comparison tools/sr_assembly/mira.py @ 4:117cce3296af

Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent. The Galaxy wrapper will no longer work with MIRA v3.2.x - if you are still using the old version of MIRA, please continue to use v0.0.2 of the wrapper.

3:298f5c1d9521

def stop_err(msg, err=1):
    sys.stderr.write(msg+"\n")
    sys.exit(err)

def tcs_to_tabular(old, new):
    in_handle = open(old, "rU")
    out_handle = open(new, "w")
    assert in_handle.readline() == "#TCS V1.0\n"
    assert in_handle.readline() == "#\n"
    assert in_handle.readline() == "# contig name          padPos  upadPos | B  Q | tcov covA covC covG covT cov* | qA qC qG qT q* |  S | Tags\n"
    assert in_handle.readline() == "#\n"
    out_handle.write("#%s\n" % "\t".join(["contig", "pasPos", "upadPos", "B", "Q",
                                         "tcov", "covA", "covC", "covG", "covT", "cov*",
                                         "qA", "qC", "qG", "qT", "q*", "S", "Tags"]))
    for line in in_handle:
        parts = line.rstrip("\n").split(None,22)
        assert parts[3] == parts[6] == parts[13] == parts[19] == parts[21] == "|"
        wanted = parts[:3] + parts[4:6]+parts[7:13]+parts[14:19]+parts[20:21]+parts[22:]
        out_handle.write("%s\n" % "\t".join(wanted))
    out_handle.close()
    in_handle.close()

def collect_output(temp, name):
    n3 = (temp, name, name, name)
    f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
    if not os.path.isdir(f):
        stop_err("Missing output folder")
    if not os.listdir(f):
        stop_err("Empty output folder")
    for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta),
                     ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual),
                     ("%s/%s_out.wig" % (f, name), out_wig),
                     ("%s/%s_out.caf" % (f, name), out_caf),
                     ("%s/%s_out.ace" % (f, name), out_ace)]:
        if not os.path.isfile(old):
            stop_err("Missing %s output file" % os.path.splitext(old)[-1])
        else:
            shutil.move(old, new)
    tcs_to_tabular("%s/%s_assembly/%s_d_results/%s_out.tcs" % n3, out_tcs)

def clean_up(temp, name):
    folder = "%s/%s_assembly" % (temp, name)
    if os.path.isdir(folder):
        shutil.rmtree(folder)

#TODO - Run MIRA in /tmp or a configurable directory?
#Currently Galaxy puts us somewhere safe like:
#/opt/galaxy-dist/database/job_working_directory/846/
temp = "."
name, out_fasta, out_qual, out_tcs, out_ace, out_caf, out_wig, out_log = sys.argv[1:9]

start_time = time.time()
cmd = " ".join(sys.argv[9:])

assert os.path.isdir(temp)
d = "%s_assembly" % name
assert not os.path.isdir(d)
try:
    #Check path access
    os.mkdir(d)
except Exception, err:
    sys.stderr.write("Error making directory %s\n%s" % (d, err))

#print cmd

handle = open(out_log, "w")
try:
    #Run MIRA
    child = subprocess.Popen(sys.argv[9:],
                             stdout=handle,
                             stderr=subprocess.STDOUT)
except Exception, err:
    sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
    #TODO - call clean up?

    clean_up(temp, name)
    stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
             return_code)
handle.close()

collect_output(temp, name)
clean_up(temp, name)
print "Done"

4:117cce3296af

def stop_err(msg, err=1):
    sys.stderr.write(msg+"\n")
    sys.exit(err)

def collect_output(temp, name):
    n3 = (temp, name, name, name)
    f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
    if not os.path.isdir(f):
        stop_err("Missing output folder")
    if not os.listdir(f):
        stop_err("Empty output folder")
    missing = []
    for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta),
                     ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual),
                     ("%s/%s_out.wig" % (f, name), out_wig),
                     ("%s/%s_out.caf" % (f, name), out_caf),
                     ("%s/%s_out.ace" % (f, name), out_ace)]:
        if not os.path.isfile(old):
            missing.append(os.path.splitext(old)[-1])
        else:
            shutil.move(old, new)
    if missing:
        stop_err("Missing output files: %s" % ", ".join(missing))

def clean_up(temp, name):
    folder = "%s/%s_assembly" % (temp, name)
    if os.path.isdir(folder):
        shutil.rmtree(folder)

#TODO - Run MIRA in /tmp or a configurable directory?
#Currently Galaxy puts us somewhere safe like:
#/opt/galaxy-dist/database/job_working_directory/846/
temp = "."
name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8]

start_time = time.time()
cmd_list =sys.argv[8:]
cmd = " ".join(cmd_list)

assert os.path.isdir(temp)
d = "%s_assembly" % name
assert not os.path.isdir(d), "Path %s already exists" % d
try:
    #Check path access
    os.mkdir(d)
except Exception, err:
    sys.stderr.write("Error making directory %s\n%s" % (d, err))

#print cmd

handle = open(out_log, "w")
try:
    #Run MIRA
    child = subprocess.Popen(cmd_list,
                             stdout=handle,
                             stderr=subprocess.STDOUT)
except Exception, err:
    sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
    #TODO - call clean up?

    clean_up(temp, name)
    stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
             return_code)
handle.close()

#print "Collecting output..."
collect_output(temp, name)

#print "Cleaning up..."
clean_up(temp, name)

print "Done"