Mercurial > repos > peterjc > tmhmm_and_signalp
diff tools/protein_analysis/promoter2.py @ 21:238eae32483c draft
"Check this is up to date with all 2020 changes (black etc)"
author | peterjc |
---|---|
date | Thu, 17 Jun 2021 08:21:06 +0000 |
parents | a19b3ded8f33 |
children |
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--- a/tools/protein_analysis/promoter2.py Thu Sep 21 11:35:20 2017 -0400 +++ b/tools/protein_analysis/promoter2.py Thu Jun 17 08:21:06 2021 +0000 @@ -41,8 +41,10 @@ sys.exit(os.system("promoter -V")) if len(sys.argv) != 4: - sys.exit("Require three arguments, number of threads (int), input DNA FASTA file & output tabular file. " - "Got %i arguments." % (len(sys.argv) - 1)) + sys.exit( + "Require three arguments, number of threads (int), input DNA FASTA " + "file & output tabular file. Got %i arguments." % (len(sys.argv) - 1) + ) num_threads = thread_count(sys.argv[3], default=4) fasta_file = os.path.abspath(sys.argv[2]) @@ -96,12 +98,16 @@ print("WARNING: Problem with line: %r" % line) continue # sys.exit("ERROR: Problem with line: %r" % line) - if likelihood not in ["ignored", - "Marginal prediction", - "Medium likely prediction", - "Highly likely prediction"]: + if likelihood not in [ + "ignored", + "Marginal prediction", + "Medium likely prediction", + "Highly likely prediction", + ]: sys.exit("ERROR: Problem with line: %r" % line) - out_handle.write("%s\t%s\t%s\t%s\n" % (identifier, position, score, likelihood)) + out_handle.write( + "%s\t%s\t%s\t%s\n" % (identifier, position, score, likelihood) + ) return queries @@ -114,10 +120,13 @@ # split_fasta returns an empty list (i.e. zero temp files). # We deliberately omit the FASTA descriptions to avoid a # bug in promoter2 with descriptions over 200 characters. -fasta_files = split_fasta(fasta_file, os.path.join(tmp_dir, "promoter"), FASTA_CHUNK, keep_descr=False) +fasta_files = split_fasta( + fasta_file, os.path.join(tmp_dir, "promoter"), FASTA_CHUNK, keep_descr=False +) temp_files = [f + ".out" for f in fasta_files] -jobs = ["%s %s > %s" % (bin, fasta, temp) - for fasta, temp in zip(fasta_files, temp_files)] +jobs = [ + "%s %s > %s" % (bin, fasta, temp) for fasta, temp in zip(fasta_files, temp_files) +] def clean_up(file_list): @@ -145,8 +154,11 @@ except IOError: output = "" clean_up(fasta_files + temp_files) - sys.exit("One or more tasks failed, e.g. %i from %r gave:\n%s" % (error_level, cmd, output), - error_level) + 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