comparison tools/protein_analysis/signalp3.py @ 11:99b82a2b1272 draft

Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)

10:09ff180d1615

FASTA_CHUNK = 500
MAX_LEN = 6000 #Found by trial and error

if len(sys.argv) not in  [6,8]:
   stop_err("Require five (or 7) arguments, organism, truncate, threads, "
            "input protein FASTA file & output tabular file (plus "
            "optionally cut method and GFF3 output file). "
            "Got %i arguments." % (len(sys.argv)-1))

organism = sys.argv[1]
if organism not in ["euk", "gram+", "gram-"]:
   stop_err("Organism argument %s is not one of euk, gram+ or gram-" % organism)

try:
   truncate = int(sys.argv[2])
except:
   truncate = 0
if truncate < 0:
   stop_err("Truncate argument %s is not a positive integer (or zero)" % sys.argv[2])

num_threads = thread_count(sys.argv[3], default=4)
fasta_file = sys.argv[4]
tabular_file = sys.argv[5]

if len(sys.argv) == 8:
   cut_method = sys.argv[6]
   if cut_method not in ["NN_Cmax", "NN_Ymax", "NN_Smax", "HMM_Cmax"]:
      stop_err("Invalid cut method %r" % cut_method)
   gff3_file = sys.argv[7]
else:
   cut_method = None
   gff3_file = None


tmp_dir = tempfile.mkdtemp()

def clean_tabular(raw_handle, out_handle, gff_handle=None, cut_method=None):
    """Clean up SignalP output to make it tabular."""
    if cut_method:
       cut_col = {"NN_Cmax" : 2,
                  "NN_Ymax" : 5,
                  "NN_Smax" : 8,
                  "HMM_Cmax" : 16}[cut_method]
    else:
       cut_col = None
    for line in raw_handle:
        if not line or line.startswith("#"):
            continue
        parts = line.rstrip("\r\n").split()
        assert len(parts)==21, repr(line)
        assert parts[14].startswith(parts[0])
        #Remove redundant truncated name column (col 0)
        #and put full name at start (col 14)
        parts = parts[14:15] + parts[1:14] + parts[15:]
        out_handle.write("\t".join(parts) + "\n")

    data_handle.close()
out_handle.close()

#GFF3:
if cut_method:
   make_gff(fasta_file, tabular_file, gff3_file, cut_method)

clean_up(fasta_files + temp_files)

11:99b82a2b1272

FASTA_CHUNK = 500
MAX_LEN = 6000 #Found by trial and error

if len(sys.argv) not in  [6,8]:
    stop_err("Require five (or 7) arguments, organism, truncate, threads, "
             "input protein FASTA file & output tabular file (plus "
             "optionally cut method and GFF3 output file). "
             "Got %i arguments." % (len(sys.argv)-1))

organism = sys.argv[1]
if organism not in ["euk", "gram+", "gram-"]:
    stop_err("Organism argument %s is not one of euk, gram+ or gram-" % organism)

try:
    truncate = int(sys.argv[2])
except:
    truncate = 0
if truncate < 0:
    stop_err("Truncate argument %s is not a positive integer (or zero)" % sys.argv[2])

num_threads = thread_count(sys.argv[3], default=4)
fasta_file = sys.argv[4]
tabular_file = sys.argv[5]

if len(sys.argv) == 8:
    cut_method = sys.argv[6]
    if cut_method not in ["NN_Cmax", "NN_Ymax", "NN_Smax", "HMM_Cmax"]:
        stop_err("Invalid cut method %r" % cut_method)
    gff3_file = sys.argv[7]
else:
    cut_method = None
    gff3_file = None


tmp_dir = tempfile.mkdtemp()

def clean_tabular(raw_handle, out_handle, gff_handle=None, cut_method=None):
    """Clean up SignalP output to make it tabular."""
    if cut_method:
        cut_col = {"NN_Cmax" : 2,
                   "NN_Ymax" : 5,
                   "NN_Smax" : 8,
                   "HMM_Cmax" : 16}[cut_method]
    else:
        cut_col = None
    for line in raw_handle:
        if not line or line.startswith("#"):
            continue
        parts = line.rstrip("\r\n").split()
        assert len(parts)==21, repr(line)
        assert parts[14].startswith(parts[0]), \
            "Bad entry in SignalP output, ID miss-match:\n%r" % line
        #Remove redundant truncated name column (col 0)
        #and put full name at start (col 14)
        parts = parts[14:15] + parts[1:14] + parts[15:]
        out_handle.write("\t".join(parts) + "\n")

    data_handle.close()
out_handle.close()

#GFF3:
if cut_method:
    make_gff(fasta_file, tabular_file, gff3_file, cut_method)

clean_up(fasta_files + temp_files)