tmhmm_and_signalp: tools/protein_analysis/rxlr

annotate tools/protein_analysis/rxlr_motifs.py @ 29:3cb02adf4326 draft

v0.2.9 Python style improvements

author	peterjc
date	Wed, 01 Feb 2017 09:46:14 -0500
parents	20139cb4c844
children	6d9d7cdf00fc

rev	line source
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	1 #!/usr/bin/env python
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	2 """Implements assorted RXLR motif methods from the literature
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	3
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	4 This script takes exactly four command line arguments:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	5 * Protein FASTA filename
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	6 * Number of threads
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	7 * Model name (Bhattacharjee2006, Win2007, Whisson2007)
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	8 * Output tabular filename
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	9
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	10 The model names are:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	11
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	12 Bhattacharjee2006: Simple regular expression search for RXLR
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	13 with additional requirements for positioning and signal peptide.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	14
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	15 Win2007: Simple regular expression search for RXLR, but with
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	16 different positional requirements.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	17
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	18 Whisson2007: As Bhattacharjee2006 but with a more complex regular
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	19 expression to look for RXLR-EER domain, and additionally calls HMMER.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	20
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	21 See the help text in the accompanying Galaxy tool XML file for more
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	22 details including the full references.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	23
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	24 Note:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	25
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	26 Bhattacharjee et al. (2006) and Win et al. (2007) used SignalP v2.0,
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	27 which is no longer available. The current release is SignalP v3.0
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	28 (Mar 5, 2007). We have therefore opted to use the NN Ymax position for
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	29 the predicted cleavage site, as this is expected to be more accurate.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	30 Also note that the HMM score values have changed from v2.0 to v3.0.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	31 Whisson et al. (2007) used SignalP v3.0 anyway.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	32
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	33 Whisson et al. (2007) used HMMER 2.3.2, and althought their HMM model
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	34 can still be used with hmmsearch from HMMER 3 this this does give
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	35 slightly different results. We expect the hmmsearch from HMMER 2.3.2
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	36 (the last stable release of HMMER 2) to be present on the path under
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	37 the name hmmsearch2 (allowing it to co-exist with HMMER 3).
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	38 """
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	39 import os
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	40 import sys
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	41 import re
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	42 import subprocess
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	43 from seq_analysis_utils import fasta_iterator
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	44
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	45 if "-v" in sys.argv:
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	46 print("RXLR Motifs v0.0.10")
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	47 sys.exit(0)
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	48
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	49 if len(sys.argv) != 5:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	50 sys.exit("Requires four arguments: protein FASTA filename, threads, model, and output filename")
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	51
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	52 fasta_file, threads, model, tabular_file = sys.argv[1:]
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	53 hmm_output_file = tabular_file + ".hmm.tmp"
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	54 signalp_input_file = tabular_file + ".fasta.tmp"
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	55 signalp_output_file = tabular_file + ".tabular.tmp"
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	56 min_signalp_hmm = 0.9
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	57 hmmer_search = "hmmsearch2"
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	58
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	59 if model == "Bhattacharjee2006":
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	60 signalp_trunc = 70
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	61 re_rxlr = re.compile("R.LR")
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	62 min_sp = 10
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	63 max_sp = 40
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	64 max_sp_rxlr = 100
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	65 min_rxlr_start = 1
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	66 # Allow signal peptide to be at most 40aa, and want RXLR to be
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	67 # within 100aa, therefore for the prescreen the max start is 140:
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	68 max_rxlr_start = max_sp + max_sp_rxlr
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	69 elif model == "Win2007":
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	70 signalp_trunc = 70
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	71 re_rxlr = re.compile("R.LR")
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	72 min_sp = 10
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	73 max_sp = 40
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	74 min_rxlr_start = 30
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	75 max_rxlr_start = 60
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	76 # No explicit limit on separation of signal peptide clevage
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	77 # and RXLR, but shortest signal peptide is 10, and furthest
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	78 # away RXLR is 60, so effectively limit is 50.
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	79 max_sp_rxlr = max_rxlr_start - min_sp + 1
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	80 elif model == "Whisson2007":
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	81 signalp_trunc = 0 # zero for no truncation
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	82 re_rxlr = re.compile("R.LR.{,40}[ED][ED][KR]")
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	83 min_sp = 10
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	84 max_sp = 40
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	85 max_sp_rxlr = 100
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	86 min_rxlr_start = 1
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	87 max_rxlr_start = max_sp + max_sp_rxlr
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	88 else:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	89 sys.exit("Did not recognise the model name %r\n"
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	90 "Use Bhattacharjee2006, Win2007, or Whisson2007" % model)
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	91
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	92
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	93 def get_hmmer_version(exe, required=None):
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	94 cmd = "%s -h" % exe
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	95 try:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	96 child = subprocess.Popen([exe, "-h"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	97 except OSError:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	98 raise ValueError("Could not run %s" % exe)
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	99 stdout, stderr = child.communicate()
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	100 if required:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	101 return required in stdout
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	102 elif "HMMER 2" in stdout:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	103 return 2
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	104 elif "HMMER 3" in stdout:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	105 return 3
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	106 else:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	107 raise ValueError("Could not determine version of %s" % exe)
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	108
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	109
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	110 # Run hmmsearch for Whisson et al. (2007)
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	111 if model == "Whisson2007":
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	112 hmm_file = os.path.join(os.path.split(sys.argv[0])[0],
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	113 "whisson_et_al_rxlr_eer_cropped.hmm")
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	114 if not os.path.isfile(hmm_file):
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	115 sys.exit("Missing HMM file for Whisson et al. (2007)")
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	116 if not get_hmmer_version(hmmer_search, "HMMER 2.3.2 (Oct 2003)"):
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	117 sys.exit("Missing HMMER 2.3.2 (Oct 2003) binary, %s" % hmmer_search)
18 2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	118
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	119 hmm_hits = set()
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	120 valid_ids = set()
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	121 for title, seq in fasta_iterator(fasta_file):
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	122 name = title.split(None, 1)[0]
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	123 if name in valid_ids:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	124 sys.exit("Duplicated identifier %r" % name)
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	125 else:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	126 valid_ids.add(name)
18 2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	127 if not valid_ids:
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	128 # Special case, don't need to run HMMER if there are no sequences
18 2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	129 pass
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	130 else:
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	131 # I've left the code to handle HMMER 3 in situ, in case
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	132 # we revisit the choice to insist on HMMER 2.
18 2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	133 hmmer3 = (3 == get_hmmer_version(hmmer_search))
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	134 # Using zero (or 5.6?) for bitscore threshold
18 2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	135 if hmmer3:
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	136 # The HMMER3 table output is easy to parse
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	137 # In HMMER3 can't use both -T and -E
18 2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	138 cmd = "%s -T 0 --tblout %s --noali %s %s > /dev/null" \
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	139 % (hmmer_search, hmm_output_file, hmm_file, fasta_file)
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	140 else:
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	141 # For HMMER2 we are stuck with parsing stdout
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	142 # Put 1e6 to effectively have no expectation threshold (otherwise
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	143 # HMMER defaults to 10 and the calculated e-value depends on the
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	144 # input FASTA file, and we can loose hits of interest).
18 2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	145 cmd = "%s -T 0 -E 1e6 %s %s > %s" \
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	146 % (hmmer_search, hmm_file, fasta_file, hmm_output_file)
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	147 return_code = os.system(cmd)
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	148 if return_code:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	149 sys.exit("Error %i from hmmsearch:\n%s" % (return_code, cmd), return_code)
18 2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	150
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	151 handle = open(hmm_output_file)
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	152 for line in handle:
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	153 if not line.strip():
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	154 # We expect blank lines in the HMMER2 stdout
18 2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	155 continue
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	156 elif line.startswith("#"):
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	157 # Header
18 2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	158 continue
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	159 else:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	160 name = line.split(None, 1)[0]
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	161 # Should be a sequence name in the HMMER3 table output.
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	162 # Could be anything in the HMMER2 stdout.
18 2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	163 if name in valid_ids:
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	164 hmm_hits.add(name)
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	165 elif hmmer3:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	166 sys.exit("Unexpected identifer %r in hmmsearch output" % name)
18 2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	167 handle.close()
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	168 # if hmmer3:
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	169 # print "HMMER3 hits for %i/%i" % (len(hmm_hits), len(valid_ids))
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	170 # else:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	171 # print "HMMER2 hits for %i/%i" % (len(hmm_hits), len(valid_ids))
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	172 # print "%i/%i matched HMM" % (len(hmm_hits), len(valid_ids))
18 2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools peterjc parents: 6 diff changeset	173 os.remove(hmm_output_file)
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	174 del valid_ids
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	175
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	176
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	177 # Prepare short list of candidates containing RXLR to pass to SignalP
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	178 assert min_rxlr_start > 0, "Min value one, since zero based counting"
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	179 count = 0
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	180 total = 0
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	181 handle = open(signalp_input_file, "w")
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	182 for title, seq in fasta_iterator(fasta_file):
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	183 total += 1
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	184 name = title.split(None, 1)[0]
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	185 match = re_rxlr.search(seq[min_rxlr_start - 1:].upper())
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	186 if match and min_rxlr_start - 1 + match.start() + 1 <= max_rxlr_start:
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	187 # This is a potential RXLR, depending on the SignalP results.
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	188 # Might as well truncate the sequence now, makes the temp file smaller
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	189 if signalp_trunc:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	190 handle.write(">%s (truncated)\n%s\n" % (name, seq[:signalp_trunc]))
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	191 else:
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	192 # Does it matter we don't line wrap?
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	193 handle.write(">%s\n%s\n" % (name, seq))
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	194 count += 1
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	195 handle.close()
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	196 # print "Running SignalP on %i/%i potentials." % (count, total)
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	197
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	198
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	199 # Run SignalP (using our wrapper script to get multi-core support etc)
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	200 signalp_script = os.path.join(os.path.split(sys.argv[0])[0], "signalp3.py")
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	201 if not os.path.isfile(signalp_script):
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	202 sys.exit("Error - missing signalp3.py script")
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	203 cmd = "python %s euk %i %s %s %s" % (signalp_script, signalp_trunc, threads, signalp_input_file, signalp_output_file)
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	204 return_code = os.system(cmd)
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	205 if return_code:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	206 sys.exit("Error %i from SignalP:\n%s" % (return_code, cmd))
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	207 # print "SignalP done"
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	208
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	209
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	210 def parse_signalp(filename):
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	211 """Parse SignalP output, yield tuples of ID, HMM_Sprob_score and NN predicted signal peptide length.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	212
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	213 For signal peptide length we use NN_Ymax_pos (minus one).
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	214 """
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	215 handle = open(filename)
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	216 line = handle.readline()
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	217 assert line.startswith("#ID\t"), line
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	218 for line in handle:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	219 parts = line.rstrip("\t").split("\t")
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	220 assert len(parts) == 20, repr(line)
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	221 yield parts[0], float(parts[18]), int(parts[5]) - 1
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	222 handle.close()
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	223
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	224
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	225 # Parse SignalP results and apply the strict RXLR criteria
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	226 total = 0
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	227 tally = dict()
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	228 handle = open(tabular_file, "w")
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	229 handle.write("#ID\t%s\n" % model)
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	230 signalp_results = parse_signalp(signalp_output_file)
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	231 for title, seq in fasta_iterator(fasta_file):
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	232 total += 1
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	233 rxlr = "N"
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	234 name = title.split(None, 1)[0]
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	235 match = re_rxlr.search(seq[min_rxlr_start - 1:].upper())
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	236 if match and min_rxlr_start - 1 + match.start() + 1 <= max_rxlr_start:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	237 del match
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	238 # This was the criteria for calling SignalP,
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	239 # so it will be in the SignalP results.
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	240 sp_id, sp_hmm_score, sp_nn_len = signalp_results.next()
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	241 assert name == sp_id, "%s vs %s" % (name, sp_id)
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	242 if sp_hmm_score >= min_signalp_hmm and min_sp <= sp_nn_len <= max_sp:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	243 match = re_rxlr.search(seq[sp_nn_len:].upper())
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	244 if match and match.start() + 1 <= max_sp_rxlr: # 1-based counting
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	245 rxlr_start = sp_nn_len + match.start() + 1
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	246 if min_rxlr_start <= rxlr_start <= max_rxlr_start:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	247 rxlr = "Y"
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	248 if model == "Whisson2007":
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	249 # Combine the signalp with regular expression heuristic and the HMM
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	250 if name in hmm_hits and rxlr == "N":
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	251 rxlr = "hmm" # HMM only
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	252 elif rxlr == "N":
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	253 rxlr = "neither" # Don't use N (no)
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	254 elif name not in hmm_hits and rxlr == "Y":
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	255 rxlr = "re" # Heuristic only
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	256 # Now have a four way classifier: Y, hmm, re, neither
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	257 # and count is the number of Y results (both HMM and heuristic)
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	258 handle.write("%s\t%s\n" % (name, rxlr))
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	259 try:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	260 tally[rxlr] += 1
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	261 except KeyError:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	262 tally[rxlr] = 1
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	263 handle.close()
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	264 assert sum(tally.values()) == total
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	265
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	266 # Check the iterator is finished
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	267 try:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	268 signalp_results.next()
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	269 assert False, "Unexpected data in SignalP output"
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	270 except StopIteration:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	271 pass
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	272
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	273 # Cleanup
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	274 os.remove(signalp_input_file)
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	275 os.remove(signalp_output_file)
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	276
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 18 diff changeset	277 # Short summary to stdout for Galaxy's info display
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	278 print "%s for %i sequences:" % (model, total)
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	279 print ", ".join("%s = %i" % kv for kv in sorted(tally.iteritems()))

Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/rxlr_motifs.py @ 29:3cb02adf4326 draft