tmhmm_and_signalp: tools/protein_analysis/rxlr

annotate tools/protein_analysis/rxlr_motifs.py @ 18:eb6ac44d4b8e draft

Suite v0.2.8, record Promoter 2 verion + misc internal updates

author	peterjc
date	Tue, 01 Sep 2015 09:56:36 -0400
parents	7de64c8b258d
children	f3ecd80850e2

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
a290c6d4e658 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
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).
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	38 """
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	39 import os
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	40 import sys
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	41 import re
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	42 import subprocess
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	43 from seq_analysis_utils import sys_exit, fasta_iterator
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	44
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	45 if "-v" in sys.argv:
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	46 print("RXLR Motifs v0.0.10")
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	47 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	48
a290c6d4e658 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:
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	50 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	51
a290c6d4e658 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:]
a290c6d4e658 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"
a290c6d4e658 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"
a290c6d4e658 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"
a290c6d4e658 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
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	57 hmmer_search = "hmmsearch2"
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	58
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	59 if model == "Bhattacharjee2006":
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	60 signalp_trunc = 70
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	61 re_rxlr = re.compile("R.LR")
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	62 min_sp = 10
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	63 max_sp = 40
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	64 max_sp_rxlr = 100
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	65 min_rxlr_start = 1
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	66 # 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	67 # 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	68 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	69 elif model == "Win2007":
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	70 signalp_trunc = 70
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	71 re_rxlr = re.compile("R.LR")
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	72 min_sp = 10
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	73 max_sp = 40
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	74 min_rxlr_start = 30
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	75 max_rxlr_start = 60
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	76 # 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	77 # 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	78 # 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	79 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	80 elif model == "Whisson2007":
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	81 signalp_trunc = 0 # zero for no truncation
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	82 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	83 min_sp = 10
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	84 max_sp = 40
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	85 max_sp_rxlr = 100
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	86 min_rxlr_start = 1
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	87 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	88 else:
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	89 sys_exit("Did not recognise the model name %r\n"
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	90 "Use Bhattacharjee2006, Win2007, or Whisson2007" % model)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	91
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	92
a290c6d4e658 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):
a290c6d4e658 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
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	95 try:
a290c6d4e658 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)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	97 except OSError:
a290c6d4e658 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)
a290c6d4e658 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()
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	100 if required:
a290c6d4e658 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
a290c6d4e658 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:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	103 return 2
a290c6d4e658 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:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	105 return 3
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	106 else:
a290c6d4e658 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)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	108
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	109
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	110 #Run hmmsearch for Whisson et al. (2007)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	111 if model == "Whisson2007":
a290c6d4e658 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],
a290c6d4e658 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")
a290c6d4e658 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):
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	115 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	116 if not get_hmmer_version(hmmer_search, "HMMER 2.3.2 (Oct 2003)"):
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	117 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	118
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	119 hmm_hits = set()
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	120 valid_ids = set()
a290c6d4e658 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):
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	122 name = title.split(None,1)[0]
a290c6d4e658 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:
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	124 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	125 else:
a290c6d4e658 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)
16 7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	127 if not valid_ids:
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	128 # 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	129 pass
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	130 else:
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	131 # 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	132 # 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	133 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	134 # 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	135 if hmmer3:
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	136 # 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	137 # 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	138 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	139 % (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	140 else:
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	141 # 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	142 # 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	143 # 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	144 # 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	145 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	146 % (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	147 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	148 if return_code:
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	149 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	150
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	151 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	152 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	153 if not line.strip():
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	154 # 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	155 continue
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	156 elif line.startswith("#"):
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	157 # Header
16 7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	158 continue
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	159 else:
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	160 name = line.split(None,1)[0]
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	161 #Should be a sequence name in the HMMER3 table output.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	162 #Could be anything in the HMMER2 stdout.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub peterjc parents: 6 diff changeset	163 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	164 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	165 elif hmmer3:
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	166 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	167 handle.close()
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	168 # if hmmer3:
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	169 # 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	170 # else:
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	171 # print "HMMER2 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	172 # 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	173 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	174 del valid_ids
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	175
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	176
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	177 # 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	178 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	179 count = 0
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	180 total = 0
a290c6d4e658 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")
a290c6d4e658 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):
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	183 total += 1
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	184 name = title.split(None,1)[0]
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	185 match = re_rxlr.search(seq[min_rxlr_start-1:].upper())
a290c6d4e658 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:
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	187 # 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	188 # 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	189 if signalp_trunc:
a290c6d4e658 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]))
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	191 else:
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	192 # 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	193 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	194 count += 1
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	195 handle.close()
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	196 # 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	197
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	198
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	199 # 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	200 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	201 if not os.path.isfile(signalp_script):
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	202 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	203 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	204 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	205 if return_code:
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	206 sys_exit("Error %i from SignalP:\n%s" % (return_code, cmd))
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	207 # print "SignalP done"
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	208
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	209
a290c6d4e658 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):
a290c6d4e658 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.
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	212
a290c6d4e658 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).
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	214 """
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	215 handle = open(filename)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	216 line = handle.readline()
a290c6d4e658 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
a290c6d4e658 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:
a290c6d4e658 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")
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	220 assert len(parts)==20, repr(line)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	221 yield parts[0], float(parts[18]), int(parts[5])-1
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	222 handle.close()
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	223
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	224
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	225 # 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	226 total = 0
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	227 tally = dict()
a290c6d4e658 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")
a290c6d4e658 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)
a290c6d4e658 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)
a290c6d4e658 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):
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	232 total += 1
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	233 rxlr = "N"
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	234 name = title.split(None,1)[0]
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	235 match = re_rxlr.search(seq[min_rxlr_start-1:].upper())
a290c6d4e658 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:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	237 del match
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	238 # This was the criteria for calling SignalP,
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	239 #so it will be in the SignalP results.
a290c6d4e658 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()
a290c6d4e658 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)
a290c6d4e658 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:
a290c6d4e658 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())
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	244 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	245 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	246 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	247 rxlr = "Y"
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	248 if model == "Whisson2007":
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	249 # 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	250 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	251 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	252 elif rxlr == "N":
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	253 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	254 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	255 rxlr = "re" # Heuristic only
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	256 # 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	257 # 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	258 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	259 try:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	260 tally[rxlr] += 1
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	261 except KeyError:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	262 tally[rxlr] = 1
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	263 handle.close()
a290c6d4e658 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
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	265
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	266 # 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	267 try:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	268 signalp_results.next()
a290c6d4e658 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"
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	270 except StopIteration:
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	271 pass
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	272
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	273 # Cleanup
6 a290c6d4e658 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)
a290c6d4e658 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)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	276
18 eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates peterjc parents: 16 diff changeset	277 # Short summary to stdout for Galaxy's info display
6 a290c6d4e658 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)
a290c6d4e658 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 @ 18:eb6ac44d4b8e draft