def processChunk( contig, regions ):
if contig == None: return
start = 0
end = contigs[contig]
regions = Intervals.combineIntervals( regions )
for xstart, xend in Intervals.complementIntervals( regions, start, end ):
locations.append( ("intergenic", "intergenic", contig, "+", xstart, xend, ".") )
def processChunk( gene_id, contig, strand, frame, regions ):
if gene_id == None: return
start = min( map( lambda x: x[0], regions ) )
end = max( map( lambda x: x[0], regions ) )
intervals = Intervals.complementIntervals( regions, start, end )
for start, end in intervals:
locations.append( (gene_id, gene_id, contig, strand, start, end, frame ) )
def processChunk(contig, regions):
if contig == None: return
start = 0
end = contigs[contig]
regions = Intervals.combineIntervals(regions)
for xstart, xend in Intervals.complementIntervals(regions, start, end):
locations.append(
("intergenic", "intergenic", contig, "+", xstart, xend, "."))
def processChunk(gene_id, contig, strand, frame, regions):
if gene_id == None: return
start = min(map(lambda x: x[0], regions))
end = max(map(lambda x: x[0], regions))
intervals = Intervals.complementIntervals(regions, start, end)
for start, end in intervals:
locations.append(
(gene_id, gene_id, contig, strand, start, end, frame))
def transform_complement(start, end, intervals_with_gff):
y = Intervals.combineIntervals([(x[0], x[1]) for x in intervals_with_gff])
return Intervals.complementIntervals(y, start, end)
def maskAlignment(mali, map_component2masks, map_component2extracts,
map_sample2reference, options):
"""mask an alignment.
If map_sample2reference is given, coordinates in references are used to
mask residues in sample.
"""
id = mali.getName()
if options.loglevel >= 5:
options.stdout.write("# multiple alignment %s before masking:\n" % id)
mali.writeToFile(sys.stdout)
def getMasks(id, map1, map_sample2reference):
if map_sample2reference and id in map_sample2reference:
xid = map_sample2reference[id]
if options.loglevel >= 1:
options.stdlog.write(
"# using mapped coordinates from %s for %s\n" % (xid, id))
else:
xid = id
if xid in map1:
return map1[xid]
else:
return []
############################################################################
## mask alignment
if map_component2masks:
masks = getMasks(id, map_component2masks, map_sample2reference)
if masks:
for start, end in masks:
if options.loglevel >= 1:
options.stdlog.write(
"# component: %s: masking region due to mask %i-%i\n" %
(id, start, end))
mali.maskColumns(range(start, min(end, mali.getWidth())))
############################################################################
## extract regions from an alignment by masking everything else
if map_component2extracts:
masks = getMasks(id, map_component2extracts, map_sample2reference)
if masks:
other_masks = Intervals.complementIntervals(
masks, 0, mali.getWidth())
for start, end in other_masks:
if options.loglevel >= 1:
options.stdlog.write(
"# component: %s: masking region due to extract %i-%i\n"
% (id, start, end))
mali.maskColumns(range(start, min(end, mali.getWidth())))
if options.loglevel >= 5:
options.stdout.write("# multiple alignment after masking:\n")
mali.writeToFile(sys.stdout)
if mali.getAlphabet() == "aa":
gap_chars = "Xx-"
else:
gap_chars = "XxNn-"
if options.remove_all_gaps:
width_before = mali.getNumColumns()
mali.removePattern(match_function=lambda x: x in gap_chars,
minimum_matches=mali.getNumSequences(),
search_frame=1,
delete_frame=options.remove_all_gaps)
width_after = mali.getNumColumns()
if options.loglevel >= 1:
options.stdlog.write(
"# component: %s: removed %i fully gapped/masked columns, old size=%i, new size=%i\n"
% (id, width_before - width_after, width_before, width_after))
if options.remove_any_gaps:
width_before = mali.getNumColumns()
mali.removePattern(match_function=lambda x: x in gap_chars,
minimum_matches=1,
search_frame=1,
delete_frame=options.remove_any_gaps)
width_after = mali.getNumColumns()
if options.loglevel >= 1:
options.stdlog.write(
"# component: %s: removed %i columns containing at least one gap/mask, old size=%i, new size=%i\n"
% (id, width_before - width_after, width_before, width_after))
if options.loglevel >= 5:
options.stdout.write("# multiple alignment after cleaning:\n")
mali.writeToFile(sys.stdout)
def transform_complement(start, end, intervals_with_gff):
y = Intervals.combineIntervals(
map(lambda x: (x[0], x[1]), intervals_with_gff))
return Intervals.complementIntervals(y, start, end)
def transform_complement(start, end, intervals_with_gff):
y = Intervals.combineIntervals(
map(lambda x: (x[0], x[1]), intervals_with_gff))
return Intervals.complementIntervals(y, start, end)
def transform_complement(start, end, intervals_with_gff):
y = Intervals.combineIntervals(
[(x[0], x[1]) for x in intervals_with_gff])
return Intervals.complementIntervals(y, start, end)
def maskAlignment(mali,
map_component2masks,
map_component2extracts,
map_sample2reference,
options):
"""mask an alignment.
If map_sample2reference is given, coordinates in references are used to
mask residues in sample.
"""
id = mali.getName()
if options.loglevel >= 5:
options.stdout.write("# multiple alignment %s before masking:\n" % id)
mali.writeToFile(sys.stdout)
def getMasks(id, map1, map_sample2reference):
if map_sample2reference and id in map_sample2reference:
xid = map_sample2reference[id]
if options.loglevel >= 1:
options.stdlog.write(
"# using mapped coordinates from %s for %s\n" % (xid, id))
else:
xid = id
if xid in map1:
return map1[xid]
else:
return []
##########################################################################
# mask alignment
if map_component2masks:
masks = getMasks(id, map_component2masks, map_sample2reference)
if masks:
for start, end in masks:
if options.loglevel >= 1:
options.stdlog.write(
"# component: %s: masking region due to mask %i-%i\n" % (id, start, end))
mali.maskColumns(range(start, min(end, mali.getWidth())))
##########################################################################
# extract regions from an alignment by masking everything else
if map_component2extracts:
masks = getMasks(id, map_component2extracts, map_sample2reference)
if masks:
other_masks = Intervals.complementIntervals(
masks, 0, mali.getWidth())
for start, end in other_masks:
if options.loglevel >= 1:
options.stdlog.write(
"# component: %s: masking region due to extract %i-%i\n" % (id, start, end))
mali.maskColumns(range(start, min(end, mali.getWidth())))
if options.loglevel >= 5:
options.stdout.write("# multiple alignment after masking:\n")
mali.writeToFile(sys.stdout)
if mali.getAlphabet() == "aa":
gap_chars = "Xx-"
else:
gap_chars = "XxNn-"
if options.remove_all_gaps:
width_before = mali.getNumColumns()
mali.removePattern(
match_function=lambda x: x in gap_chars,
minimum_matches=mali.getNumSequences(),
search_frame=1,
delete_frame=options.remove_all_gaps)
width_after = mali.getNumColumns()
if options.loglevel >= 1:
options.stdlog.write("# component: %s: removed %i fully gapped/masked columns, old size=%i, new size=%i\n" %
(id, width_before - width_after, width_before, width_after))
if options.remove_any_gaps:
width_before = mali.getNumColumns()
mali.removePattern(
match_function=lambda x: x in gap_chars,
minimum_matches=1,
search_frame=1,
delete_frame=options.remove_any_gaps)
width_after = mali.getNumColumns()
if options.loglevel >= 1:
options.stdlog.write("# component: %s: removed %i columns containing at least one gap/mask, old size=%i, new size=%i\n" %
(id, width_before - width_after, width_before, width_after))
if options.loglevel >= 5:
options.stdout.write("# multiple alignment after cleaning:\n")
mali.writeToFile(sys.stdout)
