Python SeqIO.write方法代碼示例

# 需要導入模塊: from Bio import SeqIO [as 別名]
# 或者: from Bio.SeqIO import write [as 別名]
def model_from_bam(args):
    """Main function for the `iss model` submodule

    This submodule write all variables necessary for building an ErrorModel
    to args.output + .npz

    Args:
        args (object): the command-line arguments from argparse
    """
    logger = logging.getLogger(__name__)
    logger.debug('iss version %s' % __version__)
    logger.debug('Using verbose logger')

    try:  # try to import bam module and write model data to file
        logger.info('Starting iss model')
        from iss import bam
    except ImportError as e:
        logger.error('Failed to import bam module: %s' % e)
        sys.exit(1)
    else:
        logger.info('Using KDE ErrorModel')
        bam.to_model(args.bam, args.output)
        logger.info('Model generation complete') 

# 需要導入模塊: from Bio import SeqIO [as 別名]
# 或者: from Bio.SeqIO import write [as 別名]
def main(args):
    for record in SeqIO.parse(args.infile, 'fasta'):
        if args.discard:
            if sum([1 for rx in args.discard if re.match(rx, record.id)]) > 0:
                continue

        subseqcounter = 0
        printlog(args.debug, "DEBUG: convert to upper case", record.id)
        sequence = str(record.seq).upper()
        printlog(args.debug, "DEBUG: split seq by Ns", record.id)
        subseqs = [ss for ss in re.split('[^ACGT]+', sequence) if len(ss) > args.minlength]
        printlog(args.debug, "DEBUG: print subseqs", record.id)
        for subseq in subseqs:
            subseqcounter += 1
            subid = '{:s}_chunk_{:d}'.format(record.id, subseqcounter)
            subrecord = SeqRecord(Seq(subseq), subid, '', '')
            SeqIO.write(subrecord, args.outfile, 'fasta') 

# 需要導入模塊: from Bio import SeqIO [as 別名]
# 或者: from Bio.SeqIO import write [as 別名]
def write_fasta_file(seq_records, outname, outdir=None, outext='.faa', force_rerun=False):
    """Write a FASTA file for a SeqRecord or a list of SeqRecord objects.

    Args:
        seq_records (SeqRecord, list): SeqRecord or a list of SeqRecord objects
        outname: Name of the output file which will have outext appended to it
        outdir: Path to directory to output sequences to
        outext: Extension of FASTA file, default ".faa"
        force_rerun: If file should be overwritten if it exists

    Returns:
        str: Path to output FASTA file.

    """

    if not outdir:
        outdir = ''
    outfile = ssbio.utils.outfile_maker(inname='', outname=outname, outdir=outdir, outext=outext)

    if ssbio.utils.force_rerun(flag=force_rerun, outfile=outfile):
        SeqIO.write(seq_records, outfile, "fasta")

    return outfile 

# 需要導入模塊: from Bio import SeqIO [as 別名]
# 或者: from Bio.SeqIO import write [as 別名]
def write_all_sequences_file(self, outname, outdir=None):
        """Write all the stored sequences as a single FASTA file. By default, sets IDs to model gene IDs.

        Args:
            outname (str): Name of the output FASTA file without the extension
            outdir (str): Path to output directory for the file, default is the sequences directory

        """

        if not outdir:
            outdir = self.sequence_dir
            if not outdir:
                raise ValueError('Output directory must be specified')

        outfile = op.join(outdir, outname + '.faa')
        SeqIO.write(self.sequences, outfile, "fasta")

        log.info('{}: wrote all protein sequences to file'.format(outfile))
        return outfile 

# 需要導入模塊: from Bio import SeqIO [as 別名]
# 或者: from Bio.SeqIO import write [as 別名]
def test_prepare_with_alignment_with_ref_name(self, test_file, test_seqs, existing_with_ref, existing_aln, ref_seq, out_file):
        """Test that, given a set of test sequences, an existing alignment, and a reference sequence name, no changes are made."""
        aln_outfile, seqs_outfile, _ = align.prepare([test_file,], existing_with_ref, out_file, ref_seq.id, None)
        assert os.path.isfile(aln_outfile), "Didn't write existing alignment where it said"
        assert aln_outfile == existing_with_ref, "Rewrote the alignment file unexpectedly"
        # Alignment file should be unchanged
        aln_output = SeqIO.to_dict(SeqIO.parse(aln_outfile, "fasta"))
        assert aln_output[ref_seq.id].seq == ref_seq.seq, "Reference sequence dropped from alignment"
        for seq in existing_aln:
            assert seq in aln_output, "Some existing alignment sequences dropped unexpectedly"
            assert aln_output[seq].seq == existing_aln[seq].seq, "Some existing alignment sequences changed unexpectedly"
        # test sequences should be unchanged
        assert os.path.isfile(seqs_outfile), "Didn't write test sequences where it said"
        seq_output = SeqIO.to_dict(SeqIO.parse(seqs_outfile, "fasta"))
        for seq in test_seqs:
            assert seq in seq_output, "Some test sequences unexpectedly dropped"
            assert seq_output[seq].seq == test_seqs[seq].seq, "Some test sequences changed unexpectedly"
        assert seq_output.keys() == test_seqs.keys() 

# 需要導入模塊: from Bio import SeqIO [as 別名]
# 或者: from Bio.SeqIO import write [as 別名]
def test_prepare_with_alignment_with_ref_seq(self, test_file, test_seqs, existing_file, existing_aln, ref_seq, ref_file, out_file):
        """Test that, given a set of test sequences, an existing alignment, and a reference sequence, the reference
        is added to the existing alignment and no other changes are made."""
        aln_outfile, seqs_outfile, ref_name = align.prepare([test_file,], existing_file, out_file, None, ref_file)
        assert ref_name == ref_seq.id, "Didn't return strain name from refrence file"
        assert os.path.isfile(aln_outfile), "Didn't write existing alignment where it said"
        assert aln_outfile != existing_aln, "Unexpectedly overwrote existing alignment"
        # Alignment file should have the reference added
        aln_output = SeqIO.to_dict(SeqIO.parse(aln_outfile, "fasta"))
        assert aln_output[ref_seq.id].seq == ref_seq.seq, "Reference sequence not added to alignment"
        for seq in existing_aln:
            assert seq in aln_output, "Some existing alignment sequences dropped unexpectedly"
            assert aln_output[seq].seq == existing_aln[seq].seq, "Some existing alignment sequences changed unexpectedly"
        # test sequences should be unchanged
        assert os.path.isfile(seqs_outfile), "Didn't write test sequences where it said"
        seq_output = SeqIO.to_dict(SeqIO.parse(seqs_outfile, "fasta"))
        for seq in test_seqs:
            assert seq in seq_output, "Some test sequences unexpectedly dropped"
            assert seq_output[seq].seq == test_seqs[seq].seq, "Some test sequences changed unexpectedly"
        assert seq_output.keys() == test_seqs.keys() 

# 需要導入模塊: from Bio import SeqIO [as 別名]
# 或者: from Bio.SeqIO import write [as 別名]
def main():
    """Make a jazz noise here"""

    args = get_args()
    regex = re.compile(args.pattern)
    out_fh = args.outfile or sys.stdout
    checked, took = 0, 0

    for fh in args.file:
        in_format = args.format or guess_format(fh.name)
        for rec in SeqIO.parse(fh, in_format):
            checked += 1
            out_fmt = args.out_format or args.format
            if any(map(regex.search, [rec.id, rec.description])):
                took += 1
                SeqIO.write(rec, out_fh, args.out_format or in_format)

    print(f'Done, checked {checked}, took {took}.', file=sys.stderr)


# -------------------------------------------------- 

# 需要導入模塊: from Bio import SeqIO [as 別名]
# 或者: from Bio.SeqIO import write [as 別名]
def base_complement(k):
    """ Return complement of base.

    Performs the subsitutions: A<=>T, C<=>G, X=>X for both upper and lower
    case. The return value is identical to the argument for all other values.

    :param k: A base.
    :returns: Complement of base.
    :rtype: str

    """
    try:
        return comp[k]
    except KeyError:
        sys.stderr.write(
            "WARNING: No reverse complement for {} found, returning argument.".format(k))
        return k 

# 需要導入模塊: from Bio import SeqIO [as 別名]
# 或者: from Bio.SeqIO import write [as 別名]
def _write_doc_template(schema):
    s = """Write to {} format.

    Parameters
    ----------
    filename : str
        File to write {} string to. If no filename is given, a {} string
        will be returned.

    sequence_col : str (default='sequence')
        Sequence column name in DataFrame.

    id_col : str (default='id')
        ID column name in DataFrame

    id_only : bool (default=False)
        If True, use only the ID column to label sequences in fasta.
    """.format(schema, schema, schema)
    return s 

# 需要導入模塊: from Bio import SeqIO [as 別名]
# 或者: from Bio.SeqIO import write [as 別名]
def depth_summary(all_genes,prefix):
    """Given the coding.depth file, calculate the average depth across the recovered sequence."""
    depths = {g:0 for g in all_genes}
    gene = "ZZZZ"
    gene_depths = []
    for line in open("coding.depth"):
        line = line.split()
        if line[0].split("-")[-1] == gene:
            gene_depths.append(int(line[2]))
        else:
            if gene == "ZZZZ":
                gene = line[0].split("-")[-1]
                gene_depths = [int(line[2])]
            else:
                mean_depth = sum(gene_depths)/float(len(gene_depths))
                depths[gene] = mean_depth
                gene_depths = []
            gene = line[0].split("-")[-1]
            
    output_list = [str(depths[key]) for key in sorted(depths)]                    
    sys.stdout.write("{}\t{}\n".format(prefix,"\t".join(output_list))) 

# 需要導入模塊: from Bio import SeqIO [as 別名]
# 或者: from Bio.SeqIO import write [as 別名]
def extract_paralogs(gene,prefix):
    
    putative_paralog_ids = list(set([x.split()[1].rstrip() for x in open(os.path.join(gene,prefix,"paralog_warning.txt"))]))
    try:
        chosen_paralog = open(os.path.join(gene,prefix,"exonerate_stats.csv")).readline().rstrip()
    except IOError:
        return 0
    
    exonerate_dict = SeqIO.to_dict(SeqIO.parse(os.path.join(gene,prefix,"exonerate_results.fasta"),'fasta'))
    
    if not os.path.isdir(os.path.join(gene,prefix,'paralogs')):
        os.mkdir(os.path.join(gene,prefix,"paralogs"))
    seqs_to_write = [exonerate_dict[x] for x in putative_paralog_ids]
    
    for seq in range(len(seqs_to_write)):
        if seqs_to_write[seq].id == chosen_paralog:
            seqs_to_write[seq].id = "{}.{}".format(prefix,"main")
            
        else:
            seqs_to_write[seq].id = "{}.{}".format(prefix,seq)
    
    SeqIO.write(seqs_to_write,os.path.join(gene,prefix,'paralogs','{}_paralogs.fasta'.format(gene)),'fasta')
    
    return len(seqs_to_write) 

# 需要導入模塊: from Bio import SeqIO [as 別名]
# 或者: from Bio.SeqIO import write [as 別名]
def concatenate_sequences(gene_dict,fastafiles,unique_names):
    '''Given a dictionary of dictionaries with complete sampling in each gene, write out concatenated sequences to stdout. Returns a list of partition lengths.'''    
    new_seq_dict = {}
    partition_lengths = []
    for gene in fastafiles:
        for name in unique_names:
            try:
                new_seq_dict[name] += gene_dict[gene][name]
            except KeyError:
                new_seq_dict[name] = gene_dict[gene][name]
        partition_lengths.append(len(next(iter(gene_dict[gene].values()))))
    for final_seq in new_seq_dict:
        SeqIO.write(new_seq_dict[final_seq],sys.stdout,'fasta')            
    final_seq_length = len(new_seq_dict[final_seq])
    sys.stderr.write("Final conatenated sequence length: {}\n".format(final_seq_length))
    return partition_lengths 

# 需要導入模塊: from Bio import SeqIO [as 別名]
# 或者: from Bio.SeqIO import write [as 別名]
def raxml_partition(fastafiles,partition_lengths,partition_type):
    '''Generate a raxml partition file for the given fastafiles. User specifies the partition type'''
    gene_start = 1
    partition_file = open("partition.raxml",'w')
    
    if partition_type == 'CODON':
        for g in range(len(fastafiles)):
            codon3_start = gene_start + 2
            codon3_end = gene_start + partition_lengths[g] - 1
            codon1_end = codon3_end - 2
            codon2_start = gene_start + 1
            codon2_end = codon3_end - 1
            partition_file.write("{},{}{}={}-{}\\3,{}-{}\\3\n".format("DNA",fastafiles[g],"12",gene_start,codon1_end,codon2_start,codon2_end))
            partition_file.write("{},{}{}={}-{}\\3\n".format("DNA",fastafiles[g],"3",codon3_start,codon3_end))
            gene_start = codon3_end + 1
    else:
        for g in range(len(fastafiles)):
            gene_end = gene_start + partition_lengths[g] - 1
            partition_file.write("{},{}={}-{}\n".format(partition_type,fastafiles[g],gene_start,gene_end))
            gene_start = gene_end + 1
        partition_file.close() 

# 需要導入模塊: from Bio import SeqIO [as 別名]
# 或者: from Bio.SeqIO import write [as 別名]
def supercontig_exonerate(supercontig,protseq,prefix,thresh=55):
    """Given a long, joined contig and a protein sequence, return the exonerate hit(s)"""
    logger = logging.getLogger("pipeline")

    exonerate_ryo = '>%ti,%qi,%qab,%qae,%pi,(%tS)\\n%tcs\\n'
    temp_prot_filename = "%s/temp.prot.fa"%prefix
    temp_contig_filename =  "%s/temp.contig.fa"%prefix
    SeqIO.write(protseq,temp_prot_filename,'fasta')
    SeqIO.write(supercontig,temp_contig_filename,'fasta')
    logger.debug("Conducting exonerate search on supercontig")
    proc = subprocess.Popen(['exonerate','-m','protein2genome','--showalignment','no','-V','0','--showvulgar','no','--ryo',exonerate_ryo,temp_prot_filename,temp_contig_filename],stdout=subprocess.PIPE,universal_newlines=True)

    proc.wait()
    #print proc.stdout.readlines()
    supercontig_cds = [i for i in SeqIO.parse(proc.stdout,'fasta') if float(i.id.split(",")[4])>thresh]
    logger.debug("Supercontig lengths: %s" % " ".join([str(len(x.seq)) for x in supercontig_cds]))
    return supercontig_cds 

# 需要導入模塊: from Bio import SeqIO [as 別名]
# 或者: from Bio.SeqIO import write [as 別名]
def make_intron_supercontig(contig_info,gene,prefix,add_N = False):
    cap3contigs = SeqIO.to_dict(SeqIO.parse("../{}_contigs.fasta".format(gene),'fasta'))
    intron_supercontig = SeqRecord(Seq(''))
    for i in contig_info:
        if i[5] == "(+)":
            intron_supercontig += cap3contigs[i[0]]
        elif i[5] == "(-)":
            intron_supercontig += cap3contigs[i[0]].reverse_complement()    
        else:
            sys.stderr.write("Strandedness not found!")
            sys.exit(1)
        if add_N and i != contig_info[-1]:
            intron_supercontig += "NNNNNNNNNN"    
    intron_supercontig.id = '{}-{}'.format(prefix,gene)
    intron_supercontig.description = ''
    SeqIO.write(intron_supercontig,'sequences/intron/{}_supercontig.fasta'.format(gene),'fasta')