diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 583932fc933fead43ef49d65b2543bd345cbb62a..f339b4e614cdaad772c6256a8f87db11a4842178 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -1,6 +1,11 @@
=========
CHANGELOG
=========
+- 1.0.6
+ No default output file, only stdout
+
+ Fixing -e and -m behavior
+
- 1.0.5
Fix version date inside RPG
diff --git a/docs/conf.py b/docs/conf.py
index 11881614d72c1a9f259f4764a2301684e32bbb49..6c548c4ab8751ef92dde0b5f67483d598d1493f0 100644
--- a/docs/conf.py
+++ b/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 ---------------------------------------------------
diff --git a/rpg/RapidPeptidesGenerator.py b/rpg/RapidPeptidesGenerator.py
index ac5b5da0ab53d827fe56c650a48e4cd5654b55fc..a8b1edc32bbaa083cfc65eba5a2c70d3ad4f5ce1 100644
--- a/rpg/RapidPeptidesGenerator.py
+++ b/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,
diff --git a/rpg/core.py b/rpg/core.py
index 046d6b9bbda9a5ae43502e56c05a1f3bf079b2b9..8c3b0ddba69fdc90846133df28f491e1c4d5671c 100644
--- a/rpg/core.py
+++ b/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 ")
diff --git a/setup.py b/setup.py
index 9e5dc87894a22c32a9b4fe689d6aef5a89b94415..ec9795783162e92b307e92d481b85c3b70e4ea88 100644
--- a/setup.py
+++ b/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)