# HG changeset patch
# User iracooke
# Date 1395194766 14400
# Node ID 1bea12973e53ee8db0d975038ffa13284cb74cf0
Uploaded
diff -r 000000000000 -r 1bea12973e53 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Tue Mar 18 22:06:06 2014 -0400
@@ -0,0 +1,1 @@
+# This is my README
diff -r 000000000000 -r 1bea12973e53 protxml_to_gff.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/protxml_to_gff.xml Tue Mar 18 22:06:06 2014 -0400
@@ -0,0 +1,81 @@
+
+
+ protk
+ blast+
+
+
+ Map peptides from a protXML file to genomic coordinates
+
+
+ protxml_to_gff.rb -p $protxml_file
+
+ -g $genome_fasta_file
+
+ -d $protein_fasta_file
+
+ -o $output
+
+ --threshold $peptide_threshold
+
+ --prot-threshold $protein_threshold
+
+ $stack_charges
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+Generates a gff file containing genomic coordinates for peptides present in a protXML file.
+
+In order for this tool to work the inputs must satisfy certain requirements.
+
+1. The genome fasta should encode the scaffold numbers as in the following example
+
+>scaffoldXXX
+
+or
+
+>scaffold_XXX
+
+where XXX represent digits encoding the scaffold number. Any number of digits are allowed
+
+2. The protXML should have been generated by searching a database generated using the protk Generate 6 frame translation tool and the extract proteins from gff3 tool. Both those tools should be run with the genomics coordinates included in the output file.
+
+
+
+----
+
+**References**
+
+
+
+
+
diff -r 000000000000 -r 1bea12973e53 repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Tue Mar 18 22:06:06 2014 -0400
@@ -0,0 +1,4 @@
+
+
+
+
diff -r 000000000000 -r 1bea12973e53 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Mar 18 22:06:06 2014 -0400
@@ -0,0 +1,10 @@
+
+
+
+
+
+
+
+
+
+