def run(start_from_here=False):
return cmdline(
join(steps.orthomcl_bin_dir, 'orthomclFilterFasta.pl'),
parameters=[
new_proteomes_dir,
min_length, max_percent_stop,
new_good_proteomes,
new_bad_proteomes])
def run():
if assembly_names:
return cmdline('prodigal',
parameters=[
'-i', filtered_assemblies,
'-a', predicted_proteomes]),
#'-o', join(steps.intermediate_dir, assembly_name + '.gff')]
else:
log.info('Skipping.')
return 0
def run():
if assembly_names:
return cmdline('prodigal',
parameters=[
'-i', filtered_assemblies, '-a',
predicted_proteomes
]),
#'-o', join(steps.intermediate_dir, assembly_name + '.gff')]
else:
log.info('Skipping.')
return 0
def run(start_from_here=False):
assemblies = [
join(p.assemblies, f)
for f in listdir(p.assemblies)
if f and f[0] != '.']
if isdir(config.proteomes_dir):
assemblies = filter_dublicated_proteomes(config.proteomes_dir, assemblies)
if assemblies == []:
log.warn(all_considered_warning % config.proteomes_dir)
exit(1)
assembly_names = [
splitext(basename(asm))[0]
for asm in assemblies]
filtered_assemblies = [
join(assemblies_dir, asm_name + '.fna')
for asm_name in assembly_names]
new_proteomes = [
join(config.proteomes_dir, asm_name + '.fasta')
for asm_name in assembly_names]
if not isdir(assemblies_dir): mkdir(assemblies_dir)
log.debug(' Created assemblies_dir ' + assemblies_dir)
total_successful_filters = 0
for assembly, filtered_asm in zip(assemblies, filtered_assemblies):
if filter_assembly(assembly,
filtered_asm,
skip=(4, 7, 10, 23, 32, 38),
skip_after=51) == 0:
total_successful_filters += 1
if total_successful_filters == 0:
log.error('No correct assemblies.')
return 1
for asm, prot, asm_name in zip(
filtered_assemblies, new_proteomes, assembly_names):
res = cmdline('prodigal',
parameters=[
'-i', asm,
'-o', join(config.intermediate_dir, asm_name),
'-a', prot])()
if res != 0:
return res
log.info('')
res = adjust_proteomes(new_proteomes, config.proteomes_dir,
prot_id_field=0)
if res != 0:
return res
# Recreate new_proteomes_directory
if exists(new_proteomes_dir):
rmtree(new_proteomes_dir)
if not isdir(new_proteomes_dir):
mkdir(new_proteomes_dir)
for prot in new_proteomes:
copy(prot, join(new_proteomes_dir, basename(prot)))
return 0
def run(start_from_here=False):
return cmdline(join(steps.orthomcl_bin_dir, 'orthomclFilterFasta.pl'),
parameters=[
new_proteomes_dir, min_length, max_percent_stop,
new_good_proteomes, new_bad_proteomes
])
def run(start_from_here=False):
assemblies = [
join(p.assemblies, f) for f in listdir(p.assemblies)
if f and f[0] != '.'
]
if isdir(config.proteomes_dir):
assemblies = filter_dublicated_proteomes(
config.proteomes_dir, assemblies)
if assemblies == []:
log.warn(all_considered_warning % config.proteomes_dir)
exit(1)
assembly_names = [splitext(basename(asm))[0] for asm in assemblies]
filtered_assemblies = [
join(assemblies_dir, asm_name + '.fna')
for asm_name in assembly_names
]
new_proteomes = [
join(config.proteomes_dir, asm_name + '.fasta')
for asm_name in assembly_names
]
if not isdir(assemblies_dir): mkdir(assemblies_dir)
log.debug(' Created assemblies_dir ' + assemblies_dir)
total_successful_filters = 0
for assembly, filtered_asm in zip(assemblies, filtered_assemblies):
if filter_assembly(assembly,
filtered_asm,
skip=(4, 7, 10, 23, 32, 38),
skip_after=51) == 0:
total_successful_filters += 1
if total_successful_filters == 0:
log.error('No correct assemblies.')
return 1
for asm, prot, asm_name in zip(filtered_assemblies, new_proteomes,
assembly_names):
res = cmdline('prodigal',
parameters=[
'-i', asm, '-o',
join(config.intermediate_dir, asm_name),
'-a', prot
])()
if res != 0:
return res
log.info('')
res = adjust_proteomes(new_proteomes,
config.proteomes_dir,
prot_id_field=0)
if res != 0:
return res
# Recreate new_proteomes_directory
if exists(new_proteomes_dir):
rmtree(new_proteomes_dir)
if not isdir(new_proteomes_dir):
mkdir(new_proteomes_dir)
for prot in new_proteomes:
copy(prot, join(new_proteomes_dir, basename(prot)))
return 0