tmhmm_and_signalp: tools/protein_analysis/rxlr

annotate tools/protein_analysis/rxlr_motifs.py @ 20:a19b3ded8f33 draft

v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes

author	peterjc
date	Thu, 21 Sep 2017 11:35:20 -0400
parents	f3ecd80850e2
children	238eae32483c

rev	line source
6 a290c6d4e658 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
a290c6d4e658 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
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	3
a290c6d4e658 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:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	5 * Protein FASTA filename
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	6 * Number of threads
a290c6d4e658 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)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	8 * Output tabular filename
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	9
a290c6d4e658 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:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	11
a290c6d4e658 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
a290c6d4e658 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.
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	14
a290c6d4e658 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
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	16 different positional requirements.
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	17
a290c6d4e658 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
a290c6d4e658 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.
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	20
a290c6d4e658 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
a290c6d4e658 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.
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	23
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	24 Note:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	25
a290c6d4e658 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,
a290c6d4e658 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
a290c6d4e658 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
a290c6d4e658 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.
a290c6d4e658 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.
a290c6d4e658 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.
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	32
a290c6d4e658 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
20 a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	34 can still be used with hmmsearch from HMMER 3, sadly this does give
6 a290c6d4e658 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
a290c6d4e658 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
a290c6d4e658 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).
20 a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	38
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	39 If using Conda, you should therefore install the special "hmmer2"
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	40 package from BioConda which provides "hmmsearch2" etc::
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	41
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	42 conda install -c bioconda hmmer2
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	43
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	44 See https://bioconda.github.io/recipes/hmmer2/README.html and
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	45 https://anaconda.org/bioconda/hmmer2
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	46 """
20 a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	47
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	48 from __future__ import print_function
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	49
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	50 import os
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	51 import re
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	52 import subprocess
20 a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	53 import sys
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	54
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	55 from seq_analysis_utils import fasta_iterator
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	56
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	57 if "-v" in sys.argv:
20 a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	58 print("RXLR Motifs v0.0.14")
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	59 sys.exit(0)
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	60
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	61 if len(sys.argv) != 5:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	62 sys.exit("Requires four arguments: protein FASTA filename, threads, model, and output filename")
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	63
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	64 fasta_file, threads, model, tabular_file = sys.argv[1:]
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	65 hmm_output_file = tabular_file + ".hmm.tmp"
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	66 signalp_input_file = tabular_file + ".fasta.tmp"
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	67 signalp_output_file = tabular_file + ".tabular.tmp"
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	68 min_signalp_hmm = 0.9
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	69 hmmer_search = "hmmsearch2"
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	70
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	71 if model == "Bhattacharjee2006":
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	72 signalp_trunc = 70
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	73 re_rxlr = re.compile("R.LR")
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	74 min_sp = 10
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	75 max_sp = 40
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	76 max_sp_rxlr = 100
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	77 min_rxlr_start = 1
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	78 # Allow signal peptide to be at most 40aa, and want RXLR to be
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	79 # within 100aa, therefore for the prescreen the max start is 140:
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	80 max_rxlr_start = max_sp + max_sp_rxlr
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	81 elif model == "Win2007":
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	82 signalp_trunc = 70
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	83 re_rxlr = re.compile("R.LR")
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	84 min_sp = 10
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	85 max_sp = 40
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	86 min_rxlr_start = 30
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	87 max_rxlr_start = 60
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	88 # No explicit limit on separation of signal peptide clevage
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	89 # and RXLR, but shortest signal peptide is 10, and furthest
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	90 # away RXLR is 60, so effectively limit is 50.
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	91 max_sp_rxlr = max_rxlr_start - min_sp + 1
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	92 elif model == "Whisson2007":
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	93 signalp_trunc = 0 # zero for no truncation
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	94 re_rxlr = re.compile("R.LR.{,40}[ED][ED][KR]")
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	95 min_sp = 10
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	96 max_sp = 40
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	97 max_sp_rxlr = 100
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	98 min_rxlr_start = 1
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	99 max_rxlr_start = max_sp + max_sp_rxlr
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	100 else:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	101 sys.exit("Did not recognise the model name %r\n"
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	102 "Use Bhattacharjee2006, Win2007, or Whisson2007" % model)
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	103
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	104
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	105 def get_hmmer_version(exe, required=None):
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	106 try:
20 a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	107 child = subprocess.Popen([exe, "-h"],
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	108 universal_newlines=True,
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	109 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	110 except OSError:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	111 raise ValueError("Could not run %s" % exe)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	112 stdout, stderr = child.communicate()
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	113 if required:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	114 return required in stdout
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	115 elif "HMMER 2" in stdout:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	116 return 2
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	117 elif "HMMER 3" in stdout:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	118 return 3
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	119 else:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	120 raise ValueError("Could not determine version of %s" % exe)
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	121
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	122
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	123 # Run hmmsearch for Whisson et al. (2007)
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	124 if model == "Whisson2007":
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	125 hmm_file = os.path.join(os.path.split(sys.argv[0])[0],
20 a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	126 "whisson_et_al_rxlr_eer_cropped.hmm")
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	127 if not os.path.isfile(hmm_file):
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	128 sys.exit("Missing HMM file for Whisson et al. (2007)")
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	129 if not get_hmmer_version(hmmer_search, "HMMER 2.3.2 (Oct 2003)"):
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	130 sys.exit("Missing HMMER 2.3.2 (Oct 2003) binary, %s" % hmmer_search)
16 7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	131
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	132 hmm_hits = set()
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	133 valid_ids = set()
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	134 for title, seq in fasta_iterator(fasta_file):
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	135 name = title.split(None, 1)[0]
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	136 if name in valid_ids:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	137 sys.exit("Duplicated identifier %r" % name)
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	138 else:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	139 valid_ids.add(name)
16 7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	140 if not valid_ids:
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	141 # Special case, don't need to run HMMER if there are no sequences
16 7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	142 pass
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	143 else:
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	144 # I've left the code to handle HMMER 3 in situ, in case
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	145 # we revisit the choice to insist on HMMER 2.
16 7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	146 hmmer3 = (3 == get_hmmer_version(hmmer_search))
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	147 # Using zero (or 5.6?) for bitscore threshold
16 7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	148 if hmmer3:
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	149 # The HMMER3 table output is easy to parse
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	150 # In HMMER3 can't use both -T and -E
16 7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	151 cmd = "%s -T 0 --tblout %s --noali %s %s > /dev/null" \
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	152 % (hmmer_search, hmm_output_file, hmm_file, fasta_file)
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	153 else:
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	154 # For HMMER2 we are stuck with parsing stdout
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	155 # Put 1e6 to effectively have no expectation threshold (otherwise
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	156 # HMMER defaults to 10 and the calculated e-value depends on the
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	157 # input FASTA file, and we can loose hits of interest).
16 7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	158 cmd = "%s -T 0 -E 1e6 %s %s > %s" \
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	159 % (hmmer_search, hmm_file, fasta_file, hmm_output_file)
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	160 return_code = os.system(cmd)
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	161 if return_code:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	162 sys.exit("Error %i from hmmsearch:\n%s" % (return_code, cmd), return_code)
16 7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	163
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	164 handle = open(hmm_output_file)
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	165 for line in handle:
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	166 if not line.strip():
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	167 # We expect blank lines in the HMMER2 stdout
16 7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	168 continue
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	169 elif line.startswith("#"):
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	170 # Header
16 7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	171 continue
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	172 else:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	173 name = line.split(None, 1)[0]
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	174 # Should be a sequence name in the HMMER3 table output.
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	175 # Could be anything in the HMMER2 stdout.
16 7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	176 if name in valid_ids:
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	177 hmm_hits.add(name)
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	178 elif hmmer3:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	179 sys.exit("Unexpected identifer %r in hmmsearch output" % name)
16 7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	180 handle.close()
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	181 # if hmmer3:
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	182 # print "HMMER3 hits for %i/%i" % (len(hmm_hits), len(valid_ids))
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	183 # else:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	184 # print "HMMER2 hits for %i/%i" % (len(hmm_hits), len(valid_ids))
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	185 # print "%i/%i matched HMM" % (len(hmm_hits), len(valid_ids))
16 7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	186 os.remove(hmm_output_file)
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	187 del valid_ids
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	188
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	189
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	190 # Prepare short list of candidates containing RXLR to pass to SignalP
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	191 assert min_rxlr_start > 0, "Min value one, since zero based counting"
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	192 count = 0
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	193 total = 0
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	194 handle = open(signalp_input_file, "w")
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	195 for title, seq in fasta_iterator(fasta_file):
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	196 total += 1
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	197 name = title.split(None, 1)[0]
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	198 match = re_rxlr.search(seq[min_rxlr_start - 1:].upper())
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	199 if match and min_rxlr_start - 1 + match.start() + 1 <= max_rxlr_start:
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	200 # This is a potential RXLR, depending on the SignalP results.
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	201 # Might as well truncate the sequence now, makes the temp file smaller
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	202 if signalp_trunc:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	203 handle.write(">%s (truncated)\n%s\n" % (name, seq[:signalp_trunc]))
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	204 else:
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	205 # Does it matter we don't line wrap?
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	206 handle.write(">%s\n%s\n" % (name, seq))
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	207 count += 1
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	208 handle.close()
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	209 # print "Running SignalP on %i/%i potentials." % (count, total)
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	210
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	211
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	212 # Run SignalP (using our wrapper script to get multi-core support etc)
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	213 signalp_script = os.path.join(os.path.split(sys.argv[0])[0], "signalp3.py")
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	214 if not os.path.isfile(signalp_script):
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	215 sys.exit("Error - missing signalp3.py script")
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	216 cmd = "python %s euk %i %s %s %s" % (signalp_script, signalp_trunc, threads, signalp_input_file, signalp_output_file)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	217 return_code = os.system(cmd)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	218 if return_code:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	219 sys.exit("Error %i from SignalP:\n%s" % (return_code, cmd))
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	220 # print "SignalP done"
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	221
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	222
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	223 def parse_signalp(filename):
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	224 """Parse SignalP output, yield tuples of ID, HMM_Sprob_score and NN predicted signal peptide length.
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	225
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	226 For signal peptide length we use NN_Ymax_pos (minus one).
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	227 """
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	228 handle = open(filename)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	229 line = handle.readline()
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	230 assert line.startswith("#ID\t"), line
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	231 for line in handle:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	232 parts = line.rstrip("\t").split("\t")
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	233 assert len(parts) == 20, repr(line)
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	234 yield parts[0], float(parts[18]), int(parts[5]) - 1
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	235 handle.close()
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	236
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	237
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	238 # Parse SignalP results and apply the strict RXLR criteria
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	239 total = 0
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	240 tally = dict()
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	241 handle = open(tabular_file, "w")
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	242 handle.write("#ID\t%s\n" % model)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	243 signalp_results = parse_signalp(signalp_output_file)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	244 for title, seq in fasta_iterator(fasta_file):
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	245 total += 1
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	246 rxlr = "N"
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	247 name = title.split(None, 1)[0]
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	248 match = re_rxlr.search(seq[min_rxlr_start - 1:].upper())
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	249 if match and min_rxlr_start - 1 + match.start() + 1 <= max_rxlr_start:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	250 del match
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	251 # This was the criteria for calling SignalP,
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	252 # so it will be in the SignalP results.
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	253 sp_id, sp_hmm_score, sp_nn_len = signalp_results.next()
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	254 assert name == sp_id, "%s vs %s" % (name, sp_id)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	255 if sp_hmm_score >= min_signalp_hmm and min_sp <= sp_nn_len <= max_sp:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	256 match = re_rxlr.search(seq[sp_nn_len:].upper())
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	257 if match and match.start() + 1 <= max_sp_rxlr: # 1-based counting
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	258 rxlr_start = sp_nn_len + match.start() + 1
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	259 if min_rxlr_start <= rxlr_start <= max_rxlr_start:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	260 rxlr = "Y"
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	261 if model == "Whisson2007":
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	262 # Combine the signalp with regular expression heuristic and the HMM
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	263 if name in hmm_hits and rxlr == "N":
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	264 rxlr = "hmm" # HMM only
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	265 elif rxlr == "N":
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	266 rxlr = "neither" # Don't use N (no)
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	267 elif name not in hmm_hits and rxlr == "Y":
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	268 rxlr = "re" # Heuristic only
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	269 # Now have a four way classifier: Y, hmm, re, neither
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	270 # and count is the number of Y results (both HMM and heuristic)
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	271 handle.write("%s\t%s\n" % (name, rxlr))
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	272 try:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	273 tally[rxlr] += 1
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	274 except KeyError:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	275 tally[rxlr] = 1
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	276 handle.close()
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	277 assert sum(tally.values()) == total
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	278
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	279 # Check the iterator is finished
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	280 try:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	281 signalp_results.next()
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	282 assert False, "Unexpected data in SignalP output"
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	283 except StopIteration:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	284 pass
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	285
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	286 # Cleanup
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	287 os.remove(signalp_input_file)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	288 os.remove(signalp_output_file)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	289
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	290 # Short summary to stdout for Galaxy's info display
20 a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	291 print("%s for %i sequences:" % (model, total))
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	292 print(", ".join("%s = %i" % kv for kv in sorted(tally.iteritems())))

Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/rxlr_motifs.py @ 20:a19b3ded8f33 draft