flowcraft/templates/process_newick.py
def main(newick):
    """Main executor of the process_newick template.

    Parameters
    ----------
    newick : str
        path to the newick file.

    """

    logger.info("Starting newick file processing")

    print(newick)

    tree = dendropy.Tree.get(file=open(newick, 'r'), schema="newick")

    tree.reroot_at_midpoint()

    to_write=tree.as_string("newick").strip().replace("[&R] ", '').replace(' ', '_').replace("'", "")

    with open(".report.json", "w") as json_report:
        json_dic = {
            "treeData": [{
                "trees": [
                    to_write
                ]
            }],
        }

        json_report.write(json.dumps(json_dic, separators=(",", ":")))

    with open(".status", "w") as status_fh:
        status_fh.write("pass")
def main(newick):
    """Main executor of the process_newick template.

    Parameters
    ----------
    newick : str
        path to the newick file.

    """

    logger.info("Starting newick file processing")

    print(newick)

    tree = dendropy.Tree.get(file=open(newick, 'r'), schema="newick")

    tree.reroot_at_midpoint()

    to_write=tree.as_string("newick").strip().replace("[&R] ", '').replace(' ', '_').replace("'", "")

    with open(".report.json", "w") as json_report:
        json_dic = {
            "treeData": [{
                "trees": [
                    to_write
                ]
            }],
        }

        json_report.write(json.dumps(json_dic, separators=(",", ":")))

    with open(".status", "w") as status_fh:
        status_fh.write("pass")
def main ( newick ) : logger . info ( "Starting newick file processing" ) print ( newick ) tree = dendropy . Tree . get ( file = open ( newick , 'r' ) , schema = "newick" ) tree . reroot_at_midpoint ( ) to_write = tree . as_string ( "newick" ) . strip ( ) . replace ( "[&R] " , '' ) . replace ( ' ' , '_' ) . replace ( "'" , "" ) with open ( ".report.json" , "w" ) as json_report : json_dic = { "treeData" : [ { "trees" : [ to_write ] } ] , } json_report . write ( json . dumps ( json_dic , separators = ( "," , ":" ) ) ) with open ( ".status" , "w" ) as status_fh : status_fh . write ( "pass" )
Main executor of the process_newick template.

    Parameters
    ----------
    newick : str
        path to the newick file.
Main executor of the process_newick template .