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How to use match_fs method in autotest

Best Python code snippet using autotest_python

music_score_parser - 副本.py

Source:music_score_parser - 副本.py

1'''2è°±ã=ãå°è*3å°èã=ãæ+ã'|'4æã=ãè¿é³+5è¿é³ã=ãé³é«[æ¶é¿]6é³é«ã=ã[åå]é³ç¬¦[å«åº¦åç§»]7æ¶é¿ã=ãæ¶å¼åæ°è®°å·+8ååã=ã'#' | 'b' | 'X' | 'bb' | '&'9é³ç¬¦ = [1-7-]10å«åº¦åç§» = å«åº¦ååç§»ã|ãå«åº¦éåç§»11å«åº¦ååç§»ã=ãå«åº¦å+12å«åº¦åã=ã'^'13å«åº¦éåç§»ã=ãå«åº¦é+14å«åº¦éã=ã'v'15'''16rex_language = '''17rex_language = line*18line = [idDefine] [comment_str] [NEWLINE]19idDefine = id '=' rex20basic_rex = plain_str | rex_str | id | group | multi_optional21multi = basic_rex | multi_bound | multi_star | multi_plus 22seq = multi+23choices = seq ('|' seq)*24rex = choices25multi_bound = basic_rex '{' num ',' [num] '}'26multi_star = basic_rex '*'27multi_plus = basic_rex '+'28multi_optional = '[' rex ']'29group = '(' rex ')'30str = rrex"'([^'\\]|\\.)*'" | rrex'"([^"\\]|\\.)*"'31plain_str = rrex'[r](?=[\'"])' str32rex_str = rrex'[r]rex(?=[\'"])' str33comment_str = rrex'#.*'34id = rrex'\b(?=[^0-9])\w+(?=[^\'"])'35num = rrex'\b[1-9])\d*(?=[^\'"])'36NEWLINE = '\n'37BEGIN = rrex'^'38END = rrex'$'39# _NOSPACES_ predefined40'''41class RexParser:42    def __init__(self):43        id = MatchForRexParserToken('id')44        num = MatchForRexParserToken('num')45        plain_str = MatchForRexParserToken('plain_str')46        rex_str = MatchForRexParserToken('rex_str')47        comment_str = MatchForRexParserToken('comment_str')48        assign = MatchForRexParserToken('spiecial_char', data = '=')49        left_small_bracket = MatchForRexParserToken('spiecial_char', data = '(')50        right_small_bracket = MatchForRexParserToken('spiecial_char', data = ')')51        left_big_bracket = MatchForRexParserToken('spiecial_char', data = '{')52        comma = MatchForRexParserToken('spiecial_char', data = ',')53        right_big_bracket = MatchForRexParserToken('spiecial_char', data = '}')54        star = MatchForRexParserToken('spiecial_char', data = '*')55        plus = MatchForRexParserToken('spiecial_char', data = '+')56        left_mid_bracket = MatchForRexParserToken('spiecial_char', data = '[')57        right_mid_bracket = MatchForRexParserToken('spiecial_char', data = ']')58        choice_char = MatchForRexParserToken('spiecial_char', data = '|')59        rex = MatchEq('rex', None)60        idDefine = MatchSequence('idDefine', [id, assign, rex])61        line = MatchSequence('line', [MatchOptional('_', idDefine), MatchOptional('_', comment_str)])62        multi_optional = MatchSequence('multi_optional', [left_mid_bracket, rex, right_mid_bracket])63        group = MatchSequence('group', [left_small_bracket, rex, right_small_bracket])64        basic_rex = MatchChoices('basic_rex', [plain_str, rex_str, id, group, multi_optional])65        multi_bound = MatchSequence('multi_bound', \66                                    [basic_rex, left_big_bracket, num, comma, \67                                     MatchOptional('_', num), right_big_bracket])68        multi_star = MatchSequence('multi_star', [basic_rex, star])69        multi_plus = MatchSequence('multi_plus', [basic_rex, plus]) 70        multi = MatchChoices('multi', [basic_rex, multi_bound, multi_star, multi_plus,])71        72        seq = MatchPlus('seq', multi)73        choices = MatchSequence('choices', \74                                [seq, MatchStar('_', MatchSequence('_', [choice_char, seq]))])75        rex.__init__('rex', choices)76        ls = list(locals().keys())77        #ls.sort()78        #self.match_fs = {name : locals()[name] for name in ls}79        match_fs = {}80        for name in ls:81            match_fs[name] = locals()[name]82        self.match_fs = match_fs83        84        return85    def idDefine2init_assign(self, idDefineResult):86        assert idDefineResult.name == 'idDefine'87        assert len(idDefineResult.data) == 388        id = idDefineResult.data[0]89        assert id.name == 'token'90        id = id.data91        assert type(id) == str92        rexResult = idDefineResult.data[-1]93        assignRightHand = self.rexResult2MatchPatternConstruct(rexResult)94        95        choicesResult = rexResult.data96        97            98    def parser(self, string):99        tk = RexTokener()100        ls = []101        match = self.match_fs['line']102        for i, line in enumerate(tk.tokenize(string)):103            r = match(line, 0, len(line))104            if r == None:105               raise Exception('parser fail at {}th line'.format(i))106            ls.append(r)107        for 108        return ls109    110 111class RexTokener:112    id = 'id'113    num = 'num'114    plain_str = 'plain_str'115    rex_str = 'rex_str'116    comment_str = 'comment_str'117    spaces = 'spaces'118    spiecial_char = 'spiecial_char'119    120    def __init__(self):121        self.special_chars = '#=(){,}*+[]|"\''122        self.plain_str_prefixes = ['r"', "r'", '"', "'"]123        self.rex_str_prefixes = ['rex"', 'rrex"', "rex'", "rrex'"]124        self.str_prefixes = self.plain_str_prefixes + self.rex_str_prefixes125        return126    127    def isSpecialChar(self, c):128        return c in self.special_chars129    def getStrPrefixes(self):130        return self.str_prefixes131    132    def matchID(self, string, start, end):133        if start != 0:134            c = string[start-1]135            if not (c.isspace() or self.isSpecialChar(c)):136                return None137            138        if start == end:139            return None140        c = string[start]141        if c.isspace() or self.isSpecialChar(c) or c.isdigit():142            return None143        144        for pre in self.getStrPrefixes():145            if string.startswith(pre, start, end):146                return None147            148        for i in range(start, end):149            c = string[i]150            if c.isspace() or self.isSpecialChar(c):151                if c in '\'"':152                    return None153                break154        else:155            i = end156        if not 0 <= start < i <= end:157            print(start, i, end)158        assert 0 <= start < i <= end159        return MatchResult(string, start, i, type=self.id, data = string[start:i])160    def matchNum(self, string, start, end):161        if start != 0:162            c = string[start-1]163            if not (c.isspace() or self.isSpecialChar(c)):164                return None165            166        if start == end or not string[start].isdigit():167            return None168        169            170        for i in range(start, end):171            c = string[i]172            if not c.isdigit():173                if c.isspace() or self.isSpecialChar(c):174                    break175                return None176        else:177            i += 1178        assert 0 <= start < i <= end179        num = int(string[start:i])180        return MatchResult(string, start, i, type=self.num, data = num)181    182    def matchStr(self, string, start, end):183        if start != 0:184            c = string[start-1]185            if not (c.isspace() or self.isSpecialChar(c)):186                return None187        for pre in self.getStrPrefixes():188            if string.startswith(pre, start, end):189                break190        else:191            return None192        close_char = pre[-1]193        name = self.rex_str if len(pre) >= 4 else self.plain_str194        is_raw_str = len(pre) in [2, 5]195        196        old_start = start197        str_start = start + len(pre)-1198        escaping = False199        for i in range(str_start+1, end):200            c = string[i]201            if c == '\\':202                escaping = not escaping203            elif c == close_char and not escaping:204                break205        else:206            return None207        i += 1208        str_end = i209        assert 0 <= str_start < str_end-1 < str_end <= end210        s = string[str_start : str_end]211        if is_raw_str:212            s = 'r' + s213        s = eval(s)214        return MatchResult(string, old_start, str_end, type=name, data = s)215    def matchSpecialCharExceptCommentChar(self, string, start, end):216        if start == end or string[start] == '#':217            return None218        219        c = string[start]220        if not self.isSpecialChar(c):221            return None222        223        return MatchResult(string, start, start+1, type=self.spiecial_char, data = c)224    225    def matchComment(self, string, start, end):226        if start == end or not string[start] == '#':227            return None228        229        return MatchResult(string, start, end, type=self.comment_str, data = string[start : end])230    231    def matchSpaces(self, string, start, end):232        if start == end or not string[start].isspace():233            return None234        235        for i in range(start, end):236            if not string[i].isspace():237                break238        else:239            i += 1240        return MatchResult(string, start, i, type=self.spaces, data = None)241    def matchOneToken(self, string, start, end):242        for f in [self.matchID, self.matchNum, self.matchStr, \243                  self.matchSpecialCharExceptCommentChar, \244                  self.matchComment, self.matchSpaces]:245            r = f(string, start, end)246            if r != None:247                return r248        return None249    250    def tokenize(self, string):251        for line in string.split('\n'):252            yield self.tokenizeLine(line)253        254    def tokenizeLine(self, line):255        line = line.strip()256        257        ls = []258        start = 0259        end = len(line)260        while True:261            r = self.matchOneToken(line, start, end)262            if r == None:263                if start != end:264                    raise ValueError('tokenizeLine fail')265                break266            if r.start == r.end:267                raise Exception('LogicError')268            if r.type == self.spaces or r.type == self.comment_str:269                # cast away270                pass271            else:272                ls.append(r)273            start = r.end274        return ls275    276            277            278import re279class MatchResult:280    def __init__(self, string, start, end, type, data):281        assert 0 <= start <= end <= len(string)282        283        self.string = string284        self.start = start285        self.end = end286        self.type = type287        self.data = data288        return289    290    def length(self):291        return self.end - self.start292    def __repr__(self):293        tpl = 'MatchResult(string={string}, start={start}, end={end}, type={type}, data={data})'294        return tpl.format(string=self.string, \295                          start=self.start, end=self.end, \296                          type=self.type, data=self.data)297def match_str(prefix, string, start, end):298    if not string.startswith(prefix, start, end):299        return None300    end = start + len(prefix)301    return MatchResult(string, start, end, type=match_str, data=prefix)302def match_rex(rex, string, start, end):303    m = re.search(rex, string[start : end])304    if not m:305        return None306    307    if not string.startswith(prefix, start, end):308        return None309    end = start + len(prefix)310    return MatchResult(string, m.start(), m.end(), type=match_rex, data=rex)311class MatchPattern:312    @staticmethod313    def default_factory():314        return MatchPattern('')315    316    def __init__(self, name):317        self.name = name318        return319    def match(self, string, start, end):320        r = self._match(string, start, end)321        if r != None:322            r.type = type(self)323        return r324    def __call__(self, string, start, end):325        return self.match(string, start, end)326    def __repr__(self):327        return '<{type}(name={name})>'.format(type=type(self), name=self.name)328class MatchEq(MatchPattern):329    @staticmethod330    def default_factory():331        return MatchPattern('', '')332    333    def __init__(self, name, matchPattern):334        super().__init__(name)335        self.matchPattern = matchPattern336        return337    def _match(self, string, start, end):338        return eq_match(self.matchPattern, string, start, end)339    340class MatchString(MatchPattern):341    @staticmethod342    def default_factory(self):343        return MatchPattern('', '')344    345    def __init__(self, name, string):346        super().__init__(name)347        self.string = string348        return349    def _match(self, string, start, end):350        return match_str(self.string, string, start, end)351class MatchRex(MatchPattern):352    @staticmethod353    def default_factory():354        return MatchPattern('', '')355    356    def __init__(self, name, rex):357        super().__init__(name)358        self.rex = rex359        return360    def _match(self, string, start, end):361        return match_rex(self.rex, string, start, end)362class MatchMulti(MatchPattern):363    @staticmethod364    def default_factory():365        return MatchPattern('', '', 0)366    367    def __init__(self, name, matchPattern, min, max=float('inf')):368        super().__init__(name)369        370        assert 0 <= min < min+1 <= max371        assert isinstance(min, int)372        373        self.matchPattern = matchPattern374        self.min = min375        self.max = max376        return377    def _match(self, string, start, end):378        return repeat_match(self.matchPattern, \379                            string, start, end, self.min, self.max)380    381class MatchSequence(MatchPattern):382    @staticmethod383    def default_factory():384        return MatchPattern('', [])385    386    def __init__(self, name, matchPatternList):387        super().__init__(name)388        self.matchPatternList = matchPatternList389        #self.match_fs = [p.match for p in matchPatternList]390        return391    def _match(self, string, start, end):392        return sequence_match(self.matchPatternList, string, start, end)393    394 395class MatchChoices(MatchPattern):396    @staticmethod397    def default_factory():398        return MatchPattern('', [])399    400    def __init__(self, name, matchPatternList):401        super().__init__(name)402        self.matchPatternList = matchPatternList403        #self.match_fs = [p.match for p in matchPatternList]404        return405    def _match(self, string, start, end):406        return choose_match(self.matchPatternList, string, start, end)407    408class MatchOptional(MatchMulti):409    @staticmethod410    def default_factory():411        return MatchPattern('', [])412    413    def __init__(self, name, matchPattern):414        super().__init__(name, matchPattern, min=0, max=1)415        return416    417class MatchStar(MatchMulti):418    @staticmethod419    def default_factory():420        return MatchPattern('', [])421    422    def __init__(self, name, matchPattern):423        super().__init__(name, matchPattern, min=0)424        return425    426class MatchPlus(MatchMulti):427    @staticmethod428    def default_factory():429        return MatchPattern('', [])430    431    def __init__(self, name, matchPattern):432        super().__init__(name, matchPattern, min=1)433        return434class MatchForRexParserToken(MatchPattern):435    @staticmethod436    def default_factory():437        return MatchPattern('', [])438    439    def __init__(self, type, data=None):440        super().__init__('token')441        self.type = type442        self.data = data443        return444    445    def _match(self, tokens, start, end):446        if start == end:447            return None448        r = tokens[start]449        if r.type != self.type:450            return None451        if self.data != None and self.data != r.data:452            return None453        return MatchResult(tokens, start, start+1, type=None, data = r)454        455def match(match_f, string, start, end):456    if not isinstance(match_f, MatchPattern):457        print(type(match_f), match_f)458    assert isinstance(match_f, MatchPattern)459    return match_f(string, start, end)460def eq_match(match_f, string, start, end):461    r = match(match_f, string, start, end)462    if r == None:463        return None464    return MatchResult(r.string, r.start, r.end, type=eq_match, data=r)465    466def repeat_match(match_f, string, start, end, min, max=float('inf')):467    assert min < max468    469    old_start = start470    ls = []471    for _ in range(min):472        r = match(match_f, string, start, end)473        if r == None:474            return None475        start = r.end476        ls.append(r)477    while len(ls) <= max:478        r = match(match_f, string, start, end)479        if r == None:480            break481        if max == float('inf') and r.start == r.end:482            raise MemoryError('match empty string infinit times')483        484        start = r.end485        ls.append(r)486        487    return MatchResult(string, old_start, start, type=repeat_match, data=ls)488def sequence_match(match_fs, string, start, end):489    assert len(match_fs)490    old_start = start491    ls = []492    for match_f in match_fs:493        r = match(match_f, string, start, end)494        if r == None:495            return None496        start = r.end497        ls.append(r)498        499    500    return MatchResult(string, old_start, start, type=sequence_match, data=ls)501def choose_match(match_fs, string, start, end):502    assert len(match_fs)503    504    ls = []505    for match_f in match_fs:506        r = match(match_f, string, start, end)507        if r == None:508            continue509        ls.append(r)510        511    if not ls:512        return None513    r = max(ls, key=lambda r:r.length())514    515    return MatchResult(r.string, r.start, r.end, type=choose_match, data=r)516'''517def star_match(match_f, string, start, end):518    return repeat_match(match_f, string, start, end, min=0)519def plus_match(match_f, string, start, end):520    return repeat_match(match_f, string, start, end, min=1)521def optional_match(match_f, string, start, end):522    return repeat_match(match_f, string, start, end, min=0, max=1)523def choose_str(strs, string, start, end):524    assert len(strs)525    assert strs == sorted(strs)526    for prefix in reversed(strs):527        r = match_str(prefix, string, start, end)528        if r != None:529            break530    else:531        return None532    return MatchResult(r.string, r.start, r.end, type=choose_str, data=r)533'''534p = RexParser()535r = p.parser(rex_language)...

article_cleaner.py

Source:article_cleaner.py

1import re2import pandas as pd3import numpy as np4import time56amino_acid_dict = {'C' : 'CYS', 'D' : 'ASP', 'S' : 'SER', 'Q' : 'GLN', 'K' : 'LYS',7    'I' : 'ILE', 'P' : 'PRO', 'T' : 'THR', 'F' : 'PHE', 'N' : 'ASN', 8    'G' : 'GLY', 'H' : 'HIS', 'L' : 'LEU', 'R' : 'ARG', 'W' : 'TRP', 9    'A' : 'ALA', 'V' : 'VAL', 'E' : 'GLU', 'Y' : 'TYR', 'M' : 'MET'}1011def amino_three(amino):12    """Return three letter amino acid from one letter"""13    return amino_acid_dict[amino]14    15def decompose_variation(variation):16    """Decompose a variation to search the three letter amino acid or use the position in regex"""1718    decompose_aa_pos_aa = re.compile("([a-z]{1,})(\d+)([a-z]{1,})")19    list_variation = decompose_aa_pos_aa.search(variation)20    if list_variation:21        aa1 = list_variation.group(1)22        aa2 = list_variation.group(3)2324        if len(aa1) + len(aa2) == 2:25            amino1 = amino_acid_dict[aa1.upper()].lower()26            position = list_variation.group(2)27            amino2 = amino_acid_dict[aa2.upper()].lower()28            return [amino1,position,amino2]29    return False3031def decompose_fusion(variation):32    """Decompose a "fusion" variation to search separately the genes fusioned"""33    decompose_g1_g2_fusion = re.compile("(\w+)\s?(\?|-)\s?(\w+)\? fusion")34    list_variation = decompose_g1_g2_fusion.search(variation)35    if list_variation:36        gene1 = list_variation.group(1)37        gene2 = list_variation.group(3)38        return "(" + gene1 + "|" + gene2 + ")"39    return False40        41    42def decompose_dup(variation):43    """Decompose a "duplication" variation"""4445    decompose_mut_pos = re.compile("([a-z]{1,})(\d+)dup")46    list_mut = decompose_mut_pos.search(variation)47    if list_mut:48        mut = list_mut.group(1)49        pos = list_mut.group(2)50        return mut + "" + pos51    return False525354def clean_text(article):55    """Clean text from extra dot ("Fig.", "...", "ie.") to enable regex to select real sentences"""56    dot3 = re.compile("[\.]{2,}")57    fig = re.compile("fig[s]?\.")58    decimal = re.compile("\d+\.\d+")    59    etal = re.compile("et al\.")60    ie = re.compile("i\.e\.")61    inc = re.compile("inc\.")62    mutation_point = re.compile("[p|c]\.")63    64    clean_article = article.lower()65    clean_article = dot3.sub(".", clean_article)66    clean_article = fig.sub("", clean_article)67    clean_article = decimal.sub("", clean_article)68    clean_article = etal.sub("", clean_article)69    clean_article = ie.sub("", clean_article)    70    clean_article = inc.sub("", clean_article)    71    clean_article = mutation_point.sub("", clean_article)    72    73    74    return clean_article7576def join_tuple_string(strings_tuple):77    return ' '.join(strings_tuple)7879def find_match(text, word):80    """Find the actual match with a regex"""81    clean = clean_text(text)82    word = word.lower()83    target_sentence = "([^.]*{}[^.]*\.)".format(word)84    before_after_target = "([^.]*\.){0,1}"    85    match_exp = re.compile(before_after_target + target_sentence + before_after_target)86    match_text = match_exp.findall(clean)87    final_match = "".join(list(map(join_tuple_string, match_text)))88    return final_match899091def extract_match(line):92    """Construction of the regex to use according to the variation"""93    94    # Cleaning text --> Already clean, no need    95    text = line["Text"]96    variation = line["Variation"]97    gene = line["Gene"].lower()98    99    if len(text) < 10000:100        return text,6101    102    if "r1627" == variation:103        return find_match(text, "162[0-9]"), 4104    if "c1385" == variation:105        return find_match(text, "p300"), 4106    107    if "hypermethylation" in variation:108        match_meth = find_match(text, "methylat")109        if len(match_meth) != 0:110            return match_meth, 2111        112    if "casp" in variation:113        match_casp = find_match(text, "casp")114        if len(match_casp) != 0:115            return match_casp, 1116    # Splice117    if "splice" in variation:118        match_splice = find_match(text, "splice")119        if len(match_splice) != 0:120            return match_splice, 2121        122    if "fs" in variation:123        match_fs = find_match(text, "frameshift")124        if len(match_fs) != 0:125            return match_fs, 2126        127    # Amplification128    if 'ampli' in variation:129        match_ampli = find_match(text, "(amplif|increse)")130        if len(match_ampli) != 0:131            return match_ampli,3132    133    # Duplication134    if "dup" in variation:135        decomp_dup = decompose_dup(variation)136        if decomp_dup:137            match_mut_pos = find_match(text, decomp_dup)138            if len(match_mut_pos) != 0:139                return match_mut_pos,2140        141        match_dup = find_match(text, "dup")142        if len(match_dup) != 0:143            return match_dup, 3144        145    # Try with * --> w802*146    if "*" in variation:147        new_var = variation.replace("*", "\\*")148        match_star = find_match(text, new_var)149        if len(match_star) != 0:150            return match_star, 1151        if "fs" in variation:152            match_fs = find_match(text, "fs\\*")153            if len(match_fs) != 0:154                return match_fs, 3155            156        match_stop_nonsense = find_match(text,"(stop|nonsense)")157        if len(match_stop_nonsense) != 0:158            return match_stop_nonsense, 2159160    # Try first match with inital variation value161    # Quality score = 1 162    initial_match = find_match(text, variation)    163    if len(initial_match) != 0:164        #print("First match ! ", variation)165        return initial_match, 1166    167    168    # deletion and insertion169    if "del" in variation or "ins" in variation:170        match_delins = find_match(text, "(deletion|insertion|delet|insert)")171        if len(match_delins) != 0:172            return match_delins,2173        174        match_delins_sentence = find_match(text, "(del|ins)(\w|\s){0,}(del|ins)")175        if len(match_delins_sentence) != 0:176            return match_delins_sentence, 3177    178    # Trunc mutations179    if "trunc" in variation:180        match_trunc = find_match(text, "trunc")181        if len(match_trunc) != 0:182            #print("Trunc", variation)183            return match_trunc, 2184        185        match_shorte = find_match(text, "(shorte|delet)")186        if len(match_shorte) != 0:187            return match_shorte,4188189190    # Fusion of two genes191    # Quality score = 2192    if "fusion" in variation:193        fusion_gene = decompose_fusion(variation)194        if fusion_gene:195            match_fusion_gene = find_match(text, fusion_gene)196            if len(match_fusion_gene) != 0:197                #print("Fusion gene1 | gene2", variation)198                return match_fusion_gene, 2199200        # Try to match the word fusion at least..201        # Quality score 4 (bad)202        match_fusion = find_match(text,"fusion")203        if len(match_fusion) != 0:204            #print("FUSION", variation)205            return match_fusion, 4206        207    aa_pos_aa = decompose_variation(variation)208    if aa_pos_aa :209        if len(aa_pos_aa) == 3:210            # If we success to split variation in 3 group --> aa1 pos aa2211            # Second try without the last amino acid --> y371212            match_variation_aa_pos = find_match(text, variation[:-1])213            if len(match_variation_aa_pos) != 0:214                #print("y371 aa_pos", variation)215                216                return match_variation_aa_pos, 2217218            # Third try with 3 letter code of amino acid --> tyr371ser219            match_aa_pos_aa = find_match(text, "".join(aa_pos_aa))220            if len(match_aa_pos_aa) != 0:221                #print("aa_pos_aa", variation)222                return match_aa_pos_aa, 1223            224            # Try with 3 letter code without the last aa --> tyr371225            match_aa_pos = find_match(text, aa_pos_aa[0] + aa_pos_aa[1])226            if len(match_aa_pos) != 0:227                #print("aa_pos", variation)228                229                return match_aa_pos,2230            231            # Match position only --> 371232            match_pos = find_match(text, aa_pos_aa[1])233            if len(match_pos) != 0:234                #print("pos", variation)235                236                return match_pos,4237            # Search word Substitution238            match_substitution = find_match(text, "substitu")239            if len(match_substitution) != 0:240                return match_substitution, 3241                242            # Match position around the real position --> 370 - 379243            match_pos_weak = find_match(text, aa_pos_aa[1][:-1] + "[0-9]")244            if len(match_pos_weak) != 0:245                #print("pos weak", variation)246                247                return match_pos_weak,5248     249    match_gene = find_match(text, gene)250    if len(match_gene) != 0:251        return match_gene, 5252            253    # score 6 ?254    return text,7255256257258def prepare_datas(file_text, file_variant, file_out, is_training):259    print("____________________________Cleaning Datas__________________________")260    print("____________________________________________________________________")261    start_time = time.perf_counter()262263    text = pd.read_csv(file_text, sep = '\|\|', engine='python')264    text.index.name = "ID"265    text.columns = ["Text"]266    variant = pd.read_csv(file_variant)267    variant.set_index("ID",inplace = True)268    269    concatenate_data = pd.merge(variant, text, on="ID").dropna()270    concatenate_data["Text"] = concatenate_data.apply(lambda line: clean_text(line["Text"]), axis = 1)271    concatenate_data["Variation"] = variant["Variation"].apply(lambda line: line.lower())272   273274    clean_match_data = concatenate_data.apply(lambda x: extract_match(x), axis = 1)275    clean_match = pd.DataFrame(list(clean_match_data), columns = ["Text","Score"], index = clean_match_data.index)276    clean_match.index.name = "ID"277278    new_data = pd.merge(concatenate_data,clean_match, on = "ID")279    if(is_training):280        final_data = new_data.loc[:,["Gene","Variation","Class","Text_y","Score"]]281        final_data.columns = ["Gene","Variation","Class","Text","Score"]282        dtf = pd.merge(pd.DataFrame(final_data.index), final_data, on ="ID")283        np.savetxt(file_out,dtf, fmt = "%d|||%s|||%s|||%d|||%s|||%d", header= "|||".join(dtf.columns), comments='')284    else:285        final_data = new_data.loc[:,["Gene","Variation","Text_y","Score"]]286        final_data.columns = ["Gene","Variation","Text","Score"]287        dtf = pd.merge(pd.DataFrame(final_data.index), final_data, on ="ID")288        np.savetxt(file_out,dtf, fmt = "%d|||%s|||%s|||%s|||%d", header= "|||".join(dtf.columns), comments='')289290   291    stop_time = time.perf_counter()292    print("____________________________________________________________________")293    print("Cleaning datas finished in {} seconds".format(stop_time-start_time))294295296297def main(is_training):298    if is_training:299        file_text = "datas/training_text"300        file_variant = "datas/training_variants"301        file_out = "datas/training_clean"302    else:303        file_text = "datas/test_text"304        file_variant = "datas/test_variants"305        file_out = "datas/test_clean"306    prepare_datas(file_text, file_variant, file_out, is_training)307308if __name__ == "__main__":
...

MatchPattern.py

Source:MatchPattern.py

1import re2import abc3from abc import abstractmethod, ABCMeta4from MatchResult import MatchResult5__all__ = ['MatchChoices', 'MatchEq', 'MatchMulti', 'MatchOptional',6           'MatchPattern', 'MatchPlus', 'MatchResult', 'MatchRex',7           'MatchSequence', 'MatchStar', 'MatchString']8def match_str(prefix, string, start, end):9    if not string.startswith(prefix, start, end):10        return None11    end = start + len(prefix)12    #print('match_str', repr(prefix), repr(string[start:end]))13    return MatchResult(string, start, end, type=match_str, data=prefix, children=None)14def match_rex(rex, string, start, end):15    m = re.search(rex, string[start : end])16    if (not m) or m.start() != 0:17        return None18    end = start + (m.end() - m.start())19    #print('rex: ', string[start: end])20    return MatchResult(string, start, end, type=match_rex, data=rex, children=None)21skip_follow_chars_by_rex = r'((?=[^\n])\s)*'22class MatchPattern(metaclass=ABCMeta):23    @staticmethod24    @abstractmethod25    def default_factory():26        raise NotImplementedError('default_factory @MatchPattern abstractmethod')27    @abstractmethod28    def _match(self):29        raise NotImplementedError('_match @MatchPattern abstractmethod')30    31    32    def __init__(self, *, name='', follow=skip_follow_chars_by_rex):33        self.name = name34        self.follow = follow35##        if follow is not skip_follow_chars_by_rex:36##            print(name, repr(follow))37        return38    def match(self, string, start, end):39##        print('name = ', self.name)40##        print('type = ', type(self))41##        print('string from ', string[start:start+30])42        r = self._match(string, start, end)43        if r != None:44            r.type = type(self)45            assert not r.name46            r.set_name(self.name)47            48            if (self.follow):49                m = re.search(self.follow, r.string[r.end : end])50##                if m:51##                    print(m.group())52##                print(repr(self.follow), repr(r.string[r.end : end]), r.end, end)53                if m and m.start() == 0:54                    assert not r.follow55                    r.append_follow(r.string[r.end : r.end+m.end()])56##            print('r.follow = {!r}'.format(r.follow))57##            print('r.substring = {!r}'.format(r.string[r.start:r.end]))58##            print('r.type = {!r}'.format(r.type))59##            print('r.data = {!r}'.format(r.data))60##        else:61##            print('r = ', r)62        return r63    def __call__(self, string, start, end):64        return self.match(string, start, end)65    def __repr__(self):66        return '<{type}(name={name})>'.format(type=type(self), name=self.name)67class MatchEq(MatchPattern):68    @staticmethod69    def default_factory():70        return MatchEq(None)71    72    def __init__(self, matchPattern, *, name='', follow=skip_follow_chars_by_rex):73        super().__init__(name=name, follow=follow)74        self.matchPattern = matchPattern75        return76    def _match(self, string, start, end):77        return eq_match(self.matchPattern, string, start, end)78    79class MatchString(MatchPattern):80    @staticmethod81    def default_factory():82        return MatchString('')83    84    def __init__(self, string, *, name='', follow=skip_follow_chars_by_rex):85        super().__init__(name=name, follow=follow)86        self.string = string87        return88    def _match(self, string, start, end):89        return match_str(self.string, string, start, end)90class MatchRex(MatchPattern):91    @staticmethod92    def default_factory():93        return MatchRex('')94    95    def __init__(self, rex, *, name='', follow=skip_follow_chars_by_rex):96        super().__init__(name=name, follow=follow)97        self.rex = rex98        return99    def _match(self, string, start, end):100        return match_rex(self.rex, string, start, end)101class MatchMulti(MatchPattern):102    @staticmethod103    def default_factory():104        return MatchMulti(None, 0)105    106    def __init__(self, matchPattern, min, max=float('inf'), *, name='', follow=skip_follow_chars_by_rex):107        super().__init__(name=name, follow=follow)108        109        assert 0 <= min < min+1 <= max110        assert isinstance(min, int)111        112        self.matchPattern = matchPattern113        self.min = min114        self.max = max115        return116    def _match(self, string, start, end):117        return repeat_match(self.matchPattern, \118                            string, start, end, self.min, self.max)119    120class MatchSequence(MatchPattern):121    @staticmethod122    def default_factory():123        return MatchSequence([])124    125    def __init__(self, matchPatternList, *, name='', follow=skip_follow_chars_by_rex):126        super().__init__(name=name, follow=follow)127        self.matchPatternList = matchPatternList128        #self.match_fs = [p.match for p in matchPatternList]129        return130    def _match(self, string, start, end):131        return sequence_match(self.matchPatternList, string, start, end)132    133 134class MatchChoices(MatchPattern):135    @staticmethod136    def default_factory():137        return MatchChoices([])138    139    def __init__(self, matchPatternList, *, name='', follow=skip_follow_chars_by_rex):140        super().__init__(name=name, follow=follow)141        self.matchPatternList = matchPatternList142        #self.match_fs = [p.match for p in matchPatternList]143        return144    def _match(self, string, start, end):145        return choose_match(self.matchPatternList, string, start, end)146    147class MatchOptional(MatchMulti):148    @staticmethod149    def default_factory():150        return MatchOptional([])151    152    def __init__(self, matchPattern, *, name='', follow=skip_follow_chars_by_rex):153        super().__init__(matchPattern, min=0, max=1, name=name, follow=follow)154        return155    156class MatchStar(MatchMulti):157    @staticmethod158    def default_factory():159        return MatchStar([])160    161    def __init__(self, matchPattern, *, name='', follow=skip_follow_chars_by_rex):162        super().__init__(matchPattern, min=0, name=name, follow=follow)163        return164    165class MatchPlus(MatchMulti):166    @staticmethod167    def default_factory():168        return MatchPlus([])169    170    def __init__(self, matchPattern, *, name='', follow=skip_follow_chars_by_rex):171        super().__init__(matchPattern, min=1, name=name, follow=follow)172        return173def match(match_f, string, start, end):174    if not isinstance(match_f, MatchPattern):175        print(type(match_f), match_f)176    assert isinstance(match_f, MatchPattern)177    return match_f(string, start, end)178def eq_match(match_f, string, start, end):179    r = match(match_f, string, start, end)180    if r == None:181        return None182    rr = MatchResult(string, r.start, r.org_end, type=eq_match, data=None, children=[r])183    rr.append_follow(r.follow)184    return rr185    186def repeat_match(match_f, string, start, end, min, max=float('inf')):187    assert min < max188    189    old_start = start190    ls = []191    for _ in range(min):192        r = match(match_f, string, start, end)193        if r == None:194            return None195        start = r.end196        ls.append(r)197    while len(ls) <= max:198        r = match(match_f, string, start, end)199        if r == None:200            break201        if max == float('inf') and r.start == r.end:202            print(match_f.name)203            print(type(match_f))204            print(string[start:end])205            print(match_f.max)206            raise MemoryError('match empty string infinit times')207        208        start = r.end209        ls.append(r)210        211    return MatchResult(string, old_start, start, type=repeat_match, data=None, children=ls)212def sequence_match(match_fs, string, start, end):213    assert len(match_fs)214    old_start = start215    ls = []216    for match_f in match_fs:217        r = match(match_f, string, start, end)218        if r == None:219            return None220        start = r.end221        ls.append(r)222        223    224    return MatchResult(string, old_start, start, type=sequence_match, data=None, children=ls)225def choose_match(match_fs, string, start, end):226    assert len(match_fs)227    228    ls = []229    for i, match_f in enumerate(match_fs):230        r = match(match_f, string, start, end)231        if r == None:232            continue233        ls.append((i,r))234        235    if not ls:236        return None237    elif len(ls) > 1:238        print('Warning: choose lengthest one from matchs')239        for i, r in ls:240            f = match_fs[i]241            print('\t', f.name)242              243    ir = max(ls, key=lambda ir:ir[-1].length())244    i, r = ir245    246    cs = [None]*len(match_fs)247    cs[i] = r248    return MatchResult(r.string, r.start, r.end, type=choose_match, data=i, children=cs)...

Automation Testing Tutorials

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