def main(arguments=None):
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument(
'-V', '--version', action='version', version='alnvu {}'.format(__version__))
parser.add_argument(
"infile", type=argparse.FileType('r'), nargs='?',
default=sys.stdin,
help="Input file in fasta format (reads stdin if missing)")
parser.add_argument(
"-o", "--outfile", metavar='FILE', type=argparse.FileType('w'),
default=sys.stdout,
help="""output file for text (stdout by default, use -q/--quiet to suppress)""")
parser.add_argument(
"-q", "--quiet", dest="quiet", action='store_true', default=False,
help="Suppress output of alignment to screen.")
parser.add_argument(
"--empty-ok", action='store_true', default=False,
help="Exit with zero status if infile contains no sequences")
# layout
layout_options = parser.add_argument_group('Layout (applies to text and pdf)')
layout_options.add_argument(
"-w", "--width", dest="ncol", metavar="NUMBER", type=int, default=115,
help="""Width of sequence to display in each block 'in
characters [%(default)s]""")
layout_options.add_argument(
"-L", "--lines-per-block", dest="nrow", metavar="NUMBER", type=int, default=75,
help="Sequences (lines) per block. [%(default)s]")
# columns
column_options = parser.add_argument_group('Column selection')
column_options.add_argument(
"-x", "--exclude-invariant",
action='store_true', default=False,
help="""Show only columns with at least N non-consensus bases
(set N using '-a/--min-subs')""")
column_options.add_argument(
"-g", "--include-gapcols",
action='store_true', default=False,
help="Show columns containing only gap characters.")
column_options.add_argument(
"-r", "--range", dest="rawrange", metavar='INTERVAL',
help="Range of columns to display (eg '-r start,stop')")
column_options.add_argument(
"-R", "--trim-to", metavar='SEQUENCE',
help="""Trim alignment to the extent of this sequence
identified by name or 1-based index (use
`-i/--number-sequences` to display line numbers). """)
column_options.add_argument(
"-s", "--min-subs", dest="min_subs", metavar="NUMBER", type=int, default=1,
help="""Minimum NUMBER of substitutions required to define a
position as variable. [%(default)s]""")
# consensus
consensus_options = parser.add_argument_group(
'Consensus display and sequence appearance')
consensus_options.add_argument(
"-c", "--consensus", dest="add_consensus", action='store_true', default=False,
help="Show the consensus sequence [%(default)s]")
consensus_options.add_argument(
"-d", "--compare-to", dest="compare_to", metavar='SEQUENCE',
help="""Identify the reference sequence by name or 1-based
index (use `-i/--number-sequences` to display line
numbers). Nucleotide positions identical to the reference will
be replaced with `--simchar`. The default behavior is to use
the consensus sequence as a reference.""")
consensus_options.add_argument(
"-D", "--no-comparison", action='store_false', dest='compare',
default=True,
help='Show all bases (ie, suppress comparsion with the reference sequence).')
consensus_options.add_argument(
"-G", "--ignore-gaps", dest="include_gaps", action="store_false",
default=True, help='Ignore gaps in the calculation of a consensus.')
consensus_options.add_argument(
"-C", "--simchar", metavar='CHARACTER', default=None,
help="""Character representing a base identical to the
consensus. The default behavior is to identify differences
using lower case.""")
consensus_options.add_argument(
'-t', '--reference-top', action='store_true',
default=False,
help="Place the reference/consensus sequence on the top of the alignment")
# annotation
name_options = parser.add_argument_group('Sequence annotation')
name_options.add_argument(
"-i", "--number-sequences", dest="seqnums", action='store_true', default=False,
help="Show sequence number to left of name.")
name_options.add_argument(
"-n", "--name-max", dest="name_max", metavar="NUMBER", type=int, default=35,
help="""Maximum width of sequence name in characters [%(default)s]""")
name_options.add_argument(
"-N", "--name-split", dest="name_split", metavar="CHARACTER",
help="""Specify a character delimiting sequence names. By
default, the name of each sequence is the first
whitespace-delimited word. '--name-split=none' causes the
entire line after the '>' to be displayed.""")
name_options.add_argument(
"-S", "--sort-by-name", type=argparse.FileType('r'), metavar='FILE',
help="""File containing sequence names defining the sort-order
of the sequences in the alignment.""")
name_options.add_argument(
"--rename-from-file", type=argparse.FileType('r'), metavar='FILE',
help="""headerless csv file with columns 'old-name','new-name'
to use for renaming the input sequences. If provided, renaming
occurs immediately after reading the input sequences.""")
if util.treeorder:
name_options.add_argument(
"-T", "--sort-by-tree", type=argparse.FileType('r'), metavar='FILE',
help="""File containing a newick-format tree defining the
sort-order of the sequences in the alignment (requires
biopython).""")
# for html output
html_options = parser.add_argument_group('HTML output')
html_options.add_argument(
'--html', metavar='FILE', help="HTML output file")
if html.default_brewer:
html_options.add_argument(
'--annotation-file', type=argparse.FileType('r'), metavar='FILE',
help="""csv file with headers ("group", "col") specifying
columns that should be colored in the html output. Each row
identifies a label (group) and a corresponding column
(1-indexed). Requires installation of the 'colorbrewer'
package, which is python2 only.""")
html_options.add_argument(
'--table-only', action='store_true', default=False,
help="""Don't produce a full html document, just the
alignment table and style tags. Handy if you'd like to
include in another document.""")
html_options.add_argument(
'--color', action='store_true', default=False,
help='color nucleotides in output using default palette')
html_options.add_argument(
'--char-colors', type=argparse.FileType('r'), metavar='FILE',
help="""csv file containing mapping of characters to
HTML-defined colors (implies --color).""")
html_options.add_argument(
"--fontsize-html", metavar="NUMBER", default=7, type=int,
help="Font size for html output [%(default)s]")
# pdf options (only if reportlab is installed)
if pdf.print_pdf:
pdf_options = parser.add_argument_group(
'PDF output',
'These options require reportlab.')
pdf_options.add_argument(
'--pdf', metavar='FILE', help="PDF output file")
pdf_options.add_argument(
"-O", "--orientation", default='portrait',
choices=('portrait', 'landscape'),
help="Set page orientation; choose from portrait, landscape [%(default)s]")
pdf_options.add_argument(
"-b", "--blocks-per-page",
metavar="NUMBER", type=int, default=1,
help="Number of aligned blocks of sequence per page [%(default)s]")
pdf_options.add_argument(
"--fontsize-pdf", metavar="NUMBER", default=7, type=int,
help="Font size for pdf output [%(default)s]")
args = parser.parse_args(arguments or sys.argv[1:])
# Ignore SIGPIPE, for head support
exit_on_sigpipe()
exit_on_sigint()
seqs = util.readfasta(args.infile, name_split=args.name_split)
if not seqs:
if not args.quiet:
print('No sequences in input')
return 0 if args.empty_ok else 1
if args.sort_by_name:
sortdict = dict((line.strip(), i)
for i, line in enumerate(args.sort_by_name))
elif getattr(args, 'sort_by_tree', None):
names = util.treeorder(args.sort_by_tree)
sortdict = dict((line.strip(), i) for i, line in enumerate(names))
else:
sortdict = {}
if sortdict:
seqs = iter(sorted(seqs, key=lambda seq: (sortdict.get(seq.name), seq.name)))
if args.rename_from_file:
namedict = dict(row for row in csv.reader(args.rename_from_file))
seqs = (util.Seq(name=namedict.get(seq.name, seq.name), seq=seq.seq)
for seq in seqs)
formatted_seqs, vnumstrs, mask = util.reformat(
seqs,
add_consensus=args.add_consensus,
compare=args.compare,
compare_to=args.compare_to,
exclude_gapcols=not args.include_gapcols,
exclude_invariant=args.exclude_invariant,
min_subs=args.min_subs,
simchar=args.simchar,
count_gaps=args.include_gaps,
seqrange=get_range(args.rawrange) if args.rawrange else None,
trim_to=args.trim_to,
reference_top=args.reference_top)
if args.html:
if html.default_brewer and args.annotation_file:
annotations = html.AnnotationSet.from_mapping_file(
args.annotation_file, mask)
else:
annotations = None
if args.char_colors:
char_colors = html.parse_character_color_file(args.char_colors)
elif args.color:
with open(package_data('na_colors.csv')) as f:
char_colors = html.parse_character_color_file(f)
else:
char_colors = None
html.print_html(formatted_seqs, vnumstrs, mask,
outfile=args.html,
annotations=annotations,
fontsize=args.fontsize_html,
seqnums=args.seqnums,
charcolors=char_colors,
tableonly=args.table_only)
all_numstrs = args.exclude_invariant or not args.include_gapcols
pages = util.pagify(formatted_seqs, vnumstrs,
nrow=args.nrow,
ncol=args.ncol,
name_min=10,
name_max=args.name_max,
seqnums=args.seqnums,
all_numstrs=all_numstrs)
if not args.quiet:
for page in pages:
for line in page:
args.outfile.write(line.rstrip() + '\n')
args.outfile.write('\n')
if args.pdf:
pdf.print_pdf(
pages,
outfile=args.pdf,
fontsize=args.fontsize_pdf,
orientation=args.orientation,
blocks_per_page=args.blocks_per_page
)
for name, arg in args.__dict__.items():
if hasattr(arg, 'close') and arg not in {sys.stdin, sys.stdout}:
arg.close()
def test03(self):
seqlist, vnumstrs, mask = util.reformat(self.seqs, compare_to='H59735')
render(seqlist, vnumstrs)
def test04(self):
seqlist, vnumstrs, mask = util.reformat(self.seqs, simchar=' ')
render(seqlist, vnumstrs)
def test01(self):
seqlist, vnumstrs, mask = util.reformat(self.seqs)
render(seqlist, vnumstrs)
def test02(self):
seqlist, vnumstrs, mask = util.reformat(self.seqs, compare=False)
render(seqlist, vnumstrs)
def test06(self):
seqlist, vnumstrs, mask = util.reformat(self.seqs,
exclude_invariant=True)
render(seqlist, vnumstrs)
def test06(self):
seqlist, vnumstrs, mask = util.reformat(self.seqs, exclude_invariant=True)
render(seqlist, vnumstrs)
def test05(self):
seqlist, vnumstrs, mask = util.reformat(self.seqs, simchar='')
render(seqlist, vnumstrs)
def test03(self):
seqlist, vnumstrs, mask = util.reformat(self.seqs, compare_to='59735')
render(seqlist, vnumstrs)
def test02(self):
seqlist, vnumstrs, mask = util.reformat(self.seqs, compare=False)
render(seqlist, vnumstrs)
def test01(self):
seqlist, vnumstrs, mask = util.reformat(self.seqs)
render(seqlist, vnumstrs)
def main(arguments=None):
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument(
'-V', '--version', action='version', version='alnvu {}'.format(__version__))
parser.add_argument(
"infile", type=argparse.FileType('r'), nargs='?',
default=sys.stdin,
help="Input file in fasta format (reads stdin if missing)")
parser.add_argument(
"-o", "--outfile", metavar='FILE', type=argparse.FileType('w'),
default=sys.stdout,
help="""output file for text (stdout by default, use -q/--quiet to suppress)""")
parser.add_argument(
"-q", "--quiet", dest="quiet", action='store_true', default=False,
help="Suppress output of alignment to screen.")
parser.add_argument(
"--empty-ok", action='store_true', default=False,
help="Exit with zero status if infile contains no sequences")
# layout
layout_options = parser.add_argument_group('Layout (applies to text and pdf)')
layout_options.add_argument(
"-w", "--width", dest="ncol", metavar="NUMBER", type=int, default=115,
help="""Width of sequence to display in each block 'in
characters [%(default)s]""")
layout_options.add_argument(
"-L", "--lines-per-block", dest="nrow", metavar="NUMBER", type=int, default=75,
help="Sequences (lines) per block. [%(default)s]")
# columns
column_options = parser.add_argument_group('Column selection')
column_options.add_argument(
"-x", "--exclude-invariant",
action='store_true', default=False,
help="""Show only columns with at least N non-consensus bases
(set N using '-a/--min-subs')""")
column_options.add_argument(
"-g", "--include-gapcols",
action='store_true', default=False,
help="Show columns containing only gap characters.")
column_options.add_argument(
"-r", "--range", dest="rawrange", metavar='INTERVAL',
help="Range of columns to display (eg '-r start,stop')")
column_options.add_argument(
"-R", "--trim-to", metavar='SEQUENCE',
help="""Trim alignment to the extent of this sequence
identified by name or 1-based index (use
`-i/--number-sequences` to display line numbers). """)
column_options.add_argument(
"-s", "--min-subs", dest="min_subs", metavar="NUMBER", type=int, default=1,
help="""Minimum NUMBER of substitutions required to define a
position as variable. [%(default)s]""")
# consensus
consensus_options = parser.add_argument_group(
'Consensus display and sequence appearance')
consensus_options.add_argument(
"-c", "--consensus", dest="add_consensus", action='store_true', default=False,
help="Show the consensus sequence [%(default)s]")
consensus_options.add_argument(
"-d", "--compare-to", dest="compare_to", metavar='SEQUENCE',
help="""Identify the reference sequence by name or 1-based
index (use `-i/--number-sequences` to display line
numbers). Nucleotide positions identical to the reference will
be replaced with `--simchar`. The default behavior is to use
the consensus sequence as a reference.""")
consensus_options.add_argument(
"-D", "--no-comparison", action='store_false', dest='compare',
default=True,
help='Show all bases (ie, suppress comparsion with the reference sequence).')
consensus_options.add_argument(
"-G", "--ignore-gaps", dest="include_gaps", action="store_false",
default=True, help='Ignore gaps in the calculation of a consensus.')
consensus_options.add_argument(
"-C", "--simchar", metavar='CHARACTER', default=None,
help="""Character representing a base identical to the
consensus. The default behavior is to identify differences
using lower case.""")
consensus_options.add_argument(
'-t', '--reference-top', action='store_true',
default=False,
help="Place the reference/consensus sequence on the top of the alignment")
# annotation
name_options = parser.add_argument_group('Sequence annotation')
name_options.add_argument(
"-i", "--number-sequences", dest="seqnums", action='store_true', default=False,
help="Show sequence number to left of name.")
name_options.add_argument(
"-n", "--name-max", dest="name_max", metavar="NUMBER", type=int, default=35,
help="""Maximum width of sequence name in characters [%(default)s]""")
name_options.add_argument(
"-N", "--name-split", dest="name_split", metavar="CHARACTER",
help="""Specify a character delimiting sequence names. By
default, the name of each sequence is the first
whitespace-delimited word. '--name-split=none' causes the
entire line after the '>' to be displayed.""")
name_options.add_argument(
"-S", "--sort-by-name", type=argparse.FileType('r'), metavar='FILE',
help="""File containing sequence names defining the sort-order
of the sequences in the alignment.""")
name_options.add_argument(
"--rename-from-file", type=argparse.FileType('r'), metavar='FILE',
help="""headerless csv file with columns 'old-name','new-name'
to use for renaming the input sequences. If provided, renaming
occurs immediately after reading the input sequences.""")
if util.treeorder:
name_options.add_argument(
"-T", "--sort-by-tree", type=argparse.FileType('r'), metavar='FILE',
help="""File containing a newick-format tree defining the
sort-order of the sequences in the alignment (requires
biopython).""")
# for html output
html_options = parser.add_argument_group('HTML output')
html_options.add_argument(
'--html', metavar='FILE', help="HTML output file")
if html.default_brewer:
html_options.add_argument(
'--annotation-file', type=argparse.FileType('r'), metavar='FILE',
help="""csv file with headers ("group", "col") specifying
columns that should be colored in the html output. Each row
identifies a label (group) and a corresponding column
(1-indexed). Requires installation of the 'colorbrewer'
package, which is python2 only.""")
html_options.add_argument(
'--table-only', action='store_true', default=False,
help="""Don't produce a full html document, just the
alignment table and style tags. Handy if you'd like to
include in another document.""")
html_options.add_argument(
'--color', action='store_true', default=False,
help='color nucleotides in output using default palette')
html_options.add_argument(
'--char-colors', type=argparse.FileType('r'), metavar='FILE',
help="""csv file containing mapping of characters to
HTML-defined colors (implies --color).""")
html_options.add_argument(
"--fontsize-html", metavar="NUMBER", default=7, type=int,
help="Font size for html output [%(default)s]")
# pdf options (only if reportlab is installed)
if pdf.print_pdf:
pdf_options = parser.add_argument_group(
'PDF output',
'These options require reportlab.')
pdf_options.add_argument(
'--pdf', metavar='FILE', help="PDF output file")
pdf_options.add_argument(
"-O", "--orientation", default='portrait',
choices=('portrait', 'landscape'),
help="Set page orientation; choose from portrait, landscape [%(default)s]")
pdf_options.add_argument(
"-b", "--blocks-per-page",
metavar="NUMBER", type=int, default=1,
help="Number of aligned blocks of sequence per page [%(default)s]")
pdf_options.add_argument(
"--fontsize-pdf", metavar="NUMBER", default=7, type=int,
help="Font size for pdf output [%(default)s]")
args = parser.parse_args(arguments or sys.argv[1:])
# Ignore SIGPIPE, for head support
exit_on_sigpipe()
exit_on_sigint()
seqs = util.readfasta(args.infile, name_split=args.name_split)
if not seqs:
if not args.quiet:
print('No sequences in input')
return 0 if args.empty_ok else 1
if args.rename_from_file:
namedict = dict(row for row in csv.reader(args.rename_from_file))
seqs = (util.Seq(name=namedict.get(seq.name, seq.name), seq=seq.seq)
for seq in seqs)
if args.sort_by_name:
sortdict = dict((line.strip(), i)
for i, line in enumerate(args.sort_by_name))
elif getattr(args, 'sort_by_tree', None):
names = util.treeorder(args.sort_by_tree)
sortdict = dict((line.strip(), i) for i, line in enumerate(names))
else:
sortdict = {}
if sortdict:
seqs.sort(key=lambda seq: (sortdict.get(seq.name), seq.name))
formatted_seqs, vnumstrs, mask = util.reformat(
seqs,
add_consensus=args.add_consensus,
compare=args.compare,
compare_to=args.compare_to,
exclude_gapcols=not args.include_gapcols,
exclude_invariant=args.exclude_invariant,
min_subs=args.min_subs,
simchar=args.simchar,
count_gaps=args.include_gaps,
seqrange=get_range(args.rawrange) if args.rawrange else None,
trim_to=args.trim_to,
reference_top=args.reference_top)
if args.html:
if html.default_brewer and args.annotation_file:
annotations = html.AnnotationSet.from_mapping_file(
args.annotation_file, mask)
else:
annotations = None
if args.char_colors:
char_colors = html.parse_character_color_file(args.char_colors)
elif args.color:
with open(package_data('na_colors.csv')) as f:
char_colors = html.parse_character_color_file(f)
else:
char_colors = None
html.print_html(formatted_seqs, vnumstrs, mask,
outfile=args.html,
annotations=annotations,
fontsize=args.fontsize_html,
seqnums=args.seqnums,
charcolors=char_colors,
tableonly=args.table_only)
all_numstrs = args.exclude_invariant or not args.include_gapcols
pages = util.pagify(formatted_seqs, vnumstrs,
nrow=args.nrow,
ncol=args.ncol,
name_min=10,
name_max=args.name_max,
seqnums=args.seqnums,
all_numstrs=all_numstrs)
if not args.quiet:
for page in pages:
for line in page:
args.outfile.write(line + '\n')
args.outfile.write('\n')
if args.pdf:
pdf.print_pdf(
pages,
outfile=args.pdf,
fontsize=args.fontsize_pdf,
orientation=args.orientation,
blocks_per_page=args.blocks_per_page
)
for name, arg in args.__dict__.items():
if hasattr(arg, 'close') and arg not in {sys.stdin, sys.stdout}:
arg.close()
