def process_sequences_for_script(in_fpath_seq, file_format, pipeline,
configuration, out_fpath, in_fpath_qual=None):
'''It returns a repr file with the processed sequences
The pipeline and configuration should be pickled object.
'''
pipeline = pickle.loads(pipeline)
configuration = pickle.loads(configuration)
#the pipeline is now a list of strs we should convert it into a list of
#dicts
steps = dict([(step['name'], step) for step in STEPS])
#the pipeline step do not have real functions because they were not
#pickeable, so we have to put the functions again in the steps
for step in pipeline:
step_name = step['name']
step['function'] = steps[step_name]['function']
if in_fpath_qual:
in_fhand_qual = open(in_fpath_qual)
else:
in_fhand_qual = None
processed_seqs = _process_sequences(open(in_fpath_seq),
in_fhand_qual=in_fhand_qual,
file_format=file_format,
pipeline=pipeline,
configuration=configuration)
#now we write all seq in the file
out_fhand = open(out_fpath, 'a')
writer = SequenceWriter(fhand=out_fhand,
file_format='pickle')
for sequence in processed_seqs:
writer.write(sequence)
out_fhand.close()
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