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changeset 23:e1996f0f4e85 draft default tip

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"v0.2.13 - Python 3 fix for raising StopIteration"
author peterjc
date Thu, 17 Jun 2021 17:59:33 +0000
parents e1afa4b0b682
children
files tools/protein_analysis/README.rst tools/protein_analysis/promoter2.xml tools/protein_analysis/psortb.xml tools/protein_analysis/rxlr_motifs.py tools/protein_analysis/rxlr_motifs.xml tools/protein_analysis/seq_analysis_utils.py tools/protein_analysis/signalp3.py tools/protein_analysis/signalp3.xml tools/protein_analysis/tmhmm2.py tools/protein_analysis/tmhmm2.xml tools/protein_analysis/wolf_psort.py tools/protein_analysis/wolf_psort.xml
diffstat 12 files changed, 12 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/tools/protein_analysis/README.rst	Thu Jun 17 08:34:58 2021 +0000
+++ b/tools/protein_analysis/README.rst	Thu Jun 17 17:59:33 2021 +0000
@@ -197,6 +197,7 @@
         - Reduce number of temp files if SignalP is run with one thread.
         - Applied black style to the Python code
         - Python 3 fixes with next function vs method.
+v0.2.13 - Python 3 fix for raising StopIteration.
 ======= ======================================================================
 
 
--- a/tools/protein_analysis/promoter2.xml	Thu Jun 17 08:34:58 2021 +0000
+++ b/tools/protein_analysis/promoter2.xml	Thu Jun 17 17:59:33 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="promoter2" name="Promoter 2.0" version="0.0.12">
+<tool id="promoter2" name="Promoter 2.0" version="0.0.13">
     <description>Find eukaryotic PolII promoters in DNA sequences</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <!-- Using 2000 per chunk so 4 threads each doing 500 is ideal -->
--- a/tools/protein_analysis/psortb.xml	Thu Jun 17 08:34:58 2021 +0000
+++ b/tools/protein_analysis/psortb.xml	Thu Jun 17 17:59:33 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="Psortb" name="psortb" version="0.0.9">
+<tool id="Psortb" name="psortb" version="0.0.10">
     <description>Determines sub-cellular localisation of bacterial/archaeal protein sequences</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
--- a/tools/protein_analysis/rxlr_motifs.py	Thu Jun 17 08:34:58 2021 +0000
+++ b/tools/protein_analysis/rxlr_motifs.py	Thu Jun 17 17:59:33 2021 +0000
@@ -52,7 +52,7 @@
 from seq_analysis_utils import fasta_iterator
 
 if "-v" in sys.argv:
-    print("RXLR Motifs v0.0.16")
+    print("RXLR Motifs v0.0.17")
     sys.exit(0)
 
 if len(sys.argv) != 5:
--- a/tools/protein_analysis/rxlr_motifs.xml	Thu Jun 17 08:34:58 2021 +0000
+++ b/tools/protein_analysis/rxlr_motifs.xml	Thu Jun 17 17:59:33 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.15">
+<tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.17">
     <description>Find RXLR Effectors of Plant Pathogenic Oomycetes</description>
     <requirements>
         <!-- Need SignalP for all the models -->
--- a/tools/protein_analysis/seq_analysis_utils.py	Thu Jun 17 08:34:58 2021 +0000
+++ b/tools/protein_analysis/seq_analysis_utils.py	Thu Jun 17 17:59:33 2021 +0000
@@ -19,7 +19,7 @@
 if sys.version_info[0] < 3:
     range = xrange  # noqa: F821
 
-__version__ = "0.0.4"
+__version__ = "0.0.5"
 
 try:
     from multiprocessing import cpu_count
@@ -108,7 +108,6 @@
                 % (title.split()[0], len(seq), max_len)
             )
         yield title, seq
-    raise StopIteration
 
 
 def split_fasta(
--- a/tools/protein_analysis/signalp3.py	Thu Jun 17 08:34:58 2021 +0000
+++ b/tools/protein_analysis/signalp3.py	Thu Jun 17 17:59:33 2021 +0000
@@ -67,7 +67,7 @@
 MAX_LEN = 6000  # Found by trial and error
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    print("SignalP Galaxy wrapper version 0.0.19")
+    print("SignalP Galaxy wrapper version 0.0.20")
     sys.exit(os.system("signalp -version"))
 
 if len(sys.argv) not in [6, 8]:
--- a/tools/protein_analysis/signalp3.xml	Thu Jun 17 08:34:58 2021 +0000
+++ b/tools/protein_analysis/signalp3.xml	Thu Jun 17 17:59:33 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="signalp3" name="SignalP 3.0" version="0.0.19">
+<tool id="signalp3" name="SignalP 3.0" version="0.0.20">
     <description>Find signal peptides in protein sequences</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
--- a/tools/protein_analysis/tmhmm2.py	Thu Jun 17 08:34:58 2021 +0000
+++ b/tools/protein_analysis/tmhmm2.py	Thu Jun 17 17:59:33 2021 +0000
@@ -52,7 +52,7 @@
 FASTA_CHUNK = 500
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    sys.exit("TMHMM wrapper version 0.0.16")
+    sys.exit("TMHMM wrapper version 0.0.17")
 
 if len(sys.argv) != 4:
     sys.exit(
--- a/tools/protein_analysis/tmhmm2.xml	Thu Jun 17 08:34:58 2021 +0000
+++ b/tools/protein_analysis/tmhmm2.xml	Thu Jun 17 17:59:33 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.16">
+<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.17">
     <description>Find transmembrane domains in protein sequences</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
--- a/tools/protein_analysis/wolf_psort.py	Thu Jun 17 08:34:58 2021 +0000
+++ b/tools/protein_analysis/wolf_psort.py	Thu Jun 17 17:59:33 2021 +0000
@@ -66,7 +66,7 @@
 """
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    sys.exit("WoLF-PSORT wrapper version 0.0.11")
+    sys.exit("WoLF-PSORT wrapper version 0.0.12")
 
 if len(sys.argv) != 5:
     sys.exit(
--- a/tools/protein_analysis/wolf_psort.xml	Thu Jun 17 08:34:58 2021 +0000
+++ b/tools/protein_analysis/wolf_psort.xml	Thu Jun 17 17:59:33 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="wolf_psort" name="WoLF PSORT" version="0.0.11">
+<tool id="wolf_psort" name="WoLF PSORT" version="0.0.12">
     <description>Eukaryote protein subcellular localization prediction</description>
     <requirements>
         <requirement type="package">wolfpsort</requirement>