def parse_args(args):
op = ArgumentParser(description='Find groups of orthologous genes.')
#op.add_argument(dest='directory')
op.add_argument('-o', '--out', '--dir', dest='out', required=True)
op.add_argument('-g', '--gbs', '--annotations', dest='annotations')
op.add_argument('-p', '--proteins', '--proteomes', dest='proteomes')
op.add_argument('--no-download', dest='download_anno', action='store_false', default=True)
op.add_argument('-s', '--species', '--species-list', dest='species_list')
op.add_argument('-i', '--ids', '--ids-list', dest='ids_list')
op.add_argument('--prot-id-field', dest='prot_id_field', default=1)
op.usage = '''Finding orthogroups for a list of annotations / proteomes / ref ids / species.
Test runs:
python scenario_1.py --ids test_input/ids.txt -o test_ids
python scenario_1.py --proteomes test_input/proteins -o test_proteomes
Usage: %s [-p <proteomes dir>] [-a <.gb files dir>] [-i <gb ids file>] [-s <strain names file>]
[-o <dir>] [--jobs 30] [--start-from <step num>]
-o Output directory.
-g Directory with .gb files for references with annotations.
-p Directory with fasta (or faa, fa) files of protein sequences. If they
are named by their reference ids (i.e. NC_005816.1.fasta), annotations
will be downloaded from NCBI.
-i File with reference ids (will be fetched from NCBI).
-s File with a list of organism names as in Genbank.
--prot-id-field
When specifying proteomes, use this fasta id field number
to retrieve protein ids (default if 1, like >NC_005816.1|NP_995567.1 ...).
''' % basename(__file__)
#-a --annotations-dir Directory with .gb files.
#-p --proteomes-dir Directory with fasta files of proteomes.
#-i --ids-list File with reference ids (will be fetched from Genbank).
#-s --species-list File with a list of organism names as in Genbank.
# For example, "Salmonella enterica subsp. enterica serovar Typhi str. P-stx-12".
#'''
#indent = ' ' * len('usage: ' + basename(__file__) + ' ')
#op.usage = basename(__file__) + ' [--annotations-dir DIR]\n' + \
# indent + '[--proteomes-dir DIR]\n' + \
# indent + '[--ids-file FILE]\n' + \
# indent + '[--species-file FILE]\n'
add_common_arguments(op)
p = op.parse_args(args)
check_common_args(p)
if not p.out:
arg_parse_error('Specify output directory with -o.')
if isfile(expanduser(p.out)):
arg_parse_error('%s is a file' % p.out)
p.out = abspath(expanduser(p.out))
if not isdir(p.out):
makedirs(p.out)
if p.species_list:
check_file(expanduser(p.species_list))
p.species_list = abspath(expanduser(p.species_list))
if p.ids_list:
check_file(expanduser(p.ids_list))
p.ids_list = abspath(expanduser(p.ids_list))
if p.proteomes:
check_dir(expanduser(p.proteomes))
p.proteomes = abspath(expanduser(p.proteomes))
if p.annotations:
check_dir(expanduser(p.annotations))
p.annotations = abspath(expanduser(p.annotations))
#if p.species_list or p.ids_list:
# if not isdir(p.out):
# mkdir(p.out)
#else:
# if not p.directory:
# arg_parse_error('Directory or file must be specified.')
# check_dir(p.directory)
return p
def parse_args(args):
import argparse
op = argparse.ArgumentParser(description='Find groups of orthologous genes.')
#op.add_argument(dest='directory', required=False)
op.add_argument('-s1o', dest='directory', required=True)
op.add_argument('-s2o', '-o', dest='out_dir', required=False)
op.add_argument('-a', '--assemblies', dest='assemblies')
op.add_argument('-g', '--annotations', '--gbs', dest='annotations')
op.add_argument('-p', '--proteomes', '--proteins', dest='proteomes')
op.add_argument('-i', '--ids', '--ids-list', dest='ids_list')
op.add_argument('--prot-id-field', dest='prot_id_field', default=1)
op.add_argument('--skip-blast-singletones', dest='blast_singletones',
action='store_false', default=True)
op.add_argument('--blastdb', '--blast-db', dest='blastdb')
#-o: Output directory (if not specified, the input directory will be used).
op.usage = '''Extends an orthogroup database and orthogroups files.
First argument is a path to existed Scenario 1 output.
Test runs:
python scenario_2.py -s1o test_ids -s2o test_ids_new_ids --ids test_input/new_ids.txt
python scenario_2.py -s1o test_proteomes -s2o test_prots_new_prots --proteomes test_input/new_proteins
Usage: %s -s1o <scenario_1 result dir> -s2o <new output dir> [-a <assembies dir>] [-p <proteomes dir]
[-a <.gb files dir>] [-i <gb ids file>] [-s <strain names file>]
[--jobs 30] [--start-from <step num>]
[--blast-singletones] [--blast-db <path>]
-s1o Path to existed Scenario 1 output.
-s2o Output directory (optional, if ommited, the input directory will be used).
-a --assemblies: Directory with assemblies in fasta format.
-g Directory with .gb files for references with annotations.
-p Directory with fasta (or faa, fa) files of protein sequences. If they
are named by their reference ids (i.e. NC_005816.1.fasta), annotations
will be downloaded from NCBI.
-i File with reference ids (will be fetched from NCBI).
-s File with a list of organism names as in Genbank.
--prot-id-field
When specifying proteomes, use this fasta id field number
to retrieve protein ids (default if 1, like >NC_005816.1|NP_995567.1 ...).
--blast-singletones
Search newly added proteins agains NCBI database, if they did not fit
any group with known proteins.
--blastdb
Local BLAST database path. If not set, "blastdb" value in config.txt will be used.
If it was not set either, remote NCBI will be used.
''' % basename(__file__)
#indent = ' ' * len('usage: ' + basename(__file__) + ' ')
#op.usage = basename(__file__) + ' [--existing-blast-results TSV]\n' + \
# indent + '[--existing_proteomes DIR]\n' + \
# indent + '[--assembly FASTA]\n' + \
# indent + '[--genes GFF]\n' + \
# indent + '[--proteome FASTA]\n'
add_common_arguments(op)
p = op.parse_args(args)
check_common_args(p)
if p.assemblies:
check_dir(expanduser(p.assemblies))
p.assemblies = abspath(expanduser(p.assemblies))
if p.proteomes:
check_dir(expanduser(p.proteomes))
p.proteomes = abspath(expanduser(p.proteomes))
if p.ids_list:
check_file(expanduser(p.ids_list))
p.ids_list = abspath(expanduser(p.ids_list))
if p.annotations:
check_dir(expanduser(p.annotations))
p.annotations = abspath(expanduser(p.annotations))
if p.blastdb:
p.blastdb = abspath(expanduser(p.blastdb))
if not isdir(expanduser(p.directory)):
arg_parse_error('Directory %s does not exist.' % p.directory)
p.directory = abspath(expanduser(p.directory))
if not p.out_dir:
p.out_dir = p.directory
#arg_parse_error('Specify output directory with -o.')
if isfile(expanduser(p.out_dir)):
arg_parse_error('%s is a file' % p.out_dir)
p.out_dir = abspath(expanduser(p.out_dir))
return p
def parse_args(args):
op = ArgumentParser(description='Find groups of orthologous genes.')
#op.add_argument(dest='directory')
op.add_argument('-o', '--out', '--dir', dest='out', required=True)
op.add_argument('-g', '--gbs', '--annotations', dest='annotations')
op.add_argument('-p', '--proteins', '--proteomes', dest='proteomes')
op.add_argument('--no-download',
dest='download_anno',
action='store_false',
default=True)
op.add_argument('-s', '--species', '--species-list', dest='species_list')
op.add_argument('-i', '--ids', '--ids-list', dest='ids_list')
op.add_argument('--prot-id-field', dest='prot_id_field', default=1)
op.usage = '''Finding orthogroups for a list of annotations / proteomes / ref ids / species.
Test runs:
python scenario_1.py --ids test_input/ids.txt -o test_ids
python scenario_1.py --proteomes test_input/proteins -o test_proteomes
Usage: %s [-p <proteomes dir>] [-a <.gb files dir>] [-i <gb ids file>] [-s <strain names file>]
[-o <dir>] [--jobs 30] [--start-from <step num>]
-o Output directory.
-g Directory with .gb files for references with annotations.
-p Directory with fasta (or faa, fa) files of protein sequences. If they
are named by their reference ids (i.e. NC_005816.1.fasta), annotations
will be downloaded from NCBI.
-i File with reference ids (will be fetched from NCBI).
-s File with a list of organism names as in Genbank.
--prot-id-field
When specifying proteomes, use this fasta id field number
to retrieve protein ids (default if 1, like >NC_005816.1|NP_995567.1 ...).
''' % basename(__file__)
#-a --annotations-dir Directory with .gb files.
#-p --proteomes-dir Directory with fasta files of proteomes.
#-i --ids-list File with reference ids (will be fetched from Genbank).
#-s --species-list File with a list of organism names as in Genbank.
# For example, "Salmonella enterica subsp. enterica serovar Typhi str. P-stx-12".
#'''
#indent = ' ' * len('usage: ' + basename(__file__) + ' ')
#op.usage = basename(__file__) + ' [--annotations-dir DIR]\n' + \
# indent + '[--proteomes-dir DIR]\n' + \
# indent + '[--ids-file FILE]\n' + \
# indent + '[--species-file FILE]\n'
add_common_arguments(op)
p = op.parse_args(args)
check_common_args(p)
if not p.out:
arg_parse_error('Specify output directory with -o.')
if isfile(expanduser(p.out)):
arg_parse_error('%s is a file' % p.out)
p.out = abspath(expanduser(p.out))
if not isdir(p.out):
makedirs(p.out)
if p.species_list:
check_file(expanduser(p.species_list))
p.species_list = abspath(expanduser(p.species_list))
if p.ids_list:
check_file(expanduser(p.ids_list))
p.ids_list = abspath(expanduser(p.ids_list))
if p.proteomes:
check_dir(expanduser(p.proteomes))
p.proteomes = abspath(expanduser(p.proteomes))
if p.annotations:
check_dir(expanduser(p.annotations))
p.annotations = abspath(expanduser(p.annotations))
#if p.species_list or p.ids_list:
# if not isdir(p.out):
# mkdir(p.out)
#else:
# if not p.directory:
# arg_parse_error('Directory or file must be specified.')
# check_dir(p.directory)
return p
def parse_args(args):
import argparse
op = argparse.ArgumentParser(
description='Find groups of orthologous genes.')
#op.add_argument(dest='directory', required=False)
op.add_argument('-s1o', dest='directory', required=True)
op.add_argument('-s2o', '-o', dest='out_dir', required=False)
op.add_argument('-a', '--assemblies', dest='assemblies')
op.add_argument('-g', '--annotations', '--gbs', dest='annotations')
op.add_argument('-p', '--proteomes', '--proteins', dest='proteomes')
op.add_argument('-i', '--ids', '--ids-list', dest='ids_list')
op.add_argument('--prot-id-field', dest='prot_id_field', default=1)
op.add_argument('--skip-blast-singletones',
dest='blast_singletones',
action='store_false',
default=True)
op.add_argument('--blastdb', '--blast-db', dest='blastdb')
#-o: Output directory (if not specified, the input directory will be used).
op.usage = '''Extends an orthogroup database and orthogroups files.
First argument is a path to existed Scenario 1 output.
Test runs:
python scenario_2.py -s1o test_ids -s2o test_ids_new_ids --ids test_input/new_ids.txt
python scenario_2.py -s1o test_proteomes -s2o test_prots_new_prots --proteomes test_input/new_proteins
Usage: %s -s1o <scenario_1 result dir> -s2o <new output dir> [-a <assembies dir>] [-p <proteomes dir]
[-a <.gb files dir>] [-i <gb ids file>] [-s <strain names file>]
[--jobs 30] [--start-from <step num>]
[--blast-singletones] [--blast-db <path>]
-s1o Path to existed Scenario 1 output.
-s2o Output directory (optional, if ommited, the input directory will be used).
-a --assemblies: Directory with assemblies in fasta format.
-g Directory with .gb files for references with annotations.
-p Directory with fasta (or faa, fa) files of protein sequences. If they
are named by their reference ids (i.e. NC_005816.1.fasta), annotations
will be downloaded from NCBI.
-i File with reference ids (will be fetched from NCBI).
-s File with a list of organism names as in Genbank.
--prot-id-field
When specifying proteomes, use this fasta id field number
to retrieve protein ids (default if 1, like >NC_005816.1|NP_995567.1 ...).
--blast-singletones
Search newly added proteins agains NCBI database, if they did not fit
any group with known proteins.
--blastdb
Local BLAST database path. If not set, "blastdb" value in config.txt will be used.
If it was not set either, remote NCBI will be used.
''' % basename(__file__)
#indent = ' ' * len('usage: ' + basename(__file__) + ' ')
#op.usage = basename(__file__) + ' [--existing-blast-results TSV]\n' + \
# indent + '[--existing_proteomes DIR]\n' + \
# indent + '[--assembly FASTA]\n' + \
# indent + '[--genes GFF]\n' + \
# indent + '[--proteome FASTA]\n'
add_common_arguments(op)
p = op.parse_args(args)
check_common_args(p)
if p.assemblies:
check_dir(expanduser(p.assemblies))
p.assemblies = abspath(expanduser(p.assemblies))
if p.proteomes:
check_dir(expanduser(p.proteomes))
p.proteomes = abspath(expanduser(p.proteomes))
if p.ids_list:
check_file(expanduser(p.ids_list))
p.ids_list = abspath(expanduser(p.ids_list))
if p.annotations:
check_dir(expanduser(p.annotations))
p.annotations = abspath(expanduser(p.annotations))
if p.blastdb:
p.blastdb = abspath(expanduser(p.blastdb))
if not isdir(expanduser(p.directory)):
arg_parse_error('Directory %s does not exist.' % p.directory)
p.directory = abspath(expanduser(p.directory))
if not p.out_dir:
p.out_dir = p.directory
#arg_parse_error('Specify output directory with -o.')
if isfile(expanduser(p.out_dir)):
arg_parse_error('%s is a file' % p.out_dir)
p.out_dir = abspath(expanduser(p.out_dir))
return p
