# HG changeset patch
# User bgruening
# Date 1511172561 18000
# Node ID cd211b8c2e510b40f13eb14dfc83f5a04300364b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties commit 6767a5ffb02052c844e9d862c79912f998f39d8e
diff -r 000000000000 -r cd211b8c2e51 protein_properties.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/protein_properties.py Mon Nov 20 05:09:21 2017 -0500
@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+
+import sys
+from Bio import SeqIO
+from Bio.SeqUtils.ProtParam import ProteinAnalysis
+
+sys.stdout.write("ID\tMW\tIP\tgravy\tlength\tinstability\tmonoisotpoic\tSequence\n")
+
+for record in SeqIO.parse(sys.stdin, "fasta"):
+ a = ProteinAnalysis(str(record.seq))
+
+ properties = list()
+ properties.append(record.id)
+ properties.append(a.molecular_weight())
+ properties.append(a.isoelectric_point())
+ properties.append(a.gravy())
+ properties.append(a.length)
+ properties.append(a.instability_index())
+ properties.append(a.aromaticity())
+ # always last column to make the output more readable
+ properties.append(a.sequence)
+ sys.stdout.write( '\t'.join(map(str, properties))+"\n" )
+
diff -r 000000000000 -r cd211b8c2e51 protein_properties.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/protein_properties.xml Mon Nov 20 05:09:21 2017 -0500
@@ -0,0 +1,43 @@
+
+
+
+ biopython
+
+ '$output'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+ `_.
+
+ ]]>
+
+ 10.1093/bioinformatics/btp163
+
+
diff -r 000000000000 -r cd211b8c2e51 test-data/Q9LHB9.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Q9LHB9.fasta Mon Nov 20 05:09:21 2017 -0500
@@ -0,0 +1,9 @@
+>sp|Q9LHB9|PER32_ARATH Peroxidase 32 OS=Arabidopsis thaliana GN=PER32 PE=1 SV=3
+MNFSYSSLSTWTTLMTLGCLLLHSSISSAQLTPTFYDNTCPSVFTIVRDTIVNELRSDPR
+IAASILRLHFHDCFVNGCDASILLDNTTSFRTEKDAAPNANSARGFPVIDRMKAAVETAC
+PRTVSCADILTIAAQQAVNLAGGPSWRVPLGRRDSLQAFFALANTNLPAPFFTLPQLKAS
+FQNVGLDRPSDLVALSGGHTFGKNQCQFIMDRLYNFSNTGLPDPTLNTTYLQTLRGQCPR
+NGNQTVLVDFDLRTPTVFDNKYYVNLKELKGLIQTDQELFSSPNATDTIPLVREYADGTQ
+KFFNAFVEAMNRMGNITPLTGTQGQIRQNCRVVNSNSLLHDVVEIVDFVSSM
+>sp|Q9LHB9|PER32_ARATH short
+MNFSYSSLSTWTTLMTLGCLLLHSSISSAQLTPTFYDNTCPSVFTIVRDTIVNELRSDPR
diff -r 000000000000 -r cd211b8c2e51 test-data/protein_properties_result1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/protein_properties_result1.tabular Mon Nov 20 05:09:21 2017 -0500
@@ -0,0 +1,3 @@
+ID MW IP gravy length instability monoisotpoic Sequence
+sp|Q9LHB9|PER32_ARATH 38846.6361 6.20635986328 -0.0943181818182 352 31.0301420455 0.0880681818182 MNFSYSSLSTWTTLMTLGCLLLHSSISSAQLTPTFYDNTCPSVFTIVRDTIVNELRSDPRIAASILRLHFHDCFVNGCDASILLDNTTSFRTEKDAAPNANSARGFPVIDRMKAAVETACPRTVSCADILTIAAQQAVNLAGGPSWRVPLGRRDSLQAFFALANTNLPAPFFTLPQLKASFQNVGLDRPSDLVALSGGHTFGKNQCQFIMDRLYNFSNTGLPDPTLNTTYLQTLRGQCPRNGNQTVLVDFDLRTPTVFDNKYYVNLKELKGLIQTDQELFSSPNATDTIPLVREYADGTQKFFNAFVEAMNRMGNITPLTGTQGQIRQNCRVVNSNSLLHDVVEIVDFVSSM
+sp|Q9LHB9|PER32_ARATH 6733.5899 5.41021728516 0.13 60 35.0618333333 0.1 MNFSYSSLSTWTTLMTLGCLLLHSSISSAQLTPTFYDNTCPSVFTIVRDTIVNELRSDPR
diff -r 000000000000 -r cd211b8c2e51 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Nov 20 05:09:21 2017 -0500
@@ -0,0 +1,6 @@
+
+
+
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+