def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(
version=
"%prog version: $Id: tree2patterns.py 2781 2009-09-10 11:33:14Z andreas $",
usage=globals()["__doc__"])
parser.add_option("-t",
"--reference-tree",
dest="reference_tree",
type="string",
help="reference tree to read.")
parser.add_option("-s",
"--sort-order",
dest="sort_order",
type="string",
help="output order of OTU.")
parser.set_defaults(
reference_tree=None,
sort_order=[],
)
(options, args) = E.Start(parser)
if not options.sort_order:
for nx in reference_tree.get_terminals():
options.sort_order.append(reference_tree.node(nx).get_data().taxon)
else:
options.sort_order = options.sort_order.split(",")
if not options.reference_tree:
raise "no reference tree defined."
nexus = TreeTools.Newick2Nexus(options.reference_tree)
reference_tree = nexus.trees[0]
if options.loglevel >= 3:
print "# reference tree:"
print reference_tree.display()
patterns = TreeTools.calculatePatternsFromTree(tree, options.sort_order)
for p in patterns:
print p
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(version="%prog version: $Id: tree2patterns.py 2781 2009-09-10 11:33:14Z andreas $",
usage=globals()["__doc__"])
parser.add_option("-t", "--reference-tree", dest="reference_tree", type="string",
help="reference tree to read.")
parser.add_option("-s", "--sort-order", dest="sort_order", type="string",
help="output order of OTU.")
parser.set_defaults(
reference_tree=None,
sort_order=[],
)
(options, args) = E.Start(parser)
if not options.sort_order:
for nx in reference_tree.get_terminals():
options.sort_order.append(reference_tree.node(nx).get_data().taxon)
else:
options.sort_order = options.sort_order.split(",")
if not options.reference_tree:
raise "no reference tree defined."
nexus = TreeTools.Newick2Nexus(options.reference_tree)
reference_tree = nexus.trees[0]
if options.loglevel >= 3:
print "# reference tree:"
print reference_tree.display()
patterns = TreeTools.calculatePatternsFromTree(tree, options.sort_order)
for p in patterns:
print p
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv == None: argv = sys.argv
parser = E.OptionParser(
version=
"%prog version: $Id: optic/count_orgs.py 1706 2007-12-11 16:46:11Z andreas $",
usage=globals()["__doc__"])
parser.add_option("-t",
"--reference-tree",
dest="reference_tree",
type="string",
help="reference tree to read.")
parser.add_option("-p",
"--filename-patterns",
dest="filename_patterns",
type="string",
help="filename with patterns to output.")
parser.add_option("-u",
"--filename-summary",
dest="filename_summary",
type="string",
help="filename with summary to output.")
parser.add_option("-f",
"--format",
dest="format",
type="choice",
choices=("map", "links", "trees"),
help="output format.")
parser.add_option("-o",
"--organisms",
dest="column2org",
type="string",
help="sorted list of organisms.")
parser.add_option(
"-s",
"--species-regex",
dest="species_regex",
type="string",
help="regular expression to extract species from identifier.")
parser.add_option(
"-g",
"--gene-regex",
dest="gene_regex",
type="string",
help="regular expression to extract gene from identifier.")
parser.set_defaults(
reference_tree=None,
format="map",
filename_patterns=None,
column2org=None,
species_regex="^([^|]+)\|",
gene_regex="^[^|]+\|[^|]+\|([^|]+)\|",
separator="|",
filename_summary=None,
)
(options, args) = E.Start(parser)
if options.reference_tree:
if options.reference_tree[0] == "(":
nexus = TreeTools.Newick2Nexus(options.reference_tree)
else:
nexus = TreeTools.Newick2Nexus(open(options.reference_tree, "r"))
reference_tree = nexus.trees[0]
if options.loglevel >= 3:
print "# reference tree:"
print reference_tree.display()
else:
reference_tree = None
clusters = {}
if options.format == "map":
for line in sys.stdin:
if line[0] == "#": continue
id, r = line[:-1].split("\t")
if r not in clusters: clusters[r] = []
clusters[r].append(id)
elif options.format == "trees":
nexus = TreeTools.Newick2Nexus(sys.stdin)
for tree in nexus.trees:
clusters[tree.name] = tree.get_taxa()
elif options.format == "links":
members = set()
id = None
for line in sys.stdin:
if line[0] == "#": continue
if line[0] == ">":
if id: clusters[id] = members
x = re.match(">cluster #(\d+)", line[:-1])
if x:
id = x.groups()[0]
else:
id = line[1:-1]
members = set()
continue
data = line[:-1].split("\t")[:2]
members.add(data[0])
members.add(data[1])
if id: clusters[id] = members
if len(clusters) == 0:
raise "empty input."
########################################################################
########################################################################
########################################################################
## sort out reference tree
########################################################################
rs = re.compile(options.species_regex)
rg = re.compile(options.gene_regex)
extract_species = lambda x: rs.search(x).groups()[0]
## prune tree to species present
species_set = set()
for cluster, members in clusters.items():
species_set = species_set.union(set(map(extract_species, members)))
if reference_tree:
TreeTools.PruneTree(reference_tree, species_set)
if options.loglevel >= 1:
options.stdlog.write("# Tree after pruning: %i taxa.\n" %
len(reference_tree.get_taxa()))
if options.column2org:
options.column2org = options.column2org.split(",")
elif reference_tree:
options.column2org = []
for nx in reference_tree.get_terminals():
options.column2org.append(reference_tree.node(nx).get_data().taxon)
else:
options.column2org = []
for x in species_set:
options.column2org.append(x)
options.org2column = {}
for x in range(len(options.column2org)):
options.org2column[options.column2org[x]] = x
if reference_tree:
reference_patterns = TreeTools.calculatePatternsFromTree(
reference_tree, options.column2org)
if options.loglevel >= 3:
print "# reference patterns:"
print reference_patterns
##############################################################################
notus = len(options.column2org)
patterns = {}
species_counts = [SpeciesCounts() for x in options.column2org]
## first genes, then transcripts
options.stdout.write(
"mali\tpattern\tpresent\tngenes\t%s\tntranscripts\t%s\n" %
("\t".join(options.column2org), "\t".join(options.column2org)))
keys = clusters.keys()
keys.sort()
for cluster in keys:
members = clusters[cluster]
count_genes = [{} for x in range(len(options.org2column))]
count_transcripts = [0] * len(options.org2column)
for m in members:
data = m.split(options.separator)
if len(data) == 4:
s, t, g, q = data
elif len(data) == 2:
s, g = data
t = g
if s not in options.org2column:
raise "unknown species %s" % s
col = options.org2column[s]
count_transcripts[col] += 1
if g not in count_genes[col]:
count_genes[col][g] = 0
count_genes[col][g] += 1
species_counts[col].mGenes.add(g)
species_counts[col].mTranscripts.add(t)
species_counts[col].mTrees.add(cluster)
ntotal_transcripts = reduce(lambda x, y: x + y, count_transcripts)
npresent_transcripts = len(filter(lambda x: x > 0, count_transcripts))
ntotal_genes = reduce(lambda x, y: x + y, map(len, count_genes))
npresent_genes = len(filter(lambda x: x > 0, map(len, count_genes)))
pattern = GetPattern(count_transcripts, notus)
if pattern not in patterns: patterns[pattern] = 0
patterns[pattern] += 1
options.stdout.write(
string.join(
(cluster, pattern, str(npresent_genes), str(ntotal_genes),
string.join(map(str, map(len, count_genes)), "\t"),
str(ntotal_transcripts),
string.join(map(str, count_transcripts), "\t")), "\t") + "\n")
#######################################################################################
#######################################################################################
#######################################################################################
## write pattern summary
#######################################################################################
xx = patterns.keys()
xx.sort()
if options.filename_patterns:
outfile = open(options.filename_patterns, "w")
else:
outfile = sys.stdout
for x in range(len(options.column2org)):
outfile.write("# %i = %s\n" % (x, options.column2org[x]))
if reference_tree:
outfile.write("pattern\tcounts\tisok\n")
else:
outfile.write("pattern\tcounts\n")
for x in xx:
if reference_tree:
if x in reference_patterns:
is_ok = "1"
else:
is_ok = "0"
outfile.write("%s\t%s\t%s\n" % (x, patterns[x], is_ok))
else:
outfile.write("%s\t%s\n" % (x, patterns[x]))
if outfile != sys.stdout: outfile.close()
#######################################################################################
#######################################################################################
#######################################################################################
## write summary counts per species
#######################################################################################
if options.filename_summary:
outfile = open(options.filename_summary, "w")
else:
outfile = sys.stdout
outfile.write("species\tntranscripts\tngenes\tntrees\n")
for species, col in options.org2column.items():
outfile.write(
"%s\t%i\t%i\t%i\n" %
(species, len(species_counts[col].mTranscripts),
len(species_counts[col].mGenes), len(species_counts[col].mTrees)))
if outfile != sys.stdout: outfile.close()
E.Stop()
def main( argv = None ):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv == None: argv = sys.argv
parser = E.OptionParser( version = "%prog version: $Id: optic/count_orgs.py 1706 2007-12-11 16:46:11Z andreas $",
usage = globals()["__doc__"])
parser.add_option("-t", "--reference-tree", dest="reference_tree", type="string",
help="reference tree to read." )
parser.add_option("-p", "--filename-patterns", dest="filename_patterns", type="string",
help="filename with patterns to output." )
parser.add_option("-u", "--filename-summary", dest="filename_summary", type="string",
help="filename with summary to output." )
parser.add_option("-f", "--format", dest="format", type="choice",
choices=("map", "links", "trees"),
help="output format." )
parser.add_option( "-o", "--organisms", dest="column2org", type="string" ,
help="sorted list of organisms.")
parser.add_option( "-s", "--species-regex", dest="species_regex", type="string" ,
help="regular expression to extract species from identifier.")
parser.add_option( "-g", "--gene-regex", dest="gene_regex", type="string" ,
help="regular expression to extract gene from identifier.")
parser.set_defaults(
reference_tree = None,
format="map",
filename_patterns=None,
column2org=None,
species_regex ="^([^|]+)\|",
gene_regex = "^[^|]+\|[^|]+\|([^|]+)\|",
separator = "|",
filename_summary = None,
)
(options, args) = E.Start( parser )
if options.reference_tree:
if options.reference_tree[0] == "(":
nexus = TreeTools.Newick2Nexus( options.reference_tree )
else:
nexus = TreeTools.Newick2Nexus( open(options.reference_tree, "r") )
reference_tree = nexus.trees[0]
if options.loglevel >= 3:
print "# reference tree:"
print reference_tree.display()
else:
reference_tree = None
clusters = {}
if options.format == "map":
for line in sys.stdin:
if line[0] == "#": continue
id, r = line[:-1].split("\t")
if r not in clusters: clusters[r] = []
clusters[r].append( id )
elif options.format == "trees":
nexus = TreeTools.Newick2Nexus( sys.stdin )
for tree in nexus.trees:
clusters[tree.name] = tree.get_taxa()
elif options.format == "links":
members = set()
id = None
for line in sys.stdin:
if line[0] == "#": continue
if line[0] == ">" :
if id: clusters[id] = members
x = re.match(">cluster #(\d+)", line[:-1] )
if x:
id = x.groups()[0]
else:
id = line[1:-1]
members = set()
continue
data = line[:-1].split("\t")[:2]
members.add( data[0] )
members.add( data[1] )
if id: clusters[id] = members
if len(clusters) == 0:
raise "empty input."
########################################################################
########################################################################
########################################################################
## sort out reference tree
########################################################################
rs = re.compile( options.species_regex )
rg = re.compile( options.gene_regex )
extract_species = lambda x: rs.search(x).groups()[0]
## prune tree to species present
species_set = set()
for cluster, members in clusters.items():
species_set = species_set.union( set(map( extract_species, members) ) )
if reference_tree:
TreeTools.PruneTree( reference_tree, species_set )
if options.loglevel >= 1:
options.stdlog.write("# Tree after pruning: %i taxa.\n" % len(reference_tree.get_taxa()))
if options.column2org:
options.column2org = options.column2org.split(",")
elif reference_tree:
options.column2org = []
for nx in reference_tree.get_terminals():
options.column2org.append( reference_tree.node(nx).get_data().taxon )
else:
options.column2org = []
for x in species_set:
options.column2org.append( x )
options.org2column = {}
for x in range(len(options.column2org)):
options.org2column[options.column2org[x]] = x
if reference_tree:
reference_patterns = TreeTools.calculatePatternsFromTree( reference_tree, options.column2org )
if options.loglevel >= 3:
print "# reference patterns:"
print reference_patterns
##############################################################################
notus = len(options.column2org)
patterns = {}
species_counts = [ SpeciesCounts() for x in options.column2org ]
## first genes, then transcripts
options.stdout.write("mali\tpattern\tpresent\tngenes\t%s\tntranscripts\t%s\n" % ("\t".join(options.column2org) , "\t".join(options.column2org) ))
keys = clusters.keys()
keys.sort()
for cluster in keys:
members = clusters[cluster]
count_genes = [ {} for x in range(len(options.org2column)) ]
count_transcripts = [0] * len(options.org2column)
for m in members:
data = m.split(options.separator)
if len(data) == 4:
s, t, g, q = data
elif len(data) == 2:
s, g = data
t = g
if s not in options.org2column:
raise "unknown species %s" % s
col = options.org2column[s]
count_transcripts[col] += 1
if g not in count_genes[col]:
count_genes[col][g] = 0
count_genes[col][g] += 1
species_counts[col].mGenes.add( g )
species_counts[col].mTranscripts.add( t )
species_counts[col].mTrees.add( cluster )
ntotal_transcripts = reduce( lambda x,y: x+y, count_transcripts)
npresent_transcripts = len(filter( lambda x: x > 0, count_transcripts))
ntotal_genes = reduce( lambda x,y: x+y, map(len, count_genes))
npresent_genes = len(filter( lambda x: x > 0, map(len,count_genes)))
pattern = GetPattern( count_transcripts, notus )
if pattern not in patterns: patterns[pattern] = 0
patterns[pattern] += 1
options.stdout.write( string.join( (cluster, pattern, str(npresent_genes),
str(ntotal_genes),
string.join( map(str, map(len, count_genes)), "\t"),
str(ntotal_transcripts),
string.join( map(str, count_transcripts), "\t")), "\t") + "\n")
#######################################################################################
#######################################################################################
#######################################################################################
## write pattern summary
#######################################################################################
xx = patterns.keys()
xx.sort()
if options.filename_patterns:
outfile = open(options.filename_patterns, "w")
else:
outfile = sys.stdout
for x in range(len(options.column2org)):
outfile.write("# %i = %s\n" % (x, options.column2org[x]))
if reference_tree:
outfile.write("pattern\tcounts\tisok\n")
else:
outfile.write("pattern\tcounts\n")
for x in xx:
if reference_tree:
if x in reference_patterns:
is_ok = "1"
else:
is_ok = "0"
outfile.write( "%s\t%s\t%s\n" % (x, patterns[x], is_ok) )
else:
outfile.write( "%s\t%s\n" % (x, patterns[x]) )
if outfile != sys.stdout: outfile.close()
#######################################################################################
#######################################################################################
#######################################################################################
## write summary counts per species
#######################################################################################
if options.filename_summary:
outfile = open(options.filename_summary, "w")
else:
outfile = sys.stdout
outfile.write("species\tntranscripts\tngenes\tntrees\n")
for species, col in options.org2column.items():
outfile.write("%s\t%i\t%i\t%i\n" % ( species,
len(species_counts[col].mTranscripts),
len(species_counts[col].mGenes),
len(species_counts[col].mTrees) ))
if outfile != sys.stdout: outfile.close()
E.Stop()
sort_order = [],
)
(options, args) = E.Start( parser )
if not options.sort_order:
for nx in reference_tree.get_terminals():
options.sort_order.append( reference_tree.node(nx).get_data().taxon )
else:
options.sort_order = options.sort_order.split(",")
if not options.reference_tree:
raise "no reference tree defined."
nexus = TreeTools.Newick2Nexus( options.reference_tree )
reference_tree = nexus.trees[0]
if options.loglevel >= 3:
print "# reference tree:"
print reference_tree.display()
patterns = TreeTools.calculatePatternsFromTree( tree, options.sort_order )
for p in patterns:
print p
E.Stop()
