Mercurial > repos > sanbi-uwc > build_ctb_gene
diff build_ctb_gene.py @ 10:cb322069c7bc draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit f3af88f047a6081a46925bdbb50161ad1244b4f1
| author | sanbi-uwc |
|---|---|
| date | Mon, 16 May 2016 10:34:46 -0400 |
| parents | 9cc174f0fb9f |
| children | 517691812452 |
line wrap: on
line diff
--- a/build_ctb_gene.py Mon May 16 05:45:10 2016 -0400 +++ b/build_ctb_gene.py Mon May 16 10:34:46 2016 -0400 @@ -4,45 +4,80 @@ import os import sys import glob +import shlex +import shutil +from subprocess import check_call, CalledProcessError import logging log = logging.getLogger(__name__) -def build_ctb_gene(output_file1, output_dir, input_file, mount_point): - # cmdline_str = "build_ctb_gene goterms ${}".format(input_file) - cmdline_str = "echo %s" % input_file - output_dir = mount_point - build_ctb = False - try: - os.system(cmdline_str) - build_ctb = True - except: - log.debug("Error running the build_ctb_gene goterms", file=sys.stderr) +class BuildCtbRunner(object): + + def __init__(self, args=None): + ''' + Initializes an object to run CtbRunner in Galaxy. + ''' + + # Check whether the options are specified and saves them into the object + assert args != None + self.args = args + + def build_ctb_gene(self, output_file1, output_dir, input_file, mount_point): + # cmdline_str = "build_ctb_gene goterms ${}".format(input_file) + cmdline_str = "touch /tmp/foo.bar" + build_ctb = False + cmdline_str = self.newSplit(cmdline_str) + try: + check_call(cmdline_str) + build_ctb = True + except CalledProcessError: + print("Error running the build_ctb_gene gotermS", file=sys.stderr) - # Read the files at the mount point and load the html file - if build_ctb: - files = glob.glob(mount_point) - output_file1 = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> - <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> - <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> - <title></title> - <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> - </head> - <body> - <div class="toolFormBody"> - <table> - <th>Files</th> - """ - for f in files: - output_file1 += "<tr><td>" + f + "</td></tr>" - output_file1 += """</table></div></body></html>\n""" + # Read the files at the mount point and load the html file + if build_ctb: + files = glob.glob(mount_point) + output_file1 = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> + <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> + <title></title> + <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> + </head> + <body> + <div class="toolFormBody"> + <table> + <th>Files</th> + """ + for f in files: + output_file1 += "<tr><td>" + f + "</td></tr>" + output_file1 += """</table></div></body></html>\n""" + + self.copy_output_file_to_dataset() + return output_file1 + + def newSplit(value): + lex = shlex.shlex(value) + lex.quotes = '"' + lex.whitespace_split = True + lex.commenters = '' + return list(lex) + + def copy_output_file_to_dataset(self): + ''' + Retrieves the output files from the output directory and copies them to the Galaxy output files + ''' + + # retrieve neo4j files to the working gx directory + result_file = glob.glob(self.args.mount_point + '/*') + with open(result_file[0], 'rb') as fsrc: + with open(self.args.outputdir, 'wb') as fdest: + shutil.copyfileobj(fsrc, fdest) def main(): - parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool") + parser = argparse.ArgumentParser(description="Tool used to extract data about genes using locus_tags") parser.add_argument('output_file1') parser.add_argument('--outputdir') parser.add_argument('--input_file') @@ -59,7 +94,12 @@ except: log.debug("Error exporting the NEO4J db environmental values") - build_ctb_gene(args.output_file1, args.outputdir, args.input_file, args.mount_point) + # make the output directory + if not os.path.exists(args.outputdir): + os.makedirs(args.outputdir) + + ctb_gene_runner = BuildCtbRunner(args) + ctb_gene_runner.build_ctb_gene(args.output_file1, args.outputdir, args.input_file, args.mount_point) if __name__ == "__main__": main()