def make_backbone_blast_db(project_dir, blast_db_seq, dbtype):
'It formats a blastdb when need it'
logger = logging.getLogger(LOGGER_NAME)
#the name should be the basename of the blast_db_seq
db_dir = join(project_dir, BACKBONE_DIRECTORIES['blast_databases'])
if not exists(db_dir):
makedirs(db_dir)
db_seq_fpath = join(db_dir, _get_basename(blast_db_seq))
if not exists(db_seq_fpath):
#which is the name of the new databae?
blast_db_seq_format = guess_seq_file_format(open(blast_db_seq))
if blast_db_seq_format == 'fasta':
rel_symlink(blast_db_seq, db_seq_fpath)
else:
seqio(in_seq_fhand=open(blast_db_seq),
out_seq_fhand=open(db_seq_fpath, 'w'),
out_format='fasta')
logger.info('Formatting the database %s' % db_seq_fpath)
try:
makeblastdb_plus(db_seq_fpath, dbtype=dbtype)
except RuntimeError:
msg = 'Error making blastdb. db:%s\n dbtype:%s\n' % \
(db_seq_fpath, dbtype)
remove(db_seq_fpath)
raise RuntimeError(msg)
return db_seq_fpath
def _create_temp_fasta_file(fpath):
'It creates a fasta file format temfile'
fasta_fhand = NamedTemporaryFile(suffix='.fasta', mode='a')
seqio(in_seq_fhand=open(fpath),
out_seq_fhand=fasta_fhand,
out_format='fasta')
return fasta_fhand
def main():
'The main function'
(in_seq_fhand, in_qual_fhand, in_format, out_seq_fhand, out_qual_fhand,
out_format, double_encoding) = set_parameters()
seqio(in_seq_fhand=in_seq_fhand, in_qual_fhand=in_qual_fhand,
in_format=in_format,
out_seq_fhand=out_seq_fhand, out_qual_fhand=out_qual_fhand,
out_format=out_format, double_encoding=double_encoding)
def main():
"The main part"
mira_path, iassembler_path = set_parameters()
# guess the mira files that we need
unigenes_fpath, unigenes_qual_fpath, mira_contig_read_fpath = get_mira_paths(mira_path)
# create the iassembler project dir and subdirs
if not os.path.exists(iassembler_path):
os.makedirs(iassembler_path)
mira_1_dir = os.path.join(iassembler_path, "{0:s}_Assembly".format(IASSEMBLER_INPUT_NAME), "mira")
os.makedirs(mira_1_dir)
# prepare contig readlist for iaasembler
iassembler_contig_mem_fpath = os.path.join(mira_1_dir, "CMF10")
process_contig_readlist(mira_contig_read_fpath, iassembler_contig_mem_fpath)
# copy unigene files into the iassembler project
iassembler_unigenes = os.path.join(mira_1_dir, "mira2.fa")
iassembler_unigenes_qual = os.path.join(mira_1_dir, "mira2.fa.qual")
iassembler_unigenes_fh = open(iassembler_unigenes, "w")
iassembler_unigenes_qual_fh = open(iassembler_unigenes_qual, "w")
seq_writer = SequenceWriter(
fhand=iassembler_unigenes_fh, file_format="fasta", qual_fhand=iassembler_unigenes_qual_fh
)
for seq in seqs_in_file(seq_fhand=open(unigenes_fpath), format="sfastq", qual_fhand=open(unigenes_qual_fpath)):
seq.name = "mira_{0:s}".format(seq.name.split("_", 1)[1])
seq.id = seq.name
seq_writer.write(seq)
# create iassembler input files.
seq_fhand = open(os.path.join(iassembler_path, IASSEMBLER_INPUT_NAME), "w")
qual_fhand = open(os.path.join(iassembler_path, IASSEMBLER_INPUT_NAME + ".qual"), "w")
for file_ in os.listdir(os.path.join(mira_path, "..")):
if "_in" in file_:
file_ = os.path.join(mira_path, "..", file_)
seqio(
in_seq_fhand=open(file_),
out_seq_fhand=seq_fhand,
out_qual_fhand=qual_fhand,
in_format="sfastq",
out_format="fasta",
)
msg = "To run iassembler you must use this command:\n"
msg += "iassembler -c -i {0:s}\n".format(IASSEMBLER_INPUT_NAME)
msg += "From your iassembler dir:{0:s}".format(iassembler_path)
print msg
def test_fastq_to_fastq_solexa():
'It tests the conversion using the Biopython convert function'
fcontent = '@seq1\n'
fcontent += 'CCCT\n'
fcontent += '+\n'
fcontent += ';;3;\n'
fcontent += '@SRR001666.1\n'
fcontent += 'GTTGC\n'
fcontent += '+\n'
fcontent += ';;;;;\n'
fhand = StringIO.StringIO(fcontent)
out_seq_fhand = StringIO.StringIO()
seqio(in_seq_fhand=fhand, in_format='fastq',
out_seq_fhand=out_seq_fhand, out_format='fastq-solexa')
result = '@seq1\nCCCT\n+\nZZRZ\[email protected]\nGTTGC\n+\nZZZZZ\n'
assert out_seq_fhand.getvalue() == result
def _files_to_temp_fasta(files):
'It converts the given files to a temporary fasta and qual'
fastas, quals = [], []
for file_ in files:
#are we dealing with a fastq file (with qual)
if 'fastq' in os.path.splitext(file_.name)[-1]:
qual = NamedTemporaryFile(suffix='.qual')
fasta = NamedTemporaryFile(suffix='.fasta')
seqio(in_seq_fhand=file_, out_seq_fhand=fasta,
out_qual_fhand=qual, out_format='fasta')
else:
#the file is already fasta
fasta = file_
qual = None
fastas.append(fasta)
quals.append(qual)
return fastas, quals
def test_fastq_to_fasta_qual():
'It tests the conversion from fastq to fasta'
fcontent = '@seq1\n'
fcontent += 'CCCT\n'
fcontent += '+\n'
fcontent += ';;3;\n'
fcontent += '@SRR001666.1\n'
fcontent += 'GTTGC\n'
fcontent += '+\n'
fcontent += ';;;;;\n'
fhand = StringIO.StringIO(fcontent)
out_seq_fhand = tempfile.NamedTemporaryFile(suffix='.fasta')
out_qual_fhand = tempfile.NamedTemporaryFile(suffix='.qual')
seqio(in_seq_fhand=fhand, in_format='fastq',
out_seq_fhand=out_seq_fhand, out_qual_fhand=out_qual_fhand,
out_format='fasta')
result = '>seq1\nCCCT\n>SRR001666.1\nGTTGC\n'
assert open(out_seq_fhand.name).read() == result
qual = '>seq1\n26 26 18 26\n>SRR001666.1\n26 26 26 26 26\n'
assert open(out_qual_fhand.name).read() == qual