Remove default output file, now it is stdout

CHANGELOG.rst

 =========
 CHANGELOG
 =========
+- 1.0.6
+    No default output file, only stdout
+
+    Fixing -e and -m behavior
+
 - 1.0.5
     Fix version date inside RPG
 

docs/conf.py

@@ -26,7 +26,7 @@ author = 'Nicolas Maillet'
 # The short X.Y version
 version = ''
 # The full version, including alpha/beta/rc tags
-release = '1.0.5'
+release = '1.0.6'
 
 
 # -- General configuration ---------------------------------------------------

rpg/RapidPeptidesGenerator.py

@@ -29,9 +29,9 @@
 necessary functions
 """
 
-__version_info__ = ('1', '0', '5')
+__version_info__ = ('1', '0', '6')
 __version__ = '.'.join(__version_info__)
-__revision_date__ = "2018-07-13"
+__revision_date__ = "2018-11-19"
 __author__ = "Nicolas Maillet"
 
 import argparse
@@ -39,7 +39,7 @@ import os
 import sys
 import uuid
 from pathlib import Path
-from context import rpg
+#from context import rpg
 from rpg import core
 from rpg import digest
 from rpg import enzyme
@@ -277,11 +277,10 @@ def main():
                         "overwritten.")
     group_output = parser.add_mutually_exclusive_group()
     group_output.add_argument("-o", "--outputfile", type=str, metavar="",
-                              default="peptides", help="Result file to "
-                              "output result peptides (default './peptides"
-                              ".xxx' depending of --fmt)")
+                              default="", help="Optional result file "
+                              "to output result peptides.")
     group_output.add_argument("-r", "--randomname", action="store_true",
-                              help="Random (not used) output name file")
+                              help="Random (not used) output file name")
     group_verbose = parser.add_mutually_exclusive_group()
     group_verbose.add_argument("-q", "--quiet", action="store_true",
                                help="No standard output, only error(s)")
@@ -315,6 +314,7 @@ def main():
         args.verbose = 0
 
     # --outputfile / --randomname options
+    output_file = "" # No output file (default)
     if args.randomname:
         # Generate a random file name
         output_file = str(uuid.uuid4().hex) + "." + args.fmt
@@ -322,8 +322,8 @@ def main():
         while os.path.isfile(output_file):
             # Generate a random file name
             output_file = str(uuid.uuid4().hex) + "." + args.fmt
-    # Chosen file name
-    else:
+    # Chosen file name if exist
+    elif args.outputfile:
         # Given name
         tmpname = str(args.outputfile)
         # No extension?
@@ -366,7 +366,8 @@ def main():
         print("Mode: " + mode)
         print("miscleavage ratio: " +
               str([enz.ratio_miscleavage for enz in enzymes_to_use]))
-        print("Output file: " + os.path.abspath(output_file))
+        if output_file:
+            print("Output file: " + os.path.abspath(output_file))
 
     # Make the actual digestion of input data
     results_digestion = digest.digest_from_input(args.inputdata,

rpg/core.py

@@ -138,7 +138,7 @@ def get_header(fmt="fasta"):
 def output_results(output_file, all_seq_digested, fmt, quiet, verbose):
     """Output results of digestion in file and optionally in `stdout`.
 
-    :param output_file: the file where to print results
+    :param output_file: the file where to print results, if exist
     :param all_seq_digested: results of digestions
     :param fmt: output format (`csv`, `tsv` or `fasta`)
     :param quiet: quiet mode, no `stdout` message
@@ -150,32 +150,56 @@ def output_results(output_file, all_seq_digested, fmt, quiet, verbose):
     :type verbose: int
     """
 
-    # Open output file
-    try:
-        with open(output_file, 'w') as outfile:
-            # Header
-            header = get_header(fmt)
-            # If we have a header to print (csv/tsv)
-            if header:
-                # Print it in file
-                outfile.write(header + "\n")
-                # Stdout if small verbose
-                if verbose < 2 and not quiet:
-                    print(header)
-            # Print all peptides
-            for one_seq in all_seq_digested:  # list of list of ResultOneDig
-                # For all ResultOneDigestion
-                for one_enz_res in one_seq:
-                    # Print results in file
-                    outfile.write(format(one_enz_res, fmt))
-                    # Print on stdout
-                    if verbose >= 2:
-                        # Big verbose
-                        print(one_enz_res.get_more_info())
-                        if header:
-                            print(header)
-                    # Default stdout
-                    if not quiet:
-                        print(format(one_enz_res, fmt), end='')
-    except IOError:
-        handle_errors(output_file + " can't be open in 'w' mode", 0, "File ")
+    # Not output file
+    if not output_file:
+        # Header
+        header = get_header(fmt)
+        # If we have a header to print (csv/tsv)
+        if header:
+            # Stdout if small verbose
+            if verbose < 2 and not quiet:
+                print(header)
+        # Print all peptides
+        for one_seq in all_seq_digested:  # list of list of ResultOneDig
+            # For all ResultOneDigestion
+            for one_enz_res in one_seq:
+                # Print on stdout
+                if verbose >= 2:
+                    # Big verbose
+                    print(one_enz_res.get_more_info())
+                    if header:
+                        print(header)
+                # Default stdout
+                if not quiet:
+                    print(format(one_enz_res, fmt), end='')
+    # Output file exist
+    else:
+        try:
+            with open(output_file, 'w') as outfile:
+                # Header
+                header = get_header(fmt)
+                # If we have a header to print (csv/tsv)
+                if header:
+                    # Print it in file
+                    outfile.write(header + "\n")
+                    # Stdout if small verbose
+                    if verbose < 2 and not quiet:
+                        print(header)
+                # Print all peptides
+                for one_seq in all_seq_digested:  # list of list of ResultOneDi
+                    # For all ResultOneDigestion
+                    for one_enz_res in one_seq:
+                        # Print results in file
+                        outfile.write(format(one_enz_res, fmt))
+                        # Print on stdout
+                        if verbose >= 2:
+                            # Big verbose
+                            print(one_enz_res.get_more_info())
+                            if header:
+                                print(header)
+                        # Default stdout
+                        if not quiet:
+                            print(format(one_enz_res, fmt), end='')
+        except IOError:
+            handle_errors(output_file + " can't be open in 'w' mode", 0,
+                          "File ")

setup.py

@@ -4,7 +4,7 @@ from setuptools import setup, find_packages
 
 _MAJOR = 1
 _MINOR = 0
-_MICRO = 5
+_MICRO = 6
 version = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
 release = '%d.%d' % (_MAJOR, _MINOR)