95elif sys.argv[2] == 'vc2013':96    gCompiler = 'vc2013'97    gPlatform = 'msw'98    outputDir = processExport( "vc2013", "vc2013", sys.argv[1] )99    os.chdir( outputDir + "proj\\vc2013" )100    os.system( "msbuild cinder.vcxproj /p:platform=win32 /p:configuration=debug" )101    os.system( "msbuild cinder.vcxproj /p:platform=win32 /p:configuration=release" )102    shutil.rmtree( outputDir + "proj\\vc2013\\build" )103#    os.system( "msbuild cinder.vcxproj /p:platform=x64 /p:configuration=debug" )104#    shutil.rmtree( outputDir + "vc2013\\x64\\Debug" )105#    os.system( "msbuild cinder.vcxproj /p:platform=x64 /p:configuration=release" )106#    shutil.rmtree( outputDir + "vc2013\\x64\\Release" )107    cleanupMswLibDir( outputDir + "lib\\msw\\x86\\debug" )108#    cleanupMswLibDir( outputDir + "lib\\msw\\x64" )109elif sys.argv[2] == 'vc2015':110    gCompiler = 'vc2015'111    gPlatform = 'msw'112    outputDir = processExport( "vc2015", "vc2015", sys.argv[1] )113    os.chdir( outputDir + "vc2013" )114    os.system( "msbuild cinder.vcxproj /p:platform=win32 /p:configuration=debug" )115    shutil.rmtree( outputDir + "vc2013\\Debug" )116    os.system( "msbuild cinder.vcxproj /p:platform=win32 /p:configuration=release" )117    shutil.rmtree( outputDir + "vc2013\\Release" )118    os.system( "msbuild cinder.vcxproj /p:platform=x64 /p:configuration=debug" )119    shutil.rmtree( outputDir + "vc2013\\x64\\Debug" )120    os.system( "msbuild cinder.vcxproj /p:platform=x64 /p:configuration=release" )121    shutil.rmtree( outputDir + "vc2013\\x64\\Release" )122    cleanupMswLibDir( outputDir + "lib\\msw\\x86" )123    cleanupMswLibDir( outputDir + "lib\\msw\\x64" )124else:...

Snakefile

Source:Snakefile

1inputfile = os.environ.get("INPUT")2outputdir = os.environ.get("OUTPUTDIR")3#command :  OUTPUTDIR="outputs" INPUT="tests/RAG_small.fasta" snakemake --cores all4#print(inputfile)5rule all:6    input:7        'fasta_validated.fasta',8        'table_of_contents.txt',9        f'{outputdir}/raxml/RAxML_bipartitionsBranchLabels.output_ML',10        f'{outputdir}/iqtree/standard_name.fasta.treefile',11        f'{outputdir}/compare/all_trees.treels',12        f'{outputdir}/mega/M11CC_Out/mega_tree.nwk',13        f'{outputdir}/compare/shimodaira_hasegawa.txt',14        f'{outputdir}/compare/AU_report.txt'15    message:16        'Runs sucessfully. Folders created with the respective files.'17# Clean outputs of previous runs18rule clean:19    shell:20        'rm -rf mega iqtree raxml fastas table_of_contents.txt compare outputs'21# Validate the file22rule valid_file:23    input:24        inputfile25    output:26        'fasta_validated.fasta',27        'table_of_contents.txt'28    shell:29        'python3 scripts/fasta_validator.py {input}'30# Standardize names 31rule standardized_name:32    input:33        'fasta_validated.fasta',34        'table_of_contents.txt'35    output:36        '{outputdir}/fastas/standard_name.fasta'37    run:38        shell(f'mkdir -p {outputdir}/fastas')39        shell('mv table_of_contents.txt {outputdir}')40        shell('sed "s/ .*//g" fasta_validated.fasta > {outputdir}/fastas/standard_name.fasta')41# Create trees raxml42rule create_trees_raxml:43    input:44        '{outputdir}/fastas/standard_name.fasta'45    output:46        '{outputdir}/raxml/RAxML_bipartitionsBranchLabels.output_ML'47    benchmark:48        '{outputdir}/raxml/raxml.bwa.benchmark.txt'49    run:50        shell('mkdir -p {outputdir}/raxml')51        shell('cd {outputdir}/raxml && time raxmlHPC-PTHREADS-SSE3 -T 2 -f a -s ../../{input} -m GTRGAMMA -x 2525 -p 2525 -N 100 -n output_ML')52# Create trees iqtree53rule create_trees_iqtree:54    input:55        '{outputdir}/fastas/standard_name.fasta'56    output:57        '{outputdir}/iqtree/standard_name.fasta.treefile'58    benchmark:59        '{outputdir}/iqtree/iqtree.bwa.benchmark.txt'60    run:61        shell('mkdir -p {outputdir}/iqtree')62        shell('cp {input} {outputdir}/iqtree/standard_name.fasta')63        shell('iqtree -s {outputdir}/iqtree/standard_name.fasta')64# Create trees mega65rule create_trees_mega:66    input:67        '{outputdir}/fastas/standard_name.fasta'68    output:69        '{outputdir}/mega/M11CC_Out/mega_tree.nwk'70    benchmark:71        '{outputdir}/mega/mega.bwa.benchmark.txt'72    run:73        shell('mkdir -p {outputdir}/mega')74        shell('cp {input} {outputdir}/mega/standard_name.fasta')75        shell('megacc -a files/ML_nucleotide.mao -d {outputdir}/mega/standard_name.fasta ML_tree_mega')76        shell('cat {outputdir}/mega/M11CC_Out/*.nwk > {output}')77# Concatenate all tree files78rule concatenate_trees_files:79    input:80        '{outputdir}/mega/M11CC_Out/mega_tree.nwk',81        '{outputdir}/iqtree/standard_name.fasta.treefile',82        '{outputdir}/raxml/RAxML_bipartitionsBranchLabels.output_ML'83    output:84        '{outputdir}/compare/all_trees.treels'85    run:86        shell('mkdir -p {outputdir}/compare')87        shell('cat {input} > {outputdir}/compare/all_trees.treels')88# Compare the trees using IQTree89rule compare_shimodaira_hasegawa:90    input:91        '{outputdir}/compare/all_trees.treels',92        '{outputdir}/fastas/standard_name.fasta'93    output:94        '{outputdir}/compare/shimodaira_hasegawa.txt'95    message:96        "In the eventuality of the AU scores being too similar, in their respective directories, it's accompanied the benchmarks of each tree with the times it took too create them."97        "Every user must consider this data when choosing the best program for themselfs."98    run:99        shell('iqtree -s {outputdir}/fastas/standard_name.fasta -z {outputdir}/compare/all_trees.treels -n 0 -zb 10000 -zw -au > {output}')100# Report of the AU test101rule report_AU:102    input:103        '{outputdir}/compare/shimodaira_hasegawa.txt'104    output:105        '{outputdir}/compare/AU_report.txt'106    message:107        'The results of the Au test'108    run:109        shell('grep "TreeID" -A 5 {input} > {output}')110        shell('printf "1 - MEGA\n2 - IQTREE\n3 - RAxML\n" >> {output}')...

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