def _str_hsp_header(self):
"""Print the alignment header info (PRIVATE)."""
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)
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)
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)
def _str_aln(self):
lines = []
# alignment length
aln_span = getattr_str(self, 'aln_span')
lines.append(' Fragments: 1 (%s columns)' % aln_span)
# sequences
if self.query is not None and self.hit is not None:
try:
qseq = str(self.query.seq)
except AttributeError: # query is None
qseq = '?'
try:
hseq = str(self.hit.seq)
except AttributeError: # hit is None
hseq = '?'
# similarity line
simil = ''
if 'similarity' in self.aln_annotation and \
isinstance(self.aln_annotation.get('similarity'), basestring):
simil = self.aln_annotation['similarity']
if self.aln_span <= 67:
lines.append("%10s - %s" % ('Query', qseq))
if simil:
lines.append(" %s" % simil)
lines.append("%10s - %s" % ('Hit', hseq))
else:
# adjust continuation character length, so we don't display
# the same residues twice
if self.aln_span - 66 > 3:
cont = '~' * 3
else:
cont = '~' * (self.aln_span - 66)
lines.append("%10s - %s%s%s" % ('Query',
qseq[:59], cont, qseq[-5:]))
if simil:
lines.append(" %s%s%s" %
(simil[:59], cont, simil[-5:]))
lines.append("%10s - %s%s%s" % ('Hit',
hseq[:59], cont, hseq[-5:]))
return '\n'.join(lines)
def __str__(self):
"""Return a human readable summary of the HSP object."""
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)
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)
def _str_aln(self):
lines = []
# alignment length
aln_span = getattr_str(self, "aln_span")
lines.append(" Fragments: 1 (%s columns)" % aln_span)
# sequences
if self.query is not None and self.hit is not None:
try:
qseq = str(self.query.seq)
except AttributeError: # query is None
qseq = "?"
try:
hseq = str(self.hit.seq)
except AttributeError: # hit is None
hseq = "?"
# similarity line
simil = ""
if "similarity" in self.aln_annotation and isinstance(
self.aln_annotation.get("similarity"), str
):
simil = self.aln_annotation["similarity"]
if self.aln_span <= 67:
lines.append("%10s - %s" % ("Query", qseq))
if simil:
lines.append(" %s" % simil)
lines.append("%10s - %s" % ("Hit", hseq))
else:
# adjust continuation character length, so we don't display
# the same residues twice
if self.aln_span - 66 > 3:
cont = "~" * 3
else:
cont = "~" * (self.aln_span - 66)
lines.append("%10s - %s%s%s" % ("Query", qseq[:59], cont, qseq[-5:]))
if simil:
lines.append(" %s%s%s" % (simil[:59], cont, simil[-5:]))
lines.append("%10s - %s%s%s" % ("Hit", hseq[:59], cont, hseq[-5:]))
return "\n".join(lines)
def _str_aln(self):
lines = []
# alignment length
aln_span = getattr_str(self, "aln_span")
lines.append(" Fragments: 1 (%s columns)" % aln_span)
# sequences
if self.query is not None and self.hit is not None:
try:
qseq = str(self.query.seq)
except AttributeError: # query is None
qseq = "?"
try:
hseq = str(self.hit.seq)
except AttributeError: # hit is None
hseq = "?"
# homology line
homol = ""
if "homology" in self.aln_annotation:
homol = self.aln_annotation["homology"]
if self.aln_span <= 67:
lines.append("%10s - %s" % ("Query", qseq))
if homol:
lines.append(" %s" % homol)
lines.append("%10s - %s" % ("Hit", hseq))
else:
# adjust continuation character length, so we don't display
# the same residues twice
if self.aln_span - 66 > 3:
cont = "~" * 3
else:
cont = "~" * (self.aln_span - 66)
lines.append("%10s - %s%s%s" % ("Query", qseq[:59], cont, qseq[-5:]))
if homol:
lines.append(" %s%s%s" % (homol[:59], cont, homol[-5:]))
lines.append("%10s - %s%s%s" % ("Hit", hseq[:59], cont, hseq[-5:]))
return "\n".join(lines)
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)
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)
def __str__(self):
"""Return a human readable summary of the Hit object."""
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 attributes lines
for key, value in sorted(self.attributes.items()):
lines.append(" %s: %s" % (key, value))
# set dbxrefs line
if self.dbxrefs:
lines.append("Database cross-references: " +
", ".join(self.dbxrefs))
# 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)
def __str__(self):
"""Return a human readable summary of the Hit object."""
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 attributes lines
for key, value in sorted(self.attributes.items()):
lines.append(' %s: %s' % (key, value))
# set dbxrefs line
if self.dbxrefs:
lines.append("Database cross-references: " +
", ".join(self.dbxrefs))
# 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)
def __str__(self):
lines =[]
qid_line = 'Query: %s' % self.query_id
qlength_line = 'Length: %i' % self.query_length
lines.append(qid_line)
lines.append(qlength_line)
if not self.hsps:
lines.append(' HSPs: ?')
else:
lines.append(' HSPs: %s %s %s %s %s %s %s %s %s %s' %
('-'*4, '-'*8, '-'*9, '-'*6, '-'*6, '-'*15, '-'*21, '-'*58, '-'*15, '-'*7))
pattern = '%11s %8s %9s %6s %6s %15s %21s %58s %15s %7s'
lines.append(pattern % ('#', 'E-value', 'Bit score', 'ID (%)','Span',
'Query range', 'Hit range', 'Contig', 'Contig Length', 'Strand'))
lines.append(pattern % ('-'*4, '-'*8, '-'*9, '-'*6, '-'*6, '-'*15, '-'*21, '-'*58, '-'*15, '-'*7))
for idx, hsp in enumerate(self.hsps):
# evalue
evalue = getattr_str(hsp, 'evalue', fmt='%.2g')
# bitscore
bitscore = getattr_str(hsp, 'bitscore', fmt='%.2f')
# identities
identity = getattr_str(hsp, 'identity', fmt='%4.2f')
# 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, '~]')
# contig id
contig_id = getattr_str(hsp, 'hit_id')
# contig length
contig_length = getattr_str(hsp, 'hit_length')
# strand
strand = getattr_str(hsp, 'strand')
# append the hsp row
lines.append(pattern % (str(idx), evalue, bitscore, identity, aln_span,
query_range, hit_range, contig_id, contig_length, strand))
return '\n'.join(lines)
def __str__(self):
lines = []
qid_line = 'Query: %s' % self.query_id
qlength_line = 'Length: %i' % self.query_length
lines.append(qid_line)
lines.append(qlength_line)
if not self.hsps:
lines.append(' HSPs: ?')
else:
lines.append(' HSPs: %s %s %s %s %s %s %s %s %s %s' %
('-' * 4, '-' * 8, '-' * 9, '-' * 6, '-' * 6,
'-' * 15, '-' * 21, '-' * 58, '-' * 15, '-' * 7))
pattern = '%11s %8s %9s %6s %6s %15s %21s %58s %15s %7s'
lines.append(
pattern %
('#', 'E-value', 'Bit score', 'ID (%)', 'Span', 'Query range',
'Hit range', 'Contig', 'Contig Length', 'Strand'))
lines.append(pattern %
('-' * 4, '-' * 8, '-' * 9, '-' * 6, '-' * 6,
'-' * 15, '-' * 21, '-' * 58, '-' * 15, '-' * 7))
for idx, hsp in enumerate(self.hsps):
# evalue
evalue = getattr_str(hsp, 'evalue', fmt='%.2g')
# bitscore
bitscore = getattr_str(hsp, 'bitscore', fmt='%.2f')
# identities
identity = getattr_str(hsp, 'identity', fmt='%4.2f')
# 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, '~]')
# contig id
contig_id = getattr_str(hsp, 'hit_id')
# contig length
contig_length = getattr_str(hsp, 'hit_length')
# strand
strand = getattr_str(hsp, 'strand')
# append the hsp row
lines.append(
pattern %
(str(idx), evalue, bitscore, identity, aln_span,
query_range, hit_range, contig_id, contig_length, strand))
return '\n'.join(lines)
