Mercurial > repos > peterjc > get_orfs_or_cdss

changeset 30:147353248f95 draft

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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss commit 3ab3d1a9650dec0533344d710ceb027e482d2b10-dirty
author peterjc
date Fri, 09 Nov 2018 10:54:51 -0500
parents cb2272d1a9e8
children eaf1d40eceb4
files tools/get_orfs_or_cdss/get_orfs_or_cdss.py tools/get_orfs_or_cdss/get_orfs_or_cdss.xml
diffstat 2 files changed, 8 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/tools/get_orfs_or_cdss/get_orfs_or_cdss.py	Tue Jun 06 10:20:55 2017 -0400
+++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.py	Fri Nov 09 10:54:51 2018 -0500
@@ -10,7 +10,7 @@
 
 Cock et al 2009. Biopython: freely available Python tools for computational
 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
-http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
+https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
 
 This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute
 (formerly SCRI), Dundee, UK. All rights reserved.
@@ -120,7 +120,7 @@
 
 
 def start_chop_and_trans(s, strict=True):
-    """Returns offset, trimmed nuc, protein."""
+    """Return offset, trimmed nuc, protein."""
     if strict:
         assert s[-3:] in stops, s
     assert len(s) % 3 == 0
@@ -140,7 +140,7 @@
 
 
 def break_up_frame(s):
-    """Returns offset, nuc, protein."""
+    """Return offset, nuc, protein."""
     start = 0
     for match in re_stops.finditer(s):
         index = match.start() + 3
@@ -175,7 +175,7 @@
 
 
 def get_all_peptides(nuc_seq):
-    """Returns start, end, strand, nucleotides, protein.
+    """Return start, end, strand, nucleotides, protein.
 
     Co-ordinates are Python style zero-based.
     """
@@ -199,7 +199,7 @@
 
 
 def get_top_peptides(nuc_seq):
-    """Returns all peptides of max length."""
+    """Return all peptides of max length."""
     values = list(get_all_peptides(nuc_seq))
     if not values:
         raise StopIteration
@@ -210,7 +210,7 @@
 
 
 def get_one_peptide(nuc_seq):
-    """Returns first (left most) peptide with max length."""
+    """Return first (left most) peptide with max length."""
     values = list(get_top_peptides(nuc_seq))
     if not values:
         raise StopIteration
--- a/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml	Tue Jun 06 10:20:55 2017 -0400
+++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml	Fri Nov 09 10:54:51 2018 -0500
@@ -184,14 +184,14 @@
 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
 Galaxy tools and workflows for sequence analysis with applications
 in molecular plant pathology. PeerJ 1:e167
-http://dx.doi.org/10.7717/peerj.167
+https://doi.org/10.7717/peerj.167
 
 This tool uses Biopython, so you may also wish to cite the Biopython
 application note (and Galaxy too of course):
 
 Cock et al (2009). Biopython: freely available Python tools for computational
 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
-http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
+https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
 
 This tool is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss