def phytozome(args):
"""
%prog phytozome species
Retrieve genomes and annotations from phytozome FTP. Available species
listed below. Use comma to give a list of species to download. For example:
$ %prog phytozome Athaliana,Vvinifera,Osativa,Sbicolor,Slycopersicum
"""
from jcvi.formats.gff import bed as gff_bed
from jcvi.formats.fasta import format as fasta_format
p = OptionParser(phytozome.__doc__)
p.add_option("--version", default="9.0",
help="Phytozome version [default: %default]")
p.add_option("--assembly", default=False, action="store_true",
help="Download assembly [default: %default]")
p.add_option("--format", default=False, action="store_true",
help="Format to CDS and BED for synteny inference")
opts, args = p.parse_args(args)
url = "ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v{0}/".\
format(opts.version)
valid_species = [x for x in ls_ftp(url) if "." not in x]
doc = "\n".join((phytozome.__doc__, tile(valid_species)))
p.set_usage(doc)
if len(args) != 1:
sys.exit(not p.print_help())
species, = args
if species == "all":
species = ",".join(valid_species)
species = species.split(",")
use_IDs = set()
# We have to watch out when the gene names and mRNA names mismatch, in which
# case we just extract the mRNA names
use_mRNAs = set(["Cclementina", "Creinhardtii", "Csinensis", "Fvesca",
"Lusitatissimum", "Mesculenta", "Mguttatus", "Ppersica",
"Pvirgatum", "Rcommunis", "Sitalica", "Tcacao",
"Thalophila", "Vcarteri", "Vvinifera", "Zmays"])
for s in species:
gff, fa = download_species_phytozome(s, valid_species, url,
assembly=opts.assembly)
key = "ID" if s in use_IDs else "Name"
ttype = "mRNA" if s in use_mRNAs else "gene"
if not opts.format:
continue
bedfile = s + ".bed"
cdsfile = s + ".cds"
gff_bed([gff, "--type={}".format(ttype), "--key={}".format(key),
"-o", bedfile])
fasta_format([fa, cdsfile, r"--sep=|"])
def phytozome(args):
"""
%prog phytozome species
Retrieve genomes and annotations from phytozome FTP. Available species
listed below. Use comma to give a list of species to download. For example:
$ %prog phytozome Athaliana,Vvinifera,Osativa,Sbicolor,Slycopersicum
"""
from jcvi.formats.gff import bed as gff_bed
from jcvi.formats.fasta import format as fasta_format
p = OptionParser(phytozome.__doc__)
p.add_option("--version", default="9.0",
help="Phytozome version [default: %default]")
p.add_option("--assembly", default=False, action="store_true",
help="Download assembly [default: %default]")
p.add_option("--format", default=False, action="store_true",
help="Format to CDS and BED for synteny inference")
opts, args = p.parse_args(args)
url = "ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v{0}/".\
format(opts.version)
valid_species = [x for x in ls_ftp(url) if "." not in x]
doc = "\n".join((phytozome.__doc__, tile(valid_species)))
p.set_usage(doc)
if len(args) != 1:
sys.exit(not p.print_help())
species, = args
if species == "all":
species = ",".join(valid_species)
species = species.split(",")
use_IDs = set()
# We have to watch out when the gene names and mRNA names mismatch, in which
# case we just extract the mRNA names
use_mRNAs = set(["Cclementina", "Creinhardtii", "Csinensis", "Fvesca",
"Lusitatissimum", "Mesculenta", "Mguttatus", "Ppersica",
"Pvirgatum", "Rcommunis", "Sitalica", "Tcacao",
"Thalophila", "Vcarteri", "Vvinifera", "Zmays"])
for s in species:
gff, fa = download_species_phytozome(s, valid_species, url,
assembly=opts.assembly)
key = "ID" if s in use_IDs else "Name"
ttype = "mRNA" if s in use_mRNAs else "gene"
if not opts.format:
continue
bedfile = s + ".bed"
cdsfile = s + ".cds"
gff_bed([gff, "--type={}".format(ttype), "--key={}".format(key),
"-o", bedfile])
fasta_format([fa, cdsfile, r"--sep=|"])
def phytozome(args):
"""
%prog phytozome species
Retrieve genomes and annotations from phytozome FTP. Available species
listed below. Use comma to give a list of species to download. For example:
$ %prog phytozome Athaliana,Vvinifera,Osativa,Sbicolor,Slycopersicum
"""
from jcvi.formats.gff import bed as gff_bed
from jcvi.formats.fasta import format as fasta_format
p = OptionParser(phytozome.__doc__)
p.add_option("--version",
default="9.0",
help="Phytozome version [default: %default]")
p.add_option("--assembly",
default=False,
action="store_true",
help="Download assembly [default: %default]")
p.add_option("--format",
default=False,
action="store_true",
help="Format to CDS and BED for synteny inference")
opts, args = p.parse_args(args)
url = "ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v{0}/".\
format(opts.version)
valid_species = [x for x in ls_ftp(url) if "." not in x]
doc = "\n".join((phytozome.__doc__, tile(valid_species)))
p.set_usage(doc)
if len(args) != 1:
sys.exit(not p.print_help())
species, = args
species = species.split(",")
for s in species:
gff, fa = download_species_phytozome(s,
valid_species,
url,
assembly=opts.assembly)
if not opts.format:
continue
bedfile = s + ".bed"
cdsfile = s + ".cds"
gff_bed([gff, "--phytozome", "-o", bedfile])
fasta_format([fa, cdsfile, r"--sep=|"])
def format_bed_and_cds(species, gff, cdsfa):
"""Run gff.format() and fasta.format() to generate BED and CDS files.
This prepares the input files for the MCscan synteny workflow.
https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)
Args:
species (str): Name of the species
gff (str): Path to the GFF file
fa (str): Path to the FASTA file
"""
from jcvi.formats.gff import bed as gff_bed
from jcvi.formats.fasta import format as fasta_format
# We have to watch out when the gene names and mRNA names mismatch, in which
# case we just extract the mRNA names
use_IDs = set()
use_mRNAs = set([
"Cclementina",
"Creinhardtii",
"Csinensis",
"Fvesca",
"Lusitatissimum",
"Mesculenta",
"Mguttatus",
"Ppersica",
"Pvirgatum",
"Rcommunis",
"Sitalica",
"Tcacao",
"Thalophila",
"Vcarteri",
"Vvinifera",
"Zmays",
])
key = "ID" if species in use_IDs else "Name"
ttype = "mRNA" if species in use_mRNAs else "gene"
bedfile = species + ".bed"
cdsfile = species + ".cds"
gff_bed([
gff, "--type={}".format(ttype), "--key={}".format(key), "-o", bedfile
])
fasta_format([cdsfa, cdsfile, r"--sep=|"])