snippy: snippy_core_wrapper.py comparison

planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty

comparison

equal deleted inserted replaced

-:eb46a277d64b
+:3f5ced130c5c
+#!/usr/bin/env python
+#--------------------------------------
+#
+#        snippy_core_wrapper.py
+#
+# This is an intermediary script between snippy-core.xml and snippy-core
+# It:
+#   - Copys the supplied zipped snippy output files to the working dir
+#   - Untars them to their datafile name
+#   - Builds the snippy-core command
+#   - Runs the snippy-core command
+#
+#--------------------------------------
+import os
+import sys
+import argparse
+import subprocess
+from shutil import copyfile
+def main():
+parser = argparse.ArgumentParser()
+parser.add_argument('-r', '--ref', help='Reference fasta', required=True)
+parser.add_argument('inputs', nargs='+')
+args = parser.parse_args()
+snippy_core_command_line = ['snippy-core', '--ref', args.ref]
+for input in args.inputs:
+bn = os.path.basename(input)
+sys.stderr.write(input + '\n')
+copyfile(input, bn)
+sys.stderr.write('\n'.join([input, bn]) + '\n')
+subprocess.run(['tar', '-xf', bn])
+test_list = [f.path for f in os.scandir() if f.is_dir() ]
+for dir in test_list:
+snippy_core_command_line.append(dir)
+print(snippy_core_command_line)
+subprocess.run(snippy_core_command_line)
+if __name__ == '__main__':
+main()

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