tmhmm_and_signalp: tools/protein_analysis/signalp3.py annotate

annotate tools/protein_analysis/signalp3.py @ 4:81caef04ce8b

Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository

author	peterjc
date	Tue, 07 Jun 2011 18:05:50 -0400
parents	bca9bc7fdaef
children	0f1c61998b22

rev	line source
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	1 #!/usr/bin/env python
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	2 """Wrapper for SignalP v3.0 for use in Galaxy.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	3
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	4 This script takes exactly fives command line arguments:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	5 * the organism type (euk, gram+ or gram-)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	6 * length to truncate sequences to (integer)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	7 * number of threads to use (integer)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	8 * an input protein FASTA filename
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	9 * output tabular filename.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	10
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	11 It then calls the standalone SignalP v3.0 program (not the webservice)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	12 requesting the short output (one line per protein) using both NN and HMM
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	13 for predictions.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	14
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	15 First major feature is cleaning up the output. The raw output from SignalP
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	16 v3.0 looks like this (21 columns space separated):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	17
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	18 # SignalP-NN euk predictions # SignalP-HMM euk predictions
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	19 # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? D ? # name ! Cmax pos ? Sprob ?
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	20 gi\|2781234\|pdb\|1JLY\| 0.061 17 N 0.043 17 N 0.199 1 N 0.067 N 0.055 N gi\|2781234\|pdb\|1JLY\|B Q 0.000 17 N 0.000 N
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	21 gi\|4959044\|gb\|AAD342 0.099 191 N 0.012 38 N 0.023 12 N 0.014 N 0.013 N gi\|4959044\|gb\|AAD34209.1\|AF069992_1 Q 0.000 0 N 0.000 N
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	22 gi\|671626\|emb\|CAA856 0.139 381 N 0.020 8 N 0.121 4 N 0.067 N 0.044 N gi\|671626\|emb\|CAA85685.1\| Q 0.000 0 N 0.000 N
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	23 gi\|3298468\|dbj\|BAA31 0.208 24 N 0.184 38 N 0.980 32 Y 0.613 Y 0.398 N gi\|3298468\|dbj\|BAA31520.1\| Q 0.066 24 N 0.139 N
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	24
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	25 In order to make it easier to use in Galaxy, this wrapper script reformats
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	26 this to use tab separators. Also it removes the redundant truncated name
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	27 column, and assigns unique column names in the header:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	28
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	29 #ID NN_Cmax_score NN_Cmax_pos NN_Cmax_pred NN_Ymax_score NN_Ymax_pos NN_Ymax_pred NN_Smax_score NN_Smax_pos NN_Smax_pred NN_Smean_score NN_Smean_pred NN_D_score NN_D_pred HMM_bang HMM_Cmax_score HMM_Cmax_pos HMM_Cmax_pred HMM_Sprob_score HMM_Sprob_pred
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	30 gi\|2781234\|pdb\|1JLY\|B 0.061 17 N 0.043 17 N 0.199 1 N 0.067 N 0.055 N Q 0.000 17 N 0.000 N
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	31 gi\|4959044\|gb\|AAD34209.1\|AF069992_1 0.099 191 N 0.012 38 N 0.023 12 N 0.014 N 0.013 N Q 0.000 0 N 0.000 N
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	32 gi\|671626\|emb\|CAA85685.1\| 0.139 381 N 0.020 8 N 0.121 4 N 0.067 N 0.044 N Q 0.000 0 N 0.000 N
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	33 gi\|3298468\|dbj\|BAA31520.1\| 0.208 24 N 0.184 38 N 0.980 32 Y 0.613 Y 0.398 N Q 0.066 24 N 0.139 N
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	34
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	35 The second major feature is overcoming SignalP's built in limit of 4000
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	36 sequences by breaking up the input FASTA file into chunks. This also allows
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	37 us to pre-trim the sequences since SignalP only needs their starts.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	38
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	39 The third major feature is taking advantage of multiple cores (since SignalP
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	40 v3.0 itself is single threaded) by using the individual FASTA input files to
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	41 run multiple copies of TMHMM in parallel. I would normally use Python's
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	42 multiprocessing library in this situation but it requires at least Python 2.6
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	43 and at the time of writing Galaxy still supports Python 2.4.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	44 """
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	45 import sys
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	46 import os
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	47 from seq_analysis_utils import stop_err, split_fasta, run_jobs
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	48
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	49 FASTA_CHUNK = 500
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	50 MAX_LEN = 6000 #Found by trial and error
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	51
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	52 if len(sys.argv) != 6:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	53 stop_err("Require five arguments, organism, truncate, threads, input protein FASTA file & output tabular file")
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	54
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	55 organism = sys.argv[1]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	56 if organism not in ["euk", "gram+", "gram-"]:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	57 stop_err("Organism argument %s is not one of euk, gram+ or gram-" % organism)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	58
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	59 try:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	60 truncate = int(sys.argv[2])
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	61 except:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	62 truncate = 0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	63 if truncate < 0:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	64 stop_err("Truncate argument %s is not a positive integer (or zero)" % sys.argv[2])
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	65
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	66 try:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	67 num_threads = int(sys.argv[3])
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	68 except:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	69 num_threads = 0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	70 if num_threads < 1:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	71 stop_err("Threads argument %s is not a positive integer" % sys.argv[3])
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	72
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	73 fasta_file = sys.argv[4]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	74
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	75 tabular_file = sys.argv[5]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	76
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	77 def clean_tabular(raw_handle, out_handle):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	78 """Clean up SignalP output to make it tabular."""
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	79 for line in raw_handle:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	80 if not line or line.startswith("#"):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	81 continue
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	82 parts = line.rstrip("\r\n").split()
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	83 assert len(parts)==21, repr(line)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	84 assert parts[14].startswith(parts[0])
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	85 #Remove redundant truncated name column (col 0)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	86 #and put full name at start (col 14)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	87 parts = parts[14:15] + parts[1:14] + parts[15:]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	88 out_handle.write("\t".join(parts) + "\n")
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	89
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	90 fasta_files = split_fasta(fasta_file, tabular_file, n=FASTA_CHUNK, truncate=truncate, max_len=MAX_LEN)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	91 temp_files = [f+".out" for f in fasta_files]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	92 assert len(fasta_files) == len(temp_files)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	93 jobs = ["signalp -short -t %s %s > %s" % (organism, fasta, temp)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	94 for (fasta, temp) in zip(fasta_files, temp_files)]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	95 assert len(fasta_files) == len(temp_files) == len(jobs)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	96
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	97 def clean_up(file_list):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	98 for f in file_list:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	99 if os.path.isfile(f):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	100 os.remove(f)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	101
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	102 if len(jobs) > 1 and num_threads > 1:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	103 #A small "info" message for Galaxy to show the user.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	104 print "Using %i threads for %i tasks" % (min(num_threads, len(jobs)), len(jobs))
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	105 results = run_jobs(jobs, num_threads)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	106 assert len(fasta_files) == len(temp_files) == len(jobs)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	107 for fasta, temp, cmd in zip(fasta_files, temp_files, jobs):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	108 error_level = results[cmd]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	109 try:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	110 output = open(temp).readline()
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	111 except IOError:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	112 output = ""
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	113 if error_level or output.lower().startswith("error running"):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	114 clean_up(fasta_files)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	115 clean_up(temp_files)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	116 stop_err("One or more tasks failed, e.g. %i from %r gave:\n%s" % (error_level, cmd, output),
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	117 error_level)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	118 del results
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	119
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	120 out_handle = open(tabular_file, "w")
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	121 fields = ["ID"]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	122 #NN results:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	123 for name in ["Cmax", "Ymax", "Smax"]:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	124 fields.extend(["NN_%s_score"%name, "NN_%s_pos"%name, "NN_%s_pred"%name])
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	125 fields.extend(["NN_Smean_score", "NN_Smean_pred", "NN_D_score", "NN_D_pred"])
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	126 #HMM results:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	127 fields.extend(["HMM_type", "HMM_Cmax_score", "HMM_Cmax_pos", "HMM_Cmax_pred",
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	128 "HMM_Sprob_score", "HMM_Sprob_pred"])
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	129 out_handle.write("#" + "\t".join(fields) + "\n")
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	130 for temp in temp_files:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	131 data_handle = open(temp)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	132 clean_tabular(data_handle, out_handle)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	133 data_handle.close()
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	134 out_handle.close()
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	135
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	136 clean_up(fasta_files)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	137 clean_up(temp_files)

Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/signalp3.py @ 4:81caef04ce8b