Exemple #1
0
    def _str_hsp_header(self):
        """Prints the alignment header info."""
        lines = []
        # set query id line
        qid_line = trim_str('      Query: %s %s' %
                (self.query_id, self.query_description), 80, '...')
        # set hit id line
        hid_line = trim_str('        Hit: %s %s' %
                (self.hit_id, self.hit_description), 80, '...')
        lines.append(qid_line)
        lines.append(hid_line)

        # coordinates
        query_start = getattr_str(self, 'query_start')
        query_end = getattr_str(self, 'query_end')
        hit_start = getattr_str(self, 'hit_start')
        hit_end = getattr_str(self, 'hit_end')

        # strands
        try:
            qstrand = self.query_strand
            hstrand = self.hit_strand
        except ValueError:
            qstrand = self.query_strand_all[0]
            hstrand = self.hit_strand_all[0]
        lines.append('Query range: [%s:%s] (%r)' % (query_start, query_end,
                qstrand))
        lines.append('  Hit range: [%s:%s] (%r)' % (hit_start, hit_end,
                hstrand))

        return '\n'.join(lines)
Exemple #2
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    def _str_hsp_header(self):
        """Prints the alignment header info."""
        lines = []
        # set query id line
        qid_line = trim_str(
            '      Query: %s %s' % (self.query_id, self.query_description), 80,
            '...')
        # set hit id line
        hid_line = trim_str(
            '        Hit: %s %s' % (self.hit_id, self.hit_description), 80,
            '...')
        lines.append(qid_line)
        lines.append(hid_line)

        # coordinates
        query_start = getattr_str(self, 'query_start')
        query_end = getattr_str(self, 'query_end')
        hit_start = getattr_str(self, 'hit_start')
        hit_end = getattr_str(self, 'hit_end')

        # strands
        try:
            qstrand = self.query_strand
            hstrand = self.hit_strand
        except ValueError:
            qstrand = self.query_strand_all[0]
            hstrand = self.hit_strand_all[0]
        lines.append('Query range: [%s:%s] (%r)' %
                     (query_start, query_end, qstrand))
        lines.append('  Hit range: [%s:%s] (%r)' %
                     (hit_start, hit_end, hstrand))

        return '\n'.join(lines)
Exemple #3
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    def __str__(self):
        lines = []

        # set query id line
        qid_line = 'Query: %s' % self.query_id
        if self.query_description:
            qid_line += trim_str('\n       %s' % self.query_description, 80,
                                 '...')
        lines.append(qid_line)

        # set hit id line
        hid_line = '  Hit: %s' % self.id
        if hasattr(self, 'seq_len'):
            hid_line += ' (%i)' % self.seq_len
        if self.description:
            hid_line += trim_str('\n       %s' % self.description, 80, '...')
        lines.append(hid_line)

        # set hsp line and table
        if not self.hsps:
            lines.append(' HSPs: ?')
        else:
            lines.append(
                ' HSPs: %s  %s  %s  %s  %s  %s' %
                ('-' * 4, '-' * 8, '-' * 9, '-' * 6, '-' * 15, '-' * 21))
            pattern = '%11s  %8s  %9s  %6s  %15s  %21s'
            lines.append(pattern % ('#', 'E-value', 'Bit score', 'Span',
                                    'Query range', 'Hit range'))
            lines.append(
                pattern %
                ('-' * 4, '-' * 8, '-' * 9, '-' * 6, '-' * 15, '-' * 21))
            for idx, hsp in enumerate(self.hsps):
                # evalue
                evalue = getattr_str(hsp, 'evalue', fmt='%.2g')
                # bitscore
                bitscore = getattr_str(hsp, 'bitscore', fmt='%.2f')
                # alignment length
                aln_span = getattr_str(hsp, 'aln_span')
                # query region
                query_start = getattr_str(hsp, 'query_start')
                query_end = getattr_str(hsp, 'query_end')
                query_range = '[%s:%s]' % (query_start, query_end)
                # max column length is 18
                query_range = trim_str(query_range, 15, '~]')
                # hit region
                hit_start = getattr_str(hsp, 'hit_start')
                hit_end = getattr_str(hsp, 'hit_end')
                hit_range = '[%s:%s]' % (hit_start, hit_end)
                hit_range = trim_str(hit_range, 21, '~]')
                # append the hsp row
                lines.append(pattern % (str(idx), evalue, bitscore, aln_span,
                                        query_range, hit_range))

        return '\n'.join(lines)
Exemple #4
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    def __str__(self):
        lines = []

        # set query id line
        qid_line = 'Query: %s' % self.query_id
        if self.query_description:
            qid_line += trim_str('\n       %s' %
                    self.query_description, 80, '...')
        lines.append(qid_line)

        # set hit id line
        hid_line = '  Hit: %s' % self.id
        if hasattr(self, 'seq_len'):
            hid_line += ' (%i)' % self.seq_len
        if self.description:
            hid_line += trim_str('\n       %s' % self.description,
                    80, '...')
        lines.append(hid_line)

        # set hsp line and table
        if not self.hsps:
            lines.append(' HSPs: ?')
        else:
            lines.append(' HSPs: %s  %s  %s  %s  %s  %s' %
                    ('-'*4, '-'*8, '-'*9, '-'*6, '-'*15, '-'*21))
            pattern = '%11s  %8s  %9s  %6s  %15s  %21s'
            lines.append(pattern % ('#', 'E-value', 'Bit score', 'Span',
                    'Query range', 'Hit range'))
            lines.append(pattern % ('-'*4, '-'*8, '-'*9, '-'*6, '-'*15, '-'*21))
            for idx, hsp in enumerate(self.hsps):
                # evalue
                evalue = getattr_str(hsp, 'evalue', fmt='%.2g')
                # bitscore
                bitscore = getattr_str(hsp, 'bitscore', fmt='%.2f')
                # alignment length
                aln_span = getattr_str(hsp, 'aln_span')
                # query region
                query_start = getattr_str(hsp, 'query_start')
                query_end = getattr_str(hsp, 'query_end')
                query_range = '[%s:%s]' % (query_start, query_end)
                # max column length is 18
                query_range = trim_str(query_range, 15, '~]')
                # hit region
                hit_start = getattr_str(hsp, 'hit_start')
                hit_end = getattr_str(hsp, 'hit_end')
                hit_range = '[%s:%s]' % (hit_start, hit_end)
                hit_range = trim_str(hit_range, 21, '~]')
                # append the hsp row
                lines.append(pattern % (str(idx), evalue, bitscore, aln_span,
                        query_range, hit_range))

        return '\n'.join(lines)
Exemple #5
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    def __str__(self):

        lines = []
        # set hsp info line
        statline = []
        # evalue
        evalue = getattr_str(self, 'evalue', fmt='%.2g')
        statline.append('evalue ' + evalue)
        # bitscore
        bitscore = getattr_str(self, 'bitscore', fmt='%.2f')
        statline.append('bitscore ' + bitscore)
        lines.append('Quick stats: ' + '; '.join(statline))

        if len(self.fragments) == 1:
            return '\n'.join([
                self._str_hsp_header(), '\n'.join(lines),
                self.fragments[0]._str_aln()
            ])
        else:
            lines.append('  Fragments: %s  %s  %s  %s' %
                         ('-' * 3, '-' * 14, '-' * 22, '-' * 22))
            pattern = '%16s  %14s  %22s  %22s'
            lines.append(pattern % ('#', 'Span', 'Query range', 'Hit range'))
            lines.append(pattern % ('-' * 3, '-' * 14, '-' * 22, '-' * 22))
            for idx, block in enumerate(self.fragments):
                # set hsp line and table
                # alignment span
                aln_span = getattr_str(block, 'aln_span')
                # query region
                query_start = getattr_str(block, 'query_start')
                query_end = getattr_str(block, 'query_end')
                query_range = '[%s:%s]' % (query_start, query_end)
                # max column length is 20
                query_range = trim_str(query_range, 22, '~]')
                # hit region
                hit_start = getattr_str(block, 'hit_start')
                hit_end = getattr_str(block, 'hit_end')
                hit_range = '[%s:%s]' % (hit_start, hit_end)
                hit_range = trim_str(hit_range, 22, '~]')
                # append the hsp row
                lines.append(pattern %
                             (str(idx), aln_span, query_range, hit_range))

            return self._str_hsp_header() + '\n' + '\n'.join(lines)
Exemple #6
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    def __str__(self):
        lines = []

        # set program and version line
        lines.append('Program: %s (%s)' % (self.program, self.version))

        # set query id line
        qid_line = '  Query: %s' % self.id
        if hasattr(self, 'seq_len'):
            qid_line += ' (%i)' % self.seq_len
        if self.description:
            qid_line += trim_str('\n         %s' % self.description, 80, '...')
        lines.append(qid_line)

        # set target line
        lines.append(' Target: %s' % self.target)

        # set hit lines
        if not self.hits:
            lines.append('   Hits: 0')
        else:
            lines.append('   Hits: %s  %s  %s' % ('-'*4, '-'*5, '-'*58))
            pattern = '%13s  %5s  %56s'
            lines.append(pattern % ('#', '# HSP',
                'ID + description'.ljust(58)))
            lines.append(pattern % ('-'*4, '-'*5, '-'*58))
            for idx, hit in enumerate(self.hits):
                if idx < 30:
                    hid_line = '%s  %s' % (hit.id, hit.description)
                    if len(hid_line) > 58:
                        hid_line = hid_line[:55] + '...'
                    lines.append(pattern % (idx, str(len(hit)),
                        hid_line.ljust(58)))
                elif idx > len(self.hits) - 4:
                    hid_line = '%s  %s' % (hit.id, hit.description)
                    if len(hid_line) > 58:
                        hid_line = hid_line[:55] + '...'
                    lines.append(pattern % (idx, str(len(hit)),
                        hid_line.ljust(58)))
                elif idx == 30:
                    lines.append('%14s' % '~~~')

        return '\n'.join(lines)
Exemple #7
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 def pair_as_kwarg_string(key, val):
     if isinstance(val, basestring):
         return "%s='%s'" % (key, _utils.trim_str(unicode(val), 60,
             u'...'))
     return "%s=%s" % (key, val)
Exemple #8
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 def __str__(self):
     if self.name:
         return _utils.trim_str(self.name, 40, '...')
     return self.__class__.__name__
Exemple #9
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 def pair_as_kwarg_string(key, val):
     if isinstance(val, basestring):
         return "%s='%s'" % (key,
                             _utils.trim_str(unicode(val), 60, u'...'))
     return "%s=%s" % (key, val)
Exemple #10
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 def __str__(self):
     if self.name:
         return _utils.trim_str(self.name, 40, '...')
     return self.__class__.__name__