complete util functions

PanACoTA/utils.py

@@ -522,6 +522,8 @@ def write_lstinfo(list_file, genomes, outdir):
         for genome, values in sorted(genomes.items(), key=sort_genomes_byname_l90_nbcont):
             gembase, _, to_annote, gsize, nbcont, l90 = [str(x) for x in values]
             outf.write("\t".join([gembase, genome, to_annote, gsize, nbcont, l90]) + "\n")
+    return outlst
+
 
 def sort_genomes_by_name(x):
     """
@@ -943,7 +945,7 @@ def cat(list_files, output, title=None):
         widgets = [title + ': ', progressbar.Bar(marker='█', left='', right='', fill=' '),
                    ' ', progressbar.Counter(), f"/{nbfiles}" ' (',
                    progressbar.Percentage(), ") - ", progressbar.Timer()]
-        bar = progressbar.ProgressBar(widgets=widgets, max_value=nbfiles, term_width=100).start()
+        bar = progressbar.ProgressBar(widgets=widgets, max_value=nbfiles, term_width=79).start()
         curnum = 1
     with open(output, "w") as outf:
         for file in list_files:

PanACoTA/utils_argparse.py

@@ -43,6 +43,7 @@ April 2017
 from PanACoTA import utils
 import argparse
 
+
 def gen_name(param):
     if not utils.check_format(param):
         msg = ("The genome name must contain 4 characters. For example, this name can "
@@ -136,3 +137,15 @@ def percentage(param):
                    "be in [0, 1]. Invalid value: {}".format(param))
             raise argparse.ArgumentTypeError(msg)
         return param
+
+
+def perc_id(param):
+    try:
+        param = float(param)
+    except Exception:
+        msg = "argument -i percentage_id: invalid float value: {}".format(param)
+        raise argparse.ArgumentTypeError(msg)
+    if param < 0 or param > 1:
+        msg = ("The minimum %% of identity must be in [0, 1]. Invalid value: {}".format(param))
+        raise argparse.ArgumentTypeError(msg)
+    return param