Beispiel #1
0
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)
Beispiel #2
0
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)
Beispiel #3
0
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)