def prep_genbank_files(templateFile, fasta_files, annotDir,
master_source_table=None, comment=None, sequencing_tech=None,
coverage_table=None, biosample_map=None):
''' Prepare genbank submission files. Requires .fasta and .tbl files as input,
as well as numerous other metadata files for the submission. Creates a
directory full of files (.sqn in particular) that can be sent to GenBank.
'''
# get coverage map
coverage = {}
if coverage_table:
for row in util.file.read_tabfile_dict(coverage_table):
if row.get('sample') and row.get('aln2self_cov_median'):
coverage[row['sample']] = row['aln2self_cov_median']
# get biosample id map
biosample = {}
if biosample_map:
for row in util.file.read_tabfile_dict(biosample_map):
if row.get('sample') and row.get('BioSample'):
biosample[row['sample']] = row['BioSample']
# make output directory
util.file.mkdir_p(annotDir)
for fn in fasta_files:
if not fn.endswith('.fasta'):
raise Exception("fasta files must end in .fasta")
sample_base = os.path.basename(fn)[:-6]
# for each segment/chromosome in the fasta file,
# create a separate new *.fsa file
with open(fn, "r") as inf:
asm_fasta = Bio.SeqIO.parse(inf, 'fasta')
for idx, seq_obj in enumerate(asm_fasta):
sample = sample_base + "-" + str(idx+1)
# write the segment to a temp .fasta file
# in the same dir so fasta2fsa functions as expected
out_file_name = os.path.join(os.path.dirname(fn),sample+".fasta")
with open(out_file_name, "w") as out_chr_fasta:
Bio.SeqIO.write(seq_obj, out_chr_fasta, "fasta")
# make .fsa files
fasta2fsa(out_file_name, annotDir, biosample=biosample.get(sample))
# remove the .fasta file
os.unlink(out_file_name)
# make .src files
if master_source_table:
shutil.copy(master_source_table, os.path.join(annotDir, sample + '.src'))
# make .cmt files
make_structured_comment_file(os.path.join(annotDir, sample + '.cmt'),
name=sample,
coverage=coverage.get(sample),
seq_tech=sequencing_tech)
# run tbl2asn (relies on filesnames matching by prefix)
tbl2asn = tools.tbl2asn.Tbl2AsnTool()
tbl2asn.execute(templateFile, annotDir, comment=comment, per_genome_comment=True)
def prep_genbank_files(templateFile,
fasta_files,
annotDir,
master_source_table=None,
comment=None,
sequencing_tech=None,
coverage_table=None,
biosample_map=None):
''' Prepare genbank submission files. Requires .fasta and .tbl files as input,
as well as numerous other metadata files for the submission. Creates a
directory full of files (.sqn in particular) that can be sent to GenBank.
'''
# get coverage map
coverage = {}
if coverage_table:
for row in util.file.read_tabfile_dict(coverage_table):
if row.get('sample') and row.get('aln2self_cov_median'):
coverage[row['sample']] = row['aln2self_cov_median']
# get biosample id map
biosample = {}
if biosample_map:
for row in util.file.read_tabfile_dict(biosample_map):
if row.get('sample') and row.get('BioSample'):
biosample[row['sample']] = row['BioSample']
# make output directory
util.file.mkdir_p(annotDir)
for fn in fasta_files:
if not fn.endswith('.fasta'):
raise Exception("fasta files must end in .fasta")
sample = os.path.basename(fn)[:-6]
# make .fsa files
fasta2fsa(fn, annotDir, biosample=biosample.get(sample))
# make .src files
if master_source_table:
shutil.copy(master_source_table,
os.path.join(annotDir, sample + '.src'))
# make .cmt files
make_structured_comment_file(os.path.join(annotDir, sample + '.cmt'),
name=sample,
coverage=coverage.get(sample),
seq_tech=sequencing_tech)
# run tbl2asn
tbl2asn = tools.tbl2asn.Tbl2AsnTool()
tbl2asn.execute(templateFile,
annotDir,
comment=comment,
per_genome_comment=True)
def prep_genbank_files(templateFile, fasta_files, annotDir,
master_source_table=None, comment=None, sequencing_tech=None,
coverage_table=None, biosample_map=None):
''' Prepare genbank submission files. Requires .fasta and .tbl files as input,
as well as numerous other metadata files for the submission. Creates a
directory full of files (.sqn in particular) that can be sent to GenBank.
'''
# get coverage map
coverage = {}
if coverage_table:
for row in util.file.read_tabfile_dict(coverage_table):
if row.get('sample') and row.get('aln2self_cov_median'):
coverage[row['sample']] = row['aln2self_cov_median']
# get biosample id map
biosample = {}
if biosample_map:
for row in util.file.read_tabfile_dict(biosample_map):
if row.get('sample') and row.get('BioSample'):
biosample[row['sample']] = row['BioSample']
# make output directory
util.file.mkdir_p(annotDir)
for fn in fasta_files:
if not fn.endswith('.fasta'):
raise Exception("fasta files must end in .fasta")
sample = os.path.basename(fn)[:-6]
# make .fsa files
fasta2fsa(fn, annotDir, biosample=biosample.get(sample))
# make .src files
if master_source_table:
shutil.copy(master_source_table, os.path.join(annotDir, sample + '.src'))
# make .cmt files
make_structured_comment_file(os.path.join(annotDir, sample + '.cmt'),
name=sample,
coverage=coverage.get(sample),
seq_tech=sequencing_tech)
# run tbl2asn
tbl2asn = tools.tbl2asn.Tbl2AsnTool()
tbl2asn.execute(templateFile, annotDir, comment=comment, per_genome_comment=True)