Mercurial > repos > peterjc > tmhmm_and_signalp
diff tools/protein_analysis/tmhmm2.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 | 99b82a2b1272 |
children | f3ecd80850e2 |
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--- a/tools/protein_analysis/tmhmm2.py Fri Nov 21 08:19:09 2014 -0500 +++ b/tools/protein_analysis/tmhmm2.py Tue Sep 01 09:56:36 2015 -0400 @@ -43,12 +43,12 @@ import sys import os import tempfile -from seq_analysis_utils import stop_err, split_fasta, run_jobs, thread_count +from seq_analysis_utils import sys_exit, split_fasta, run_jobs, thread_count FASTA_CHUNK = 500 if len(sys.argv) != 4: - stop_err("Require three arguments, number of threads (int), input protein FASTA file & output tabular file") + sys_exit("Require three arguments, number of threads (int), input protein FASTA file & output tabular file") num_threads = thread_count(sys.argv[1], default=4) fasta_file = sys.argv[2] @@ -68,7 +68,7 @@ identifier, length, expAA, first60, predhel, topology = parts except: assert len(parts)!=6 - stop_err("Bad line: %r" % line) + sys_exit("Bad line: %r" % line) assert length.startswith("len="), line length = length[4:] assert expAA.startswith("ExpAA="), line @@ -112,7 +112,7 @@ except IOError: output = "" clean_up(fasta_files + temp_files) - stop_err("One or more tasks failed, e.g. %i from %r gave:\n%s" % (error_level, cmd, output), + sys_exit("One or more tasks failed, e.g. %i from %r gave:\n%s" % (error_level, cmd, output), error_level) del results del jobs @@ -125,7 +125,7 @@ data_handle.close() if not count: clean_up(fasta_files + temp_files) - stop_err("No output from tmhmm2") + sys_exit("No output from tmhmm2") out_handle.close() clean_up(fasta_files + temp_files)