How to use _switch method in lisa

Best Python code snippet using lisa_python

repository_rules.bzl

Source:repository_rules.bzl

...99    rules = {}100    #101    # Common102    #103    rules["proto_library_with_info"] = _switch(104        gapic,105        "@com_google_api_codegen//rules_gapic:gapic.bzl",106    )107    rules["moved_proto_library"] = _switch(108        gapic,109        "@com_google_api_codegen//rules_gapic:gapic.bzl",110    )111    #112    # Java113    #114    rules["java_proto_library"] = _switch(115        java,116        "native.java_proto_library",117    )118    rules["java_grpc_library"] = _switch(119        java and grpc,120        "@io_grpc_grpc_java//:java_grpc_library.bzl",121    )122    rules["java_gapic_library"] = _switch(123        java and grpc and gapic,124        "@com_google_api_codegen//rules_gapic/java:java_gapic.bzl",125    )126    rules["java_resource_name_proto_library"] = _switch(127        java and grpc and gapic,128        "@com_google_api_codegen//rules_gapic/java:java_gapic.bzl",129    )130    rules["java_gapic_test"] = _switch(131        java and grpc and gapic,132        "@com_google_api_codegen//rules_gapic/java:java_gapic.bzl",133    )134    rules["java_gapic_assembly_gradle_pkg"] = _switch(135        java and grpc and gapic,136        "@com_google_api_codegen//rules_gapic/java:java_gapic_pkg.bzl",137    )138    #139    # Python140    #141    rules["py_proto_library"] = _switch(142        python,143        "@com_github_grpc_grpc//bazel:python_rules.bzl",144    )145    rules["py_grpc_library"] = _switch(146        python and grpc,147        "@com_github_grpc_grpc//bazel:python_rules.bzl",148    )149    rules["py_gapic_library"] = _switch(150        python and grpc and gapic,151        "@com_google_api_codegen//rules_gapic/python:py_gapic.bzl",152    )153    rules["py_gapic_assembly_pkg"] = _switch(154        python and grpc and gapic,155        "@com_google_api_codegen//rules_gapic/python:py_gapic_pkg.bzl",156    )157    rules["py_gapic_library2"] = _switch(158        python and grpc and gapic,159        "@gapic_generator_python//rules_python_gapic:py_gapic.bzl",160        "py_gapic_library",161    )162    rules["py_gapic_assembly_pkg2"] = _switch(163        python and grpc and gapic,164        "@gapic_generator_python//rules_python_gapic:py_gapic_pkg.bzl",165        "py_gapic_assembly_pkg",166    )167    #168    # Go169    #170    rules["go_proto_library"] = _switch(171        go,172        "@io_bazel_rules_go//proto:def.bzl",173    )174    rules["go_library"] = _switch(175        go,176        "@io_bazel_rules_go//go:def.bzl",177    )178    rules["go_test"] = _switch(179        go and grpc and gapic,180        "@io_bazel_rules_go//go:def.bzl",181    )182    rules["go_gapic_library"] = _switch(183        go and grpc and gapic,184        "@com_googleapis_gapic_generator_go//rules_go_gapic:go_gapic.bzl",185    )186    rules["go_gapic_assembly_pkg"] = _switch(187        go and grpc and gapic,188        "@com_googleapis_gapic_generator_go//rules_go_gapic:go_gapic_pkg.bzl",189    )190    #191    # C++192    #193    rules["cc_proto_library"] = _switch(194        cc,195        "native.cc_proto_library",196    )197    rules["cc_grpc_library"] = _switch(198        cc and grpc,199        "@com_github_grpc_grpc//bazel:cc_grpc_library.bzl",200    )201    rules["cc_gapic_library"] = _switch(False)202    #203    # PHP204    #205    rules["php_proto_library"] = _switch(206        php,207        "@com_google_api_codegen//rules_gapic/php:php_gapic.bzl",208    )209    rules["php_grpc_library"] = _switch(210        php and grpc,211        "@com_google_api_codegen//rules_gapic/php:php_gapic.bzl",212    )213    rules["php_gapic_library"] = _switch(214        php and grpc and gapic,215        "@com_google_api_codegen//rules_gapic/php:php_gapic.bzl",216    )217    rules["php_gapic_assembly_pkg"] = _switch(218        php and grpc and gapic,219        "@com_google_api_codegen//rules_gapic/php:php_gapic_pkg.bzl",220    )221    #222    # Node.js223    #224    rules["nodejs_gapic_library"] = _switch(225        nodejs and grpc and gapic,226        "@gapic_generator_typescript//rules_typescript_gapic:typescript_gapic.bzl",227        "typescript_gapic_library",228    )229    rules["nodejs_gapic_assembly_pkg"] = _switch(230        nodejs and grpc and gapic,231        "@gapic_generator_typescript//rules_typescript_gapic:typescript_gapic_pkg.bzl",232        "typescript_gapic_assembly_pkg",233    )234    #235    # Ruby236    #237    rules["ruby_proto_library"] = _switch(238        ruby,239        "@gapic_generator_ruby//rules_ruby_gapic:ruby_gapic.bzl",240    )241    rules["ruby_grpc_library"] = _switch(242        ruby and grpc,243        "@gapic_generator_ruby//rules_ruby_gapic:ruby_gapic.bzl",244    )245    rules["ruby_gapic_library"] = _switch(246        ruby and grpc and gapic,247        "@com_google_api_codegen//rules_gapic/ruby:ruby_gapic.bzl",248    )249    rules["ruby_ads_gapic_library"] = _switch(250        ruby and grpc and gapic,251        "@gapic_generator_ruby//rules_ruby_gapic:ruby_gapic.bzl",252    )253    rules["ruby_cloud_gapic_library"] = _switch(254        ruby and grpc and gapic,255        "@gapic_generator_ruby//rules_ruby_gapic:ruby_gapic.bzl",256    )257    rules["ruby_gapic_assembly_pkg"] = _switch(258        ruby and grpc and gapic,259        "@com_google_api_codegen//rules_gapic/ruby:ruby_gapic_pkg.bzl",260    )261    #262    # C#263    #264    rules["csharp_proto_library"] = _switch(265        csharp,266        "@gapic_generator_csharp//rules_csharp_gapic:csharp_gapic.bzl",267    )268    rules["csharp_grpc_library"] = _switch(269        csharp and grpc,270        "@gapic_generator_csharp//rules_csharp_gapic:csharp_gapic.bzl",271    )272    rules["csharp_gapic_library"] = _switch(273        csharp and grpc and gapic,274        "@gapic_generator_csharp//rules_csharp_gapic:csharp_gapic.bzl",275    )276    rules["csharp_gapic_assembly_pkg"] = _switch(277        csharp and grpc and gapic,278        "@gapic_generator_csharp//rules_csharp_gapic:csharp_gapic_pkg.bzl",279    )280    rules.update(rules_override)281    switched_rules(282        name = name,283        rules = rules,284    )285def _switch(enabled, enabled_value = "", actual_name = ""):286    if enabled:287        return [enabled_value, actual_name]288    else:...

_Dialign.py

Source:_Dialign.py

1# Copyright 2009 by Cymon J. Cox.  All rights reserved.2# This code is part of the Biopython distribution and governed by its3# license.  Please see the LICENSE file that should have been included4# as part of this package.5"""6Bio.Application command line for the multiple alignment program DIALIGN2-2.7http://bibiserv.techfak.uni-bielefeld.de/dialign/welcome.html8Citations:9B. Morgenstern (2004). DIALIGN: Multiple DNA and Protein Sequence Alignment10at BiBiServ. Nucleic Acids Research 32, W33-W36.11Last checked against version: 2.212"""13from Bio import Application14from Bio.Application import _Option, _Argument, _Switch, AbstractCommandline15class DialignCommandline(AbstractCommandline):16    """Command line wrapper for the multiple alignment program DIALIGN2-2."""17    def __init__(self, cmd="dialign2-2", **kwargs):18        self.program_name = cmd19        self.parameters = \20            [21            _Switch(["-afc", "afc"], ["input"],22                    "Creates additional output file '*.afc' " + \23                    "containing data of all fragments considered " + \24                    "for alignment WARNING: this file can be HUGE !"),25            _Switch(["-afc_v", "afc_v"], ["input"],26                    "Like '-afc' but verbose: fragments are explicitly " + \27                    "printed. WARNING: this file can be EVEN BIGGER !"),28            _Switch(["-anc", "anc"], ["input"],29                    "Anchored alignment. Requires a file <seq_file>.anc " + \30                    "containing anchor points."),31            _Switch(["-cs", "cs"], ["input"],32                    "If segments are translated, not only the `Watson " + \33                    "strand' but also the `Crick strand' is looked at."),34            _Switch(["-cw", "cw"], ["input"],35                    "Additional output file in CLUSTAL W format."),36            _Switch(["-ds", "ds"], ["input"],37                    "`dna alignment speed up' - non-translated nucleic acid " + \38                    "fragments are taken into account only if they start " + \39                    "with at least two matches. Speeds up DNA alignment at " + \40                    "the expense of sensitivity."),41            _Switch(["-fa", "fa"], ["input"],42                    "Additional output file in FASTA format."),43            _Switch(["-ff", "ff"], ["input"],44                    "Creates file *.frg containing information about all " + \45                    "fragments that are part of the respective optimal " + \46                    "pairwise alignmnets plus information about " + \47                    "consistency in the multiple alignment"),48            _Option(["-fn", "fn"], ["input"],49                    None,50                    0,51                    "Output files are named <out_file>.<extension>.",52                    0),53            _Switch(["-fop", "fop"], ["input"],54                    "Creates file *.fop containing coordinates of all " + \55                    "fragments that are part of the respective pairwise alignments."),56            _Switch(["-fsm", "fsm"], ["input"],57                    "Creates file *.fsm containing coordinates of all " + \58                    "fragments that are part of the final alignment"),59            _Switch(["-iw", "iw"], ["input"],60                    "Overlap weights switched off (by default, overlap " + \61                    "weights are used if up to 35 sequences are aligned). " + \62                    "This option speeds up the alignment but may lead " + \63                    "to reduced alignment quality."),64            _Switch(["-lgs", "lgs"], ["input"],65                    "`long genomic sequences' - combines the following " + \66                    "options: -ma, -thr 2, -lmax 30, -smin 8, -nta, -ff, " + \67                    "-fop, -ff, -cs, -ds, -pst "),68            _Switch(["-lgs_t", "lgs_t"], ["input"],69                    "Like '-lgs' but with all segment pairs assessed " + \70                    "at the peptide level (rather than 'mixed alignments' " + \71                    "as with the '-lgs' option). Therefore faster than " + \72                    "-lgs but not very sensitive for non-coding regions."),73            _Option(["-lmax", "lmax"], ["input"],74                    lambda x: isinstance(x, int),75                    0,76                    "Maximum fragment length = x  (default: x = 40 or " + \77                    "x = 120 for `translated' fragments). Shorter x " + \78                    "speeds up the program but may affect alignment quality.",79                    0),80            _Switch(["-lo", "lo"], ["input"],81                    "(Long Output) Additional file *.log with information " + \82                    "about fragments selected for pairwise alignment and " + \83                    "about consistency in multi-alignment proceedure."),84            _Switch(["-ma", "ma"], ["input"],85                    "`mixed alignments' consisting of P-fragments and " + \86                    "N-fragments if nucleic acid sequences are aligned."),87            _Switch(["-mask", "mask"], ["input"],88                    "Residues not belonging to selected fragments are " + \89                    "replaced by `*' characters in output alignment " + \90                    "(rather than being printed in lower-case characters)"),91            _Switch(["-mat", "mat"], ["input"],92                    "Creates file *mat with substitution counts derived " + \93                    "from the fragments that have been selected for alignment."),94            _Switch(["-mat_thr", "mat_thr"], ["input"],95                    "Like '-mat' but only fragments with weight score " + \96                    "> t are considered"),97            _Switch(["-max_link", "max_link"], ["input"],98                    "'maximum linkage' clustering used to construct " + \99                    "sequence tree (instead of UPGMA)."),100            _Switch(["-min_link", "min_link"], ["input"],101                    "'minimum linkage' clustering used."),102            _Option(["-mot", "mot"], ["input"],103                    None, 104                    0,105                    "'motif' option.",106                    0),107            _Switch(["-msf", "msf"], ["input"],108                    "Separate output file in MSF format."),109            _Switch(["-n", "n"], ["input"],110                    "Input sequences are nucleic acid sequences. " + \111                    "No translation of fragments."),112            _Switch(["-nt", "nt"], ["input"],113                    "Input sequences are nucleic acid sequences and " + \114                    "`nucleic acid segments' are translated to `peptide " + \115                    "segments'."),116            _Switch(["-nta", "nta"], ["input"],117                    "`no textual alignment' - textual alignment suppressed. " + \118                    "This option makes sense if other output files are of " + \119                    "intrest -- e.g. the fragment files created with -ff, " + \120                    "-fop, -fsm or -lo."),121            _Switch(["-o", "o"], ["input"],122                    "Fast version, resulting alignments may be slightly " + \123                    "different."),124            _Switch(["-ow", "ow"], ["input"],125                    "Overlap weights enforced (By default, overlap weights " + \126                    "are used only if up to 35 sequences are aligned since " + \127                    "calculating overlap weights is time consuming)."),128            _Switch(["-pst", "pst"], ["input"],129                    "'print status'. Creates and updates a file *.sta with " + \130                    "information about the current status of the program " + \131                    "run.  This option is recommended if large data sets " + \132                    "are aligned since it allows the user to estimate the " + \133                    "remaining running time."),134            _Switch(["-smin", "smin"], ["input"],135                    "Minimum similarity value for first residue pair " + \136                    "(or codon pair) in fragments. Speeds up protein " + \137                    "alignment or alignment of translated DNA fragments " + \138                    "at the expense of sensitivity."),139            _Option(["-stars", "stars"], ["input"],140                    lambda x: x in range(0,10),141                    0,142                    "Maximum number of `*' characters indicating degree " + \143                    "of local similarity among sequences. By default, no " + \144                    "stars are used but numbers between 0 and 9, instead.",145                    0),146            _Switch(["-stdo", "stdo"], ["input"],147                    "Results written to standard output."),148            _Switch(["-ta", "ta"], ["input"],149                    "Standard textual alignment printed (overrides " + \150                    "suppression of textual alignments in special " + \151                    "options, e.g. -lgs)"),152            _Option(["-thr", "thr"], ["input"],153                    lambda x: isinstance(x, int),154                    0,155                    "Threshold T = x.",156                    0),157            _Switch(["-xfr", "xfr"], ["input"],158                    "'exclude fragments' - list of fragments can be " + \159                    "specified that are NOT considered for pairwise alignment"),160            _Argument(["input"], ["input", "file"], None, 1,161                      "Input file name. Must be FASTA format")162            ]...

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