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# Copyright 1999 by Jeffrey Chang.  All rights reserved.
# Copyright 2000 by Jeffrey Chang.  All rights reserved.
# Revisions Copyright 2007 by Peter Cock.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.
"""Module for working with Prosite files from ExPASy (OBSOLETE).

Most of the functionality in this module has moved to Bio.ExPASy.Prosite;
please see

Bio.ExPASy.Prosite.read          To read a Prosite file containing one entry.
Bio.ExPASy.Prosite.parse         Iterates over entries in a Prosite file.
Bio.ExPASy.Prosite.Record        Holds Prosite data.

scan_sequence_expasy  Scan a sequence for occurrences of Prosite patterns.
_extract_pattern_hits Extract Prosite patterns from a web page.
PatternHit            Holds data from a hit against a Prosite pattern.
please see the new module Bio.ExPASy.ScanProsite.

The other functions and classes in Bio.Prosite (including
Bio.Prosite.index_file and Bio.Prosite.Dictionary) are considered deprecated,
and were not moved to Bio.ExPASy.Prosite. If you use this functionality,
please contact the Biopython developers at biopython-dev@biopython.org to
avoid permanent removal of this module from Biopython.

This module provides code to work with the prosite dat file from

Tested with:
Release 15.0, July 1998
Release 16.0, July 1999
Release 17.0, Dec 2001
Release 19.0, Mar 2006

parse                 Iterates over entries in a Prosite file.
scan_sequence_expasy  Scan a sequence for occurrences of Prosite patterns.
index_file            Index a Prosite file for a Dictionary.
_extract_record       Extract Prosite data from a web page.
_extract_pattern_hits Extract Prosite patterns from a web page.

Record                Holds Prosite data.
PatternHit            Holds data from a hit against a Prosite pattern.
Dictionary            Accesses a Prosite file using a dictionary interface.
RecordParser          Parses a Prosite record into a Record object.
Iterator              Iterates over entries in a Prosite file; DEPRECATED.

_Scanner              Scans Prosite-formatted data.
_RecordConsumer       Consumes Prosite data to a Record object.

from types import *
import re
import sgmllib
from Bio import File
from Bio import Index
from Bio.ParserSupport import *

# There is probably a cleaner way to write the read/parse functions
# if we don't use the "parser = RecordParser(); parser.parse(handle)"
# approach. Leaving that for the next revision of Bio.Prosite.
def parse(handle):
    import cStringIO
    parser = RecordParser()
    text = ""
    for line in handle:
        text += line
        if line[:2]=='//':
            handle = cStringIO.StringIO(text)
            record = parser.parse(handle)
            text = ""
            if not record: # Then this was the copyright notice
            yield record

def read(handle):
    parser = RecordParser()
        record = parser.parse(handle)
    except ValueError, error:
        if error.message=="There doesn't appear to be a record":
            raise ValueError("No Prosite record found")
            raise error
    # We should have reached the end of the record by now
    remainder = handle.read()
    if remainder:
        raise ValueError("More than one Prosite record found")
    return record

00099 class Record:
    """Holds information from a Prosite record.

    name           ID of the record.  e.g. ADH_ZINC
    type           Type of entry.  e.g. PATTERN, MATRIX, or RULE
    accession      e.g. PS00387
    created        Date the entry was created.  (MMM-YYYY)
    data_update    Date the 'primary' data was last updated.
    info_update    Date data other than 'primary' data was last updated.
    pdoc           ID of the PROSITE DOCumentation.
    description    Free-format description.
    pattern        The PROSITE pattern.  See docs.
    matrix         List of strings that describes a matrix entry.
    rules          List of rule definitions (from RU lines).  (strings)
    prorules       List of prorules (from PR lines). (strings)

    nr_sp_release  SwissProt release.
    nr_sp_seqs     Number of seqs in that release of Swiss-Prot. (int)
    nr_total       Number of hits in Swiss-Prot.  tuple of (hits, seqs)
    nr_positive    True positives.  tuple of (hits, seqs)
    nr_unknown     Could be positives.  tuple of (hits, seqs)
    nr_false_pos   False positives.  tuple of (hits, seqs)
    nr_false_neg   False negatives.  (int)
    nr_partial     False negatives, because they are fragments. (int)

    cc_taxo_range  Taxonomic range.  See docs for format
    cc_max_repeat  Maximum number of repetitions in a protein
    cc_site        Interesting site.  list of tuples (pattern pos, desc.)
    cc_skip_flag   Can this entry be ignored?
    cc_version     version number (introduced in release 19.0)

    DATA BANK REFERENCES - The following are all
                           lists of tuples (swiss-prot accession,
                                            swiss-prot name)
    dr_potential   Potential hits, but fingerprint region not yet available.
    dr_unknown     Could possibly belong

    pdb_structs    List of PDB entries.

    def __init__(self):
        self.name = ''
        self.type = ''
        self.accession = ''
        self.created = ''
        self.data_update = ''
        self.info_update = ''
        self.pdoc = ''
        self.description = ''
        self.pattern = ''
        self.matrix = []
        self.rules = []
        self.prorules = []
        self.postprocessing = []

        self.nr_sp_release = ''
        self.nr_sp_seqs = ''
        self.nr_total = (None, None)
        self.nr_positive = (None, None)
        self.nr_unknown = (None, None)
        self.nr_false_pos = (None, None)
        self.nr_false_neg = None
        self.nr_partial = None

        self.cc_taxo_range = ''
        self.cc_max_repeat = ''
        self.cc_site = []
        self.cc_skip_flag = ''

        self.dr_positive = []
        self.dr_false_neg = []
        self.dr_false_pos = []
        self.dr_potential = []
        self.dr_unknown = []

        self.pdb_structs = []

00189 class PatternHit:
    """Holds information from a hit against a Prosite pattern.

    name           ID of the record.  e.g. ADH_ZINC
    accession      e.g. PS00387
    pdoc           ID of the PROSITE DOCumentation.
    description    Free-format description.
    matches        List of tuples (start, end, sequence) where
                   start and end are indexes of the match, and sequence is
                   the sequence matched.

    def __init__(self):
        self.name = None
        self.accession = None
        self.pdoc = None
        self.description = None
        self.matches = []
    def __str__(self):
        lines = []
        lines.append("%s %s %s" % (self.accession, self.pdoc, self.name))
        if len(self.matches) > 1:
            lines.append("Number of matches: %s" % len(self.matches))
        for i in range(len(self.matches)):
            start, end, seq = self.matches[i]
            range_str = "%d-%d" % (start, end)
            if len(self.matches) > 1:
                lines.append("%7d %10s %s" % (i+1, range_str, seq))
                lines.append("%7s %10s %s" % (' ', range_str, seq))
        return "\n".join(lines)
00224 class Iterator:
    """Returns one record at a time from a Prosite file.

    next   Return the next record from the stream, or None.

00231     def __init__(self, handle, parser=None):
        """__init__(self, handle, parser=None)

        Create a new iterator.  handle is a file-like object.  parser
        is an optional Parser object to change the results into another form.
        If set to None, then the raw contents of the file will be returned.

        import warnings
        warnings.warn("Bio.Prosite.Iterator is deprecated; we recommend using the function Bio.Prosite.parse instead. Please contact the Biopython developers at biopython-dev@biopython.org you cannot use Bio.Prosite.parse instead of Bio.Prosite.Iterator.",
        if type(handle) is not FileType and type(handle) is not InstanceType:
            raise ValueError("I expected a file handle or file-like object")
        self._uhandle = File.UndoHandle(handle)
        self._parser = parser

00247     def next(self):
        """next(self) -> object

        Return the next Prosite record from the file.  If no more records,
        return None.

        # Skip the copyright info, if it's the first record.
        line = self._uhandle.peekline()
        if line[:2] == 'CC':
            while 1:
                line = self._uhandle.readline()
                if not line:
                if line[:2] == '//':
                if line[:2] != 'CC':
                    raise ValueError("Oops, where's the copyright?")
        lines = []
        while 1:
            line = self._uhandle.readline()
            if not line:
            if line[:2] == '//':
        if not lines:
            return None
        data = "".join(lines)
        if self._parser is not None:
            return self._parser.parse(File.StringHandle(data))
        return data
    def __iter__(self):
        return iter(self.next, None)

00286 class Dictionary:
    """Accesses a Prosite file using a dictionary interface.

    __filename_key = '__filename'
00292     def __init__(self, indexname, parser=None):
        """__init__(self, indexname, parser=None)

        Open a Prosite Dictionary.  indexname is the name of the
        index for the dictionary.  The index should have been created
        using the index_file function.  parser is an optional Parser
        object to change the results into another form.  If set to None,
        then the raw contents of the file will be returned.

        self._index = Index.Index(indexname)
        self._handle = open(self._index[Dictionary.__filename_key])
        self._parser = parser

    def __len__(self):
        return len(self._index)

    def __getitem__(self, key):
        start, len = self._index[key]
        data = self._handle.read(len)
        if self._parser is not None:
            return self._parser.parse(File.StringHandle(data))
        return data

    def __getattr__(self, name):
        return getattr(self._index, name)

00320 class RecordParser(AbstractParser):
    """Parses Prosite data into a Record object.

    def __init__(self):
        self._scanner = _Scanner()
        self._consumer = _RecordConsumer()

    def parse(self, handle):
        self._scanner.feed(handle, self._consumer)
        return self._consumer.data

00332 class _Scanner:
    """Scans Prosite-formatted data.

    Tested with:
    Release 15.0, July 1998
00339     def feed(self, handle, consumer):
        """feed(self, handle, consumer)

        Feed in Prosite data for scanning.  handle is a file-like
        object that contains prosite data.  consumer is a
        Consumer object that will receive events as the report is scanned.

        if isinstance(handle, File.UndoHandle):
            uhandle = handle
            uhandle = File.UndoHandle(handle)

        consumer.finished = False
        while not consumer.finished:
            line = uhandle.peekline()
            if not line:
            elif is_blank_line(line):
                # Skip blank lines between records
            elif line[:2] == 'ID':
                self._scan_record(uhandle, consumer)
            elif line[:2] == 'CC':
                self._scan_copyrights(uhandle, consumer)
                raise ValueError("There doesn't appear to be a record")

    def _scan_copyrights(self, uhandle, consumer):
        self._scan_line('CC', uhandle, consumer.copyright, any_number=1)
        self._scan_terminator(uhandle, consumer)

    def _scan_record(self, uhandle, consumer):
        for fn in self._scan_fns:
            fn(self, uhandle, consumer)

            # In Release 15.0, C_TYPE_LECTIN_1 has the DO line before
            # the 3D lines, instead of the other way around.
            # Thus, I'll give the 3D lines another chance after the DO lines
            # are finished.
            if fn is self._scan_do.im_func:
                self._scan_3d(uhandle, consumer)

    def _scan_line(self, line_type, uhandle, event_fn,
                   exactly_one=None, one_or_more=None, any_number=None,
        # Callers must set exactly one of exactly_one, one_or_more, or
        # any_number to a true value.  I do not explicitly check to
        # make sure this function is called correctly.
        # This does not guarantee any parameter safety, but I
        # like the readability.  The other strategy I tried was have
        # parameters min_lines, max_lines.
        if exactly_one or one_or_more:
            read_and_call(uhandle, event_fn, start=line_type)
        if one_or_more or any_number:
            while 1:
                if not attempt_read_and_call(uhandle, event_fn,
        if up_to_one:
            attempt_read_and_call(uhandle, event_fn, start=line_type)

    def _scan_id(self, uhandle, consumer):
        self._scan_line('ID', uhandle, consumer.identification, exactly_one=1)

    def _scan_ac(self, uhandle, consumer):
        self._scan_line('AC', uhandle, consumer.accession, exactly_one=1)
    def _scan_dt(self, uhandle, consumer):
        self._scan_line('DT', uhandle, consumer.date, exactly_one=1)

    def _scan_de(self, uhandle, consumer):
        self._scan_line('DE', uhandle, consumer.description, exactly_one=1)
    def _scan_pa(self, uhandle, consumer):
        self._scan_line('PA', uhandle, consumer.pattern, any_number=1)
    def _scan_ma(self, uhandle, consumer):
        self._scan_line('MA', uhandle, consumer.matrix, any_number=1)
##        # ZN2_CY6_FUNGAL_2, DNAJ_2 in Release 15
##        # contain a CC line buried within an 'MA' line.  Need to check
##        # for that.
##        while 1:
##            if not attempt_read_and_call(uhandle, consumer.matrix, start='MA'):
##                line1 = uhandle.readline()
##                line2 = uhandle.readline()
##                uhandle.saveline(line2)
##                uhandle.saveline(line1)
##                if line1[:2] == 'CC' and line2[:2] == 'MA':
##                    read_and_call(uhandle, consumer.comment, start='CC')
##                else:
##                    break
    def _scan_pp(self, uhandle, consumer):
        #New PP line, PostProcessing, just after the MA line
        self._scan_line('PP', uhandle, consumer.postprocessing, any_number=1)
    def _scan_ru(self, uhandle, consumer):
        self._scan_line('RU', uhandle, consumer.rule, any_number=1)
    def _scan_nr(self, uhandle, consumer):
        self._scan_line('NR', uhandle, consumer.numerical_results,

    def _scan_cc(self, uhandle, consumer):
        self._scan_line('CC', uhandle, consumer.comment, any_number=1)
    def _scan_dr(self, uhandle, consumer):
        self._scan_line('DR', uhandle, consumer.database_reference,
    def _scan_3d(self, uhandle, consumer):
        self._scan_line('3D', uhandle, consumer.pdb_reference,

    def _scan_pr(self, uhandle, consumer):
        #New PR line, ProRule, between 3D and DO lines
        self._scan_line('PR', uhandle, consumer.prorule, any_number=1)

    def _scan_do(self, uhandle, consumer):
        self._scan_line('DO', uhandle, consumer.documentation, exactly_one=1)

    def _scan_terminator(self, uhandle, consumer):
        self._scan_line('//', uhandle, consumer.terminator, exactly_one=1)

    #This is a list of scan functions in the order expected in the file file.
    #The function definitions define how many times each line type is exected
    #(or if optional):
    _scan_fns = [

        # This is a really dirty hack, and should be fixed properly at
        # some point.  ZN2_CY6_FUNGAL_2, DNAJ_2 in Rel 15 and PS50309
        # in Rel 17 have lines out of order.  Thus, I have to rescan
        # these, which decreases performance.


00501 class _RecordConsumer(AbstractConsumer):
    """Consumer that converts a Prosite record to a Record object.

    data    Record with Prosite data.

    def __init__(self):
        self.data = None
    def start_record(self):
        self.data = Record()
    def end_record(self):

    def identification(self, line):
        cols = line.split()
        if len(cols) != 3:
            raise ValueError("I don't understand identification line\n%s" \
                             % line)
        self.data.name = self._chomp(cols[1])    # don't want ';'
        self.data.type = self._chomp(cols[2])    # don't want '.'
    def accession(self, line):
        cols = line.split()
        if len(cols) != 2:
            raise ValueError("I don't understand accession line\n%s" % line)
        self.data.accession = self._chomp(cols[1])
    def date(self, line):
        uprline = line.upper()
        cols = uprline.split()

        # Release 15.0 contains both 'INFO UPDATE' and 'INF UPDATE'
        if cols[2] != '(CREATED);' or \
           cols[4] != '(DATA' or cols[5] != 'UPDATE);' or \
           cols[7][:4] != '(INF' or cols[8] != 'UPDATE).':
            raise ValueError("I don't understand date line\n%s" % line)

        self.data.created = cols[1]
        self.data.data_update = cols[3]
        self.data.info_update = cols[6]
    def description(self, line):
        self.data.description = self._clean(line)
    def pattern(self, line):
        self.data.pattern = self.data.pattern + self._clean(line)
    def matrix(self, line):

    def postprocessing(self, line):
        postprocessing = self._clean(line).split(";")

    def rule(self, line):
    def numerical_results(self, line):
        cols = self._clean(line).split(";")
        for col in cols:
            if not col:
            qual, data = [word.lstrip() for word in col.split("=")]
            if qual == '/RELEASE':
                release, seqs = data.split(",")
                self.data.nr_sp_release = release
                self.data.nr_sp_seqs = int(seqs)
            elif qual == '/FALSE_NEG':
                self.data.nr_false_neg = int(data)
            elif qual == '/PARTIAL':
                self.data.nr_partial = int(data)
            elif qual in ['/TOTAL', '/POSITIVE', '/UNKNOWN', '/FALSE_POS']:
                m = re.match(r'(\d+)\((\d+)\)', data)
                if not m:
                    raise Exception("Broken data %s in comment line\n%s" \
                                    % (repr(data), line))
                hits = tuple(map(int, m.groups()))
                if(qual == "/TOTAL"):
                    self.data.nr_total = hits
                elif(qual == "/POSITIVE"):
                    self.data.nr_positive = hits
                elif(qual == "/UNKNOWN"):
                    self.data.nr_unknown = hits
                elif(qual == "/FALSE_POS"):
                    self.data.nr_false_pos = hits
                raise ValueError("Unknown qual %s in comment line\n%s" \
                                 % (repr(qual), line))
    def comment(self, line):
        #Expect CC lines like this:
        #CC   /TAXO-RANGE=??EPV; /MAX-REPEAT=2;
        #Can (normally) split on ";" and then on "="
        cols = self._clean(line).split(";")
        for col in cols:
            if not col or col[:17] == 'Automatic scaling':
                # DNAJ_2 in Release 15 has a non-standard comment line:
                # CC   Automatic scaling using reversed database
                # Throw it away.  (Should I keep it?)
            if col.count("=") == 0 :
                #Missing qualifier!  Can we recover gracefully?
                #For example, from Bug 2403, in PS50293 have:
                #CC /AUTHOR=K_Hofmann; N_Hulo
            qual, data = [word.lstrip() for word in col.split("=")]
            if qual == '/TAXO-RANGE':
                self.data.cc_taxo_range = data
            elif qual == '/MAX-REPEAT':
                self.data.cc_max_repeat = data
            elif qual == '/SITE':
                pos, desc = data.split(",")
                self.data.cc_site.append((int(pos), desc))
            elif qual == '/SKIP-FLAG':
                self.data.cc_skip_flag = data
            elif qual == '/MATRIX_TYPE':
                self.data.cc_matrix_type = data
            elif qual == '/SCALING_DB':
                self.data.cc_scaling_db = data
            elif qual == '/AUTHOR':
                self.data.cc_author = data
            elif qual == '/FT_KEY':
                self.data.cc_ft_key = data
            elif qual == '/FT_DESC':
                self.data.cc_ft_desc = data
            elif qual == '/VERSION':
                self.data.cc_version = data
                raise ValueError("Unknown qual %s in comment line\n%s" \
                                 % (repr(qual), line))
    def database_reference(self, line):
        refs = self._clean(line).split(";")
        for ref in refs:
            if not ref:
            acc, name, type = [word.strip() for word in ref.split(",")]
            if type == 'T':
                self.data.dr_positive.append((acc, name))
            elif type == 'F':
                self.data.dr_false_pos.append((acc, name))
            elif type == 'N':
                self.data.dr_false_neg.append((acc, name))
            elif type == 'P':
                self.data.dr_potential.append((acc, name))
            elif type == '?':
                self.data.dr_unknown.append((acc, name))
                raise ValueError("I don't understand type flag %s" % type)
    def pdb_reference(self, line):
        cols = line.split()
        for id in cols[1:]:  # get all but the '3D' col
    def prorule(self, line):
        #Assume that each PR line can contain multiple ";" separated rules
        rules = self._clean(line).split(";")

    def documentation(self, line):
        self.data.pdoc = self._chomp(self._clean(line))

    def terminator(self, line):
        self.finished = True

    def _chomp(self, word, to_chomp='.,;'):
        # Remove the punctuation at the end of a word.
        if word[-1] in to_chomp:
            return word[:-1]
        return word

    def _clean(self, line, rstrip=1):
        # Clean up a line.
        if rstrip:
            return line[5:].rstrip()
        return line[5:]

def scan_sequence_expasy(seq=None, id=None, exclude_frequent=None):
    """scan_sequence_expasy(seq=None, id=None, exclude_frequent=None) ->
    list of PatternHit's

    Search a sequence for occurrences of Prosite patterns.  You can
    specify either a sequence in seq or a SwissProt/trEMBL ID or accession
    in id.  Only one of those should be given.  If exclude_frequent
    is true, then the patterns with the high probability of occurring
    will be excluded.

    from Bio import ExPASy
    if (seq and id) or not (seq or id):
        raise ValueError("Please specify either a sequence or an id")
    handle = ExPASy.scanprosite1(seq, id, exclude_frequent)
    return _extract_pattern_hits(handle)

def _extract_pattern_hits(handle):
    """_extract_pattern_hits(handle) -> list of PatternHit's

    Extract hits from a web page.  Raises a ValueError if there
    was an error in the query.

    class parser(sgmllib.SGMLParser):
        def __init__(self):
            self.hits = []
            self.broken_message = 'Some error occurred'
            self._in_pre = 0
            self._current_hit = None
            self._last_found = None   # Save state of parsing
        def handle_data(self, data):
            if data.find('try again') >= 0:
                self.broken_message = data
            elif data == 'illegal':
                self.broken_message = 'Sequence contains illegal characters'
            if not self._in_pre:
            elif not data.strip():
            if self._last_found is None and data[:4] == 'PDOC':
                self._current_hit.pdoc = data
                self._last_found = 'pdoc'
            elif self._last_found == 'pdoc':
                if data[:2] != 'PS':
                    raise ValueError("Expected accession but got:\n%s" % data)
                self._current_hit.accession = data
                self._last_found = 'accession'
            elif self._last_found == 'accession':
                self._current_hit.name = data
                self._last_found = 'name'
            elif self._last_found == 'name':
                self._current_hit.description = data
                self._last_found = 'description'
            elif self._last_found == 'description':
                m = re.findall(r'(\d+)-(\d+) (\w+)', data)
                for start, end, seq in m:
                        (int(start), int(end), seq))
        def do_hr(self, attrs):
            # <HR> inside a <PRE> section means a new hit.
            if self._in_pre:
                self._current_hit = PatternHit()
                self._last_found = None
        def start_pre(self, attrs):
            self._in_pre = 1
            self.broken_message = None   # Probably not broken
        def end_pre(self):
            self._in_pre = 0
    p = parser()
    if p.broken_message:
        raise ValueError(p.broken_message)
    return p.hits

def index_file(filename, indexname, rec2key=None):
    """index_file(filename, indexname, rec2key=None)

    Index a Prosite file.  filename is the name of the file.
    indexname is the name of the dictionary.  rec2key is an
    optional callback that takes a Record and generates a unique key
    (e.g. the accession number) for the record.  If not specified,
    the id name will be used.

    import os
    if not os.path.exists(filename):
        raise ValueError("%s does not exist" % filename)

    index = Index.Index(indexname, truncate=1)
    index[Dictionary._Dictionary__filename_key] = filename
    handle = open(filename)
    records = parse(handle)
    end = 0L
    for record in records:
        start = end
        end = long(handle.tell())
        length = end - start
        if rec2key is not None:
            key = rec2key(record)
            key = record.name
        if not key:
            raise KeyError("empty key was produced")
        elif key in index:
            raise KeyError("duplicate key %s found" % key)

        index[key] = start, length

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