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How to use maker method in hypothesis

Best Python code snippet using hypothesis

makerbotHBP.py

Source:makerbotHBP.py

1import nc2import makerbot_codes as maker3import datetime4import iso_modal5import math678now = datetime.datetime.now()910################################################################################11class CreatorMakerbotHBP(iso_modal.CreatorIsoModal):12    def __init__(self):13        iso_modal.CreatorIsoModal.__init__(self)1415        self.absolute_flag = True16        self.prev_g91 = ''171819################################################################################20# program begin and end2122    def program_begin(self, id, name=''):23        self.write((maker.codes.COMMENT(now)))24        self.write((maker.codes.EXTRUDER_TEMP('220')) + (maker.codes.COMMENT('Extruder Temp')) )25        self.write((maker.codes.BUILD_BED_TEMP('110'))+ (maker.codes.COMMENT('Build Bed Temp')) )26        self.write((maker.codes.FAN_OFF()) + (maker.codes.COMMENT('Fan Off')) )27        self.write((maker.codes.METRIC()) + (maker.codes.COMMENT('Metric units')) )28        self.write((maker.codes.ABSOLUTE()) + (maker.codes.COMMENT('Absolute units')) )29        self.write('G92 X0 Y0 Z0 (You are now at 0,0,0)\n')30        self.write('G0 Z15 (Move up for warmup)\n')31        self.write((maker.codes.EXTRUDER_SPEED_PWM('255')) + (maker.codes.COMMENT('Extruder Speed')) )32        self.write('M6 T0 (Wait for tool to heat up)\n')33        self.write('G04 P5000 (Wait 5 seconds)\n')34        self.write((maker.codes.EXTRUDER_ON_FWD()) + (maker.codes.COMMENT('Extruder On')) )35        self.write('G04 P5000 (Wait 5 seconds)\n')36        self.write((maker.codes.EXTRUDER_OFF()) + (maker.codes.COMMENT('Extruder Off')) )37        self.write('M01 (The heated build platform is heating up. Wait until after the lights have turned off for the first time, clear the test extrusion, and click yes.)\n')38        self.write('G0 Z0    (Go back to zero.)\n')3940    def program_end(self):41        self.write((maker.codes.COMMENT('End of the file. Begin cool-down')))42        self.write((maker.codes.EXTRUDER_TEMP('0')) + (maker.codes.COMMENT('Extruder Temp')) )43        self.write((maker.codes.BUILD_BED_TEMP('0')) + (maker.codes.COMMENT('Build Bed Temp')) )44        self.write((maker.codes.FAN_ON()) + (maker.codes.COMMENT('Fan On')) )45        self.write('G92 Z0 (zero our z axis - hack b/c skeinforge mangles gcodes in end.txt)\n')46        self.write('G1 Z10 (go up 10 b/c it was zeroed earlier.)\n')47        self.write('G1 X0 Y0 Z10 (go to 0,0,z)\n')48        self.write((maker.codes.STEPPERS_OFF()) + (maker.codes.COMMENT('Steppers Off')) )4950    def program_stop(self):51        self.write((maker.codes.EXTRUDER_TEMP('0')))52        self.write((maker.codes.BUILD_BED_TEMP('0')))53        self.write((maker.codes.STEPPERS_OFF()))54        55################################################################################56# general57    def write_blocknum(self):58        pass5960    def set_plane(self, plane):61         pass62          63    def workplane(self, id):64        pass65        66    def spindle(self, s, clockwise):67        pass68################################################################################69# Extruder Control70        71    def extruder_on(self):72         self.write((maker.codes.EXTRUDER_ON()) + ('\n'))73        74    def extruder_off(self):75         self.write((maker.codes.EXTRUDER_OFF()) + ('\n'))76        77    def set_extruder_flowrate(self, flowrate):78         self.write((maker.codes.EXTRUDER_SPEED_PWM(flowrate)) + ('\n'))7980    def extruder_temp(self, temp):81         self.write((maker.codes.EXTRUDER_TEMP(temp)) + ('\n'))82   83################################################################################84# Build Environment Control85    def build_bed_temp(self, temp):86         self.write((maker.codes.BUILD_BED_TEMP(temp)) + ('\n'))87        88    def chamber_temp(self, temp):89         self.write((maker.codes.CHAMBER_TEMP(temp)) + ('\n'))   90         91################################################################################92# Fan Control93    def fan_on(self):94         self.write((maker.codes.FAN_ON()) + ('\n'))95        96    def fan_off(self):97         self.write((maker.codes.FAN_OFF()) + ('\n'))98        99################################################################################100# Custom routines101102    def wipe(self):103        self.write(('(This would be a good place for a custom wipe routine)\n'))104105################################################################################106# APT style INSERT- insert anything into program107108    def insert(self, text):109        self.write((text + '\n'))110111################################################################################112# tool info113    def tool_change(self, id):114    	pass115     #	self.write_blocknum()116     #  self.write((maker.codes.TOOL() % id) + '\n')117     #  self.t = id118    119    def tool_defn(self, id, name='', params=None):120	pass121############################################################################122##  Moves123124    def rapid(self, x=None, y=None, z=None, a=None, b=None, c=None ):125        self.write_blocknum()126        if self.g0123_modal:127            if self.prev_g0123 != maker.codes.RAPID():128                self.write(maker.codes.RAPID())129                self.prev_g0123 = maker.codes.RAPID()130        else:131            self.write(maker.codes.RAPID())132        self.write_preps()133        if (x != None):134            dx = x - self.x135            if (self.absolute_flag ):136                self.write(maker.codes.X() + (self.fmt % x))137            else:138                self.write(maker.codes.X() + (self.fmt % dx))139            self.x = x140        if (y != None):141            dy = y - self.y142            if (self.absolute_flag ):143                self.write(maker.codes.Y() + (self.fmt % y))144            else:145                self.write(maker.codes.Y() + (self.fmt % dy))146147            self.y = y148        if (z != None):149            dz = z - self.z150            if (self.absolute_flag ):151                self.write(maker.codes.Z() + (self.fmt % z))152            else:153                self.write(maker.codes.Z() + (self.fmt % dz))154155            self.z = z156157        if (a != None):158            da = a - self.a159            if (self.absolute_flag ):160                self.write(maker.codes.A() + (self.fmt % a))161            else:162                self.write(maker.codes.A() + (self.fmt % da))163            self.a = a164165        if (b != None):166            db = b - self.b167            if (self.absolute_flag ):168                self.write(maker.codes.B() + (self.fmt % b))169            else:170                self.write(maker.codes.B() + (self.fmt % db))171            self.b = b172173        if (c != None):174            dc = c - self.c175            if (self.absolute_flag ):176                self.write(maker.codes.C() + (self.fmt % c))177            else:178                self.write(maker.codes.C() + (self.fmt % dc))179            self.c = c180        self.write_spindle()181        self.write_misc()182        self.write('\n')183184    def feed(self, x=None, y=None, z=None, a = None, b = None, c = None):185        if self.same_xyz(x, y, z): return186        self.write_blocknum()187        if self.g0123_modal:188            if self.prev_g0123 != maker.codes.FEED():189                self.write(maker.codes.FEED())190                self.prev_g0123 = maker.codes.FEED()191        else:192            self.write(maker.codes.FEED())193        self.write_preps()194        dx = dy = dz = 0195        if (x != None):196            dx = x - self.x197            if (self.absolute_flag ):198                self.write(maker.codes.X() + (self.fmt % x))199            else:200                self.write(maker.codes.X() + (self.fmt % dx))201            self.x = x202        if (y != None):203            dy = y - self.y204            if (self.absolute_flag ):205                self.write(maker.codes.Y() + (self.fmt % y))206            else:207                self.write(maker.codes.Y() + (self.fmt % dy))208209            self.y = y210        if (z != None):211            dz = z - self.z212            if (self.absolute_flag ):213                self.write(maker.codes.Z() + (self.fmt % z))214            else:215                self.write(maker.codes.Z() + (self.fmt % dz))216217            self.z = z218        if (self.fhv) : self.calc_feedrate_hv(math.sqrt(dx*dx+dy*dy), math.fabs(dz))219        self.write_feedrate()220        self.write_spindle()221        self.write_misc()222        self.write('\n')223224    def same_xyz(self, x=None, y=None, z=None):225        if (x != None):226            if (self.fmt % x) != (self.fmt % self.x):227                return False228        if (y != None):229            if (self.fmt % y) != (self.fmt % self.y):230                return False231        if (z != None):232            if (self.fmt % z) != (self.fmt % self.z):233                return False234            235        return True236237    def arc(self, cw, x=None, y=None, z=None, i=None, j=None, k=None, r=None):238        if self.same_xyz(x, y, z): return239        self.write_blocknum()240        arc_g_code = ''241        if cw: arc_g_code = maker.codes.ARC_CW()242        else: arc_g_code = maker.codes.ARC_CCW()243        if self.g0123_modal:244            if self.prev_g0123 != arc_g_code:245                self.write(arc_g_code)246                self.prev_g0123 = arc_g_code247        else:248            self.write(arc_g_code)249        self.write_preps()250        if (x != None):251            dx = x - self.x252            if (self.absolute_flag ):253                self.write(maker.codes.X() + (self.fmt % x))254            else:255                self.write(maker.codes.X() + (self.fmt % dx))256            self.x = x257        if (y != None):258            dy = y - self.y259            if (self.absolute_flag ):260                self.write(maker.codes.Y() + (self.fmt % y))261            else:262                self.write(maker.codes.Y() + (self.fmt % dy))263            self.y = y264        if (z != None):265            dz = z - self.z266            if (self.absolute_flag ):267                self.write(maker.codes.Z() + (self.fmt % z))268            else:269                self.write(maker.codes.Z() + (self.fmt % dz))270            self.z = z271        if (i != None) : self.write(maker.codes.CENTRE_X() + (self.fmt % i))272        if (j != None) : self.write(maker.codes.CENTRE_Y() + (self.fmt % j))273        if (k != None) : self.write(maker.codes.CENTRE_Z() + (self.fmt % k))274        if (r != None) : self.write(maker.codes.RADIUS() + (self.fmt % r))275#       use horizontal feed rate276        if (self.fhv) : self.calc_feedrate_hv(1, 0)277        self.write_feedrate()278        self.write_spindle()279        self.write_misc()280        self.write('\n')281282    def arc_cw(self, x=None, y=None, z=None, i=None, j=None, k=None, r=None):283        self.arc(True, x, y, z, i, j, k, r)284285    def arc_ccw(self, x=None, y=None, z=None, i=None, j=None, k=None, r=None):286        self.arc(False, x, y, z, i, j, k, r)287288    def dwell(self, t):289        self.write_blocknum()290        self.write_preps()291        self.write(maker.codes.DWELL() + (maker.codes.TIME() % t))292        self.write_misc()293        self.write('\n')294295    def rapid_home(self, x=None, y=None, z=None, a=None, b=None, c=None):296        pass297298    def rapid_unhome(self):299        pass300301    def set_machine_coordinates(self):302        self.write(maker.codes.MACHINE_COORDINATES())303        self.prev_g0123 = ''304305nc.creator = CreatorMakerbotHBP()
...

maker.smk

Source:maker.smk

1# split the maker.gff base on the 2nd column2rule generate_output:3    input: "maker/maker_annotation.gff"4    output: "maker.gff"5    run:6        maker  = open("maker.gff", "w")7        abinit = open("abinit.gff", "w")8        other  = open("other.gff", "w")9        with open(input[0]) as f:10            for line in f:11                rec = line.strip().split('\t')12                if len(rec) < 9:13                    continue14                if rec[1] == 'maker':15                    maker.write(line)16                elif "masked" in rec[1]:17                    abinit.write(line)18                else:19                    other.write(line)20        maker.close()21        abinit.close()22        other.close()23# rule to generate maker.gff24rule maker_annotation_output:25    input: "status/maker_annotation.done"26    params:27         base_name = "maker/maker_annotation",28         dsindex = "{ds}.maker.output/{ds}_master_datastore_index.log".format(ds=specie_name)29    output: 30        gff = "maker/maker_annotation.gff",31        protein = "maker/maker_annotation.all.maker.proteins.fasta",32        transcript = "maker/maker_annotation.all.maker.transcripts.fasta" 33    shell:"""34    fasta_merge -o {params.base_name} -d {params.dsindex} && 35    gff3_merge -o {output} -d {params.dsindex}36    """37# CTL file rules38def add_param_to_setting(settings, params):39    if len(params) == 0:40        return settings41    for param in params:42        key,value = param.split("=")43        settings[key] = value44    return settings45def get_maker_config(wildcards):46    maker_ctl  = wildcards.ctl47    maker_type = wildcards.type48    json_file = ".maker_{}_{}_parameter.json".format(maker_ctl, maker_type)49    settings = dict()50    51    # maker round52    if maker_type.find("round") >= 0:53        round = int(maker_type[5:])54    elif maker_type == "base":55        round = 156    else:57        round = -1 # prediction58    # get the params59    if round > 0:60        params = config['round'+str(round)].get(maker_ctl,"")61    else:62        params = config['prediciton'].get(maker_ctl,"")63        64    if maker_ctl == "bopts" or maker_ctl == "exe": # bopts and exe65        settings =  add_param_to_setting(settings, params)66    else: # opts setting67        # default settings68        settings['genome'] = reference69        if protein is not None:70            settings['protein'] = protein71        if transcript_fasta is not None:72            settings['est'] = ','.join(transcript_fasta)    73        # set the gff3 in est_gff74        if transcript_assemble:75            settings['est_gff'] = ','.join(all_gff3)76        else:77            settings['est_gff'] = gtf 78        if maker_type == "annotation":79            # training model: setting snap, hmm 80            if training_model:81                if snap_rounds != '0':82                    settings['snaphmm'] = "gene_model/snap_round{}.hmm".format(snap_rounds[-1])83                if augustus_rounds != '0':84                    settings["augustus_species"] = specie_name85            else: 86                settings['snaphmm'] = snaphmm87                settings['augustus_species'] = augustus_species88        if maker_type == "base": # train round = 189            if snaphmm or augustus_species:90                settings['snaphmm'] = snaphmm91                settings['augustus_species'] = augustus_species92            else:93                settings['est2genome'] = '1'94                if protein is not None:95                    settings['protein2genome'] = '1'96        97        if maker_type.find("round") >= 0: #  train round > 198            if str(round-1) in snap_rounds :99                settings['snaphmm'] = "gene_model/snap_round{}.hmm".format(round-1)100            if str(round-1) in augustus_rounds :101                    settings["augustus_species"] = specie_name102        settings =  add_param_to_setting(settings, params)103    # dump the settings to json104    with open(json_file, "w") as f:105        json.dump(settings, f)106    return os.path.abspath(json_file)107# return the input base on the training_model and transcript_assemble108def get_maker_ctl_input(wildcards):109    maker_ctl  = wildcards.ctl110    maker_type = wildcards.type111    112    input_dict = {113        "ctl" : "maker_{ctl}.ctl".format(ctl=maker_ctl)114    }115    if maker_ctl == "bopts" or maker_ctl == "exe":116        return input_dict117    if maker_type == "annotation":118        if training_model:119            input_dict['train'] = "status/model_training_round{round}.done".format(round=max_round)120            #print(input_dict)121            return input_dict122        elif transcript_assemble:123            input_dict['gtf'] = "status/transcript_assemble.done"124            #print(input_dict)125            return input_dict126        elif check_gff(gtf):127            return input_dict128        else:129            log_exception("gtf not exists")130    if maker_type == "base":131        #print(input_dict)132        if transcript_assemble:133            input_dict['gtf'] = "status/transcript_assemble.done"134            return input_dict135        elif check_gff(gtf):136            return input_dict137        else:138            log_exception("gtf not exists")139    if maker_type.find("round") >= 0:140        round = int(maker_type[5:])141        input_dict['train'] = "status/model_training_round{round}.done".format(round=round-1)142        #print(input_dict)143        return input_dict144rule init_maker_ctl:145    output: "maker_opts.ctl", "maker_bopts.ctl", "maker_exe.ctl"146    shell:"maker -CTL"147rule update_maker_ctl:148    input: unpack(get_maker_ctl_input)149    params:150        script_dir = script_dir,151        opts_settings = get_maker_config152    output: "ctl/maker_{ctl}_{type}.ctl"153    shell:"""154    python {params.script_dir}/maker_ctl_updator.py {input.ctl} {output} {params.opts_settings}155    """156# annotation step157if MPI:158    rule run_maker_annotation:159        input: 160            opts = "ctl/maker_opts_annotation.ctl",161            bopts = "ctl/maker_bopts_annotation.ctl",162            exe = "ctl/maker_exe_annotation.ctl"163        output: touch("status/maker_annotation.done")164        params:165            dsname = specie_name166        threads: 40167        log: "log/maker_annotation.log"168        shell:"""169        mpiexec -n {threads} maker -quiet -base {params.dsname} {input.opts} {input.bopts} {input.exe} &> {log} 170        """171else: 172    rule run_maker_annotation:173        input: 174            opts = "ctl/maker_opts_annotation.ctl",175            bopts = "ctl/maker_bopts_annotation.ctl",176            exe = "ctl/maker_exe_annotation.ctl"177        output: touch("status/maker_annotation.done")178        params:179            dsname = specie_name,180        threads: 1181        log: "log/maker_annotation.log"182        shell:"""183        maker -quiet -base {params.dsname} {input.opts} {input.bopts} {input.exe} &> {log} 184        """185# train step: maker_loop: maker_round{2...n}.gff186rule maker_loop_output:187    input: "status/maker_round{round}.done"188    params:189        base_name =  lambda wildcards: "maker/maker_round{round}".format(round=wildcards.round),190        dsindex = "{ds}.maker.output/{ds}_master_datastore_index.log".format(ds=specie_name)191    output: 192        gff = "maker/maker_round{round}.gff",193        protein = "maker/maker_round{round}.all.maker.proteins.fasta",194        transcript = "maker/maker_round{round}.all.maker.transcripts.fasta"195    shell:"""196    fasta_merge -o {params.base_name} -d {params.dsindex} && 197    gff3_merge -o {output.gff} -d  {params.dsindex}     198    """199if MPI:200    rule run_maker_loop:201        input: 202            opts = "ctl/maker_opts_round{round}.ctl",203            bopts = "ctl/maker_bopts_round{round}.ctl",204            exe = "ctl/maker_exe_round{round}.ctl"205        output: touch("status/maker_round{round}.done")206        params:207            dsname = specie_name,208        threads: 40209        log: "log/maker_round{round}.log"210        shell:"""211        mpiexec -n {threads} maker -quiet -base {params.dsname} {input.opts} {input.bopts} {input.exe} &> {log} 212        """213else:214    rule run_maker_loop:215        input: 216            opts = "ctl/maker_opts_round{round}.ctl",217            bopts = "ctl/maker_bopts_round{round}.ctl",218            exe = "ctl/maker_exe_round{round}.ctl"219        output: touch("status/maker_round{round}.done")220        params:221            dsname = specie_name,222        threads: 1223        log: "log/maker_round{round}.log"224        shell:"""225        maker -quiet -base {params.dsname} {input.opts} {input.bopts} {input.exe} &> {log} 226        """227# maker_base.gff228if MPI:229    rule run_maker_base:230        input: 231            opts = "ctl/maker_opts_base.ctl",232            bopts = "ctl/maker_bopts_base.ctl",233            exe = "ctl/maker_exe_base.ctl"234        output: touch("status/maker_base.done")235        params:236            dsname = specie_name,237        threads: 40238        log: "log/maker_base.log"239        shell:"""240        mpiexec -n {threads} maker -quiet -base {params.dsname} {input.opts} {input.bopts} {input.exe} &> {log} 241        """242else:243    rule run_maker_base:244        input: 245            opts = "ctl/maker_opts_base.ctl",246            bopts = "ctl/maker_bopts_base.ctl",247            exe = "ctl/maker_exe_base.ctl"248        output: touch("status/maker_base.done")249        params:250            dsname = specie_name,251        threads: 1252        log: "log/maker_base.log"253        shell:"""254        maker -quiet -base {params.dsname} {input.opts} {input.bopts} {input.exe} &> {log} 255        """256rule maker_base_output:257    input: "status/maker_base.done"258    params:259        base_name = "maker/maker_base",260        dsindex = "{ds}.maker.output/{ds}_master_datastore_index.log".format(ds=specie_name)261    output: 262        gff = "maker/maker_base.gff",263        protein = "maker/maker_base.all.maker.proteins.fasta",264        transcript = "maker/maker_base.all.maker.transcripts.fasta"265    shell:"""266    fasta_merge -o {params.base_name} -d {params.dsindex} &&267    gff3_merge -o {output.gff} -d  {params.dsindex}     ...

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