Mercurial > repos > peterjc > tmhmm_and_signalp

comparison tools/protein_analysis/rxlr_motifs.py @ 18:2b35b5c4b7f4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.2.5, preview 2, fixed bug in RXLR tools
author peterjc
date Fri, 10 May 2013 07:48:26 -0400
parents 39a6e46cdda3
children 20139cb4c844
comparison
equal deleted inserted replaced
17:af3174637834 18:2b35b5c4b7f4
109 "whisson_et_al_rxlr_eer_cropped.hmm") 109 "whisson_et_al_rxlr_eer_cropped.hmm")
110 if not os.path.isfile(hmm_file): 110 if not os.path.isfile(hmm_file):
111 stop_err("Missing HMM file for Whisson et al. (2007)") 111 stop_err("Missing HMM file for Whisson et al. (2007)")
112 if not get_hmmer_version(hmmer_search, "HMMER 2.3.2 (Oct 2003)"): 112 if not get_hmmer_version(hmmer_search, "HMMER 2.3.2 (Oct 2003)"):
113 stop_err("Missing HMMER 2.3.2 (Oct 2003) binary, %s" % hmmer_searcher) 113 stop_err("Missing HMMER 2.3.2 (Oct 2003) binary, %s" % hmmer_searcher)
114 #I've left the code to handle HMMER 3 in situ, in case 114
115 #we revisit the choice to insist on HMMER 2.
116 hmmer3 = (3 == get_hmmer_version(hmmer_search))
117 #Using zero (or 5.6?) for bitscore threshold
118 if hmmer3:
119 #The HMMER3 table output is easy to parse
120 #In HMMER3 can't use both -T and -E
121 cmd = "%s -T 0 --tblout %s --noali %s %s > /dev/null" \
122 % (hmmer_search, hmm_output_file, hmm_file, fasta_file)
123 else:
124 #For HMMER2 we are stuck with parsing stdout
125 #Put 1e6 to effectively have no expectation threshold (otherwise
126 #HMMER defaults to 10 and the calculated e-value depends on the
127 #input FASTA file, and we can loose hits of interest).
128 cmd = "%s -T 0 -E 1e6 %s %s > %s" \
129 % (hmmer_search, hmm_file, fasta_file, hmm_output_file)
130 return_code = os.system(cmd)
131 if return_code:
132 stop_err("Error %i from hmmsearch:\n%s" % (return_code, cmd))
133 hmm_hits = set() 115 hmm_hits = set()
134 valid_ids = set() 116 valid_ids = set()
135 for title, seq in fasta_iterator(fasta_file): 117 for title, seq in fasta_iterator(fasta_file):
136 name = title.split(None,1)[0] 118 name = title.split(None,1)[0]
137 if name in valid_ids: 119 if name in valid_ids:
138 stop_err("Duplicated identifier %r" % name) 120 stop_err("Duplicated identifier %r" % name)
139 else: 121 else:
140 valid_ids.add(name) 122 valid_ids.add(name)
141 handle = open(hmm_output_file) 123 if not valid_ids:
142 for line in handle: 124 #Special case, don't need to run HMMER if there are no sequences
143 if not line.strip(): 125 pass
144 #We expect blank lines in the HMMER2 stdout 126 else:
145 continue 127 #I've left the code to handle HMMER 3 in situ, in case
146 elif line.startswith("#"): 128 #we revisit the choice to insist on HMMER 2.
147 #Header 129 hmmer3 = (3 == get_hmmer_version(hmmer_search))
148 continue 130 #Using zero (or 5.6?) for bitscore threshold
131 if hmmer3:
132 #The HMMER3 table output is easy to parse
133 #In HMMER3 can't use both -T and -E
134 cmd = "%s -T 0 --tblout %s --noali %s %s > /dev/null" \
135 % (hmmer_search, hmm_output_file, hmm_file, fasta_file)
149 else: 136 else:
150 name = line.split(None,1)[0] 137 #For HMMER2 we are stuck with parsing stdout
151 #Should be a sequence name in the HMMER3 table output. 138 #Put 1e6 to effectively have no expectation threshold (otherwise
152 #Could be anything in the HMMER2 stdout. 139 #HMMER defaults to 10 and the calculated e-value depends on the
153 if name in valid_ids: 140 #input FASTA file, and we can loose hits of interest).
154 hmm_hits.add(name) 141 cmd = "%s -T 0 -E 1e6 %s %s > %s" \
155 elif hmmer3: 142 % (hmmer_search, hmm_file, fasta_file, hmm_output_file)
156 stop_err("Unexpected identifer %r in hmmsearch output" % name) 143 return_code = os.system(cmd)
157 handle.close() 144 if return_code:
158 #if hmmer3: 145 stop_err("Error %i from hmmsearch:\n%s" % (return_code, cmd), return_code)
159 # print "HMMER3 hits for %i/%i" % (len(hmm_hits), len(valid_ids)) 146
160 #else: 147 handle = open(hmm_output_file)
161 # print "HMMER2 hits for %i/%i" % (len(hmm_hits), len(valid_ids)) 148 for line in handle:
162 #print "%i/%i matched HMM" % (len(hmm_hits), len(valid_ids)) 149 if not line.strip():
163 os.remove(hmm_output_file) 150 #We expect blank lines in the HMMER2 stdout
151 continue
152 elif line.startswith("#"):
153 #Header
154 continue
155 else:
156 name = line.split(None,1)[0]
157 #Should be a sequence name in the HMMER3 table output.
158 #Could be anything in the HMMER2 stdout.
159 if name in valid_ids:
160 hmm_hits.add(name)
161 elif hmmer3:
162 stop_err("Unexpected identifer %r in hmmsearch output" % name)
163 handle.close()
164 #if hmmer3:
165 # print "HMMER3 hits for %i/%i" % (len(hmm_hits), len(valid_ids))
166 #else:
167 # print "HMMER2 hits for %i/%i" % (len(hmm_hits), len(valid_ids))
168 #print "%i/%i matched HMM" % (len(hmm_hits), len(valid_ids))
169 os.remove(hmm_output_file)
164 del valid_ids 170 del valid_ids
165 171
166 172
167 #Prepare short list of candidates containing RXLR to pass to SignalP 173 #Prepare short list of candidates containing RXLR to pass to SignalP
168 assert min_rxlr_start > 0, "Min value one, since zero based counting" 174 assert min_rxlr_start > 0, "Min value one, since zero based counting"