# HG changeset patch
# User mons
# Date 1415140795 18000
# Node ID ea16c9e1196a7def4e7a14b649a1ac1328ee8a67
# Parent ddbc12fc88854374c6996e3c64b0fb2861bcdd72
Deleted selected files
diff -r ddbc12fc8885 -r ea16c9e1196a genbanktofasta-6b5153d02ac2/README.txt
--- a/genbanktofasta-6b5153d02ac2/README.txt Tue Nov 04 17:27:17 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-
-----------------
-GenBank to FASTA
-----------------
-
-This package contains the GenBank to FASTA converter.
-
---------------------------------------------------------------------
-Instructions for integration of the "GenBank to FASTA" tool into the workflow-system
-Galaxy (http://getgalaxy.org)
---------------------------------------------------------------------
-
-For best results, we recommand you to install it via the toolshed.
-
-
diff -r ddbc12fc8885 -r ea16c9e1196a genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/.hg_archival.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/.hg_archival.txt Tue Nov 04 17:39:55 2014 -0500
@@ -0,0 +1,5 @@
+repo: 6b5153d02ac202223fe4db6796a55d3fa76f258f
+node: 6b5153d02ac202223fe4db6796a55d3fa76f258f
+branch: default
+latesttag: null
+latesttagdistance: 1
diff -r ddbc12fc8885 -r ea16c9e1196a genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/README.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/README.txt Tue Nov 04 17:39:55 2014 -0500
@@ -0,0 +1,15 @@
+
+----------------
+GenBank to FASTA
+----------------
+
+This package contains the GenBank to FASTA converter.
+
+--------------------------------------------------------------------
+Instructions for integration of the "GenBank to FASTA" tool into the workflow-system
+Galaxy (http://getgalaxy.org)
+--------------------------------------------------------------------
+
+For best results, we recommand you to install it via the toolshed.
+
+
diff -r ddbc12fc8885 -r ea16c9e1196a genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/genbanktofasta.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/genbanktofasta.py Tue Nov 04 17:39:55 2014 -0500
@@ -0,0 +1,40 @@
+#!/usr/bin/env python
+"""
+Input: genbank file
+Output: fasta nucleotide or protein sequences
+This bit of code will record the full DNA nucleotide sequence for each record in the GenBank file as a fasta record.
+http://www.warwick.ac.uk/go/peter_cock/python/genbank2fasta/
+"""
+
+import sys, os
+from Bio import SeqIO
+
+
+def __main__():
+
+ infile = sys.argv[1]
+ outfile= sys.argv[2]
+ input_handle = open(infile, "r")
+ output_handle = open(outfile, "w")
+ gbk_to_fna(input_handle,output_handle)
+
+
+#Short version:
+#SeqIO.write(SeqIO.parse(input_handle, "genbank"), output_handle, "fasta")
+#Long version, allows full control of fasta output
+
+def gbk_to_fna(input_handle,output_handle):
+ for seq_record in SeqIO.parse(input_handle, "genbank") :
+ print "Dealing with GenBank record %s" % seq_record.id
+ output_handle.write(">%s %s\n%s\n" % (
+ seq_record.id,
+ seq_record.description,
+ seq_record.seq.tostring()))
+ output_handle.close()
+ input_handle.close()
+ print "Done"
+
+
+
+if __name__ == "__main__" : __main__()
+
diff -r ddbc12fc8885 -r ea16c9e1196a genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/genbanktofasta.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/genbanktofasta.xml Tue Nov 04 17:39:55 2014 -0500
@@ -0,0 +1,51 @@
+
+
+
+ to Fasta format
+
+
+
+ python
+
+
+
+ genbanktofasta.py $input $output
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+================
+GenBank to Fasta
+================
+
+-----------
+Description
+-----------
+
+ | This tool converts a GenBank file to FASTA nucleotides format.
+ | Reference: http://www.warwick.ac.uk/go/peter_cock/python/genbank2fasta/
+
+.. image:: image.jpg
+
+
+
+
diff -r ddbc12fc8885 -r ea16c9e1196a genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/image.jpg
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diff -r ddbc12fc8885 -r ea16c9e1196a genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/genbanktofasta-6b5153d02ac2/genbanktofasta-6b5153d02ac2/repository_dependencies.xml Tue Nov 04 17:39:55 2014 -0500
@@ -0,0 +1,4 @@
+
+
+
+
diff -r ddbc12fc8885 -r ea16c9e1196a genbanktofasta-6b5153d02ac2/genbanktofasta.py
--- a/genbanktofasta-6b5153d02ac2/genbanktofasta.py Tue Nov 04 17:27:17 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,40 +0,0 @@
-#!/usr/bin/env python
-"""
-Input: genbank file
-Output: fasta nucleotide or protein sequences
-This bit of code will record the full DNA nucleotide sequence for each record in the GenBank file as a fasta record.
-http://www.warwick.ac.uk/go/peter_cock/python/genbank2fasta/
-"""
-
-import sys, os
-from Bio import SeqIO
-
-
-def __main__():
-
- infile = sys.argv[1]
- outfile= sys.argv[2]
- input_handle = open(infile, "r")
- output_handle = open(outfile, "w")
- gbk_to_fna(input_handle,output_handle)
-
-
-#Short version:
-#SeqIO.write(SeqIO.parse(input_handle, "genbank"), output_handle, "fasta")
-#Long version, allows full control of fasta output
-
-def gbk_to_fna(input_handle,output_handle):
- for seq_record in SeqIO.parse(input_handle, "genbank") :
- print "Dealing with GenBank record %s" % seq_record.id
- output_handle.write(">%s %s\n%s\n" % (
- seq_record.id,
- seq_record.description,
- seq_record.seq.tostring()))
- output_handle.close()
- input_handle.close()
- print "Done"
-
-
-
-if __name__ == "__main__" : __main__()
-
diff -r ddbc12fc8885 -r ea16c9e1196a genbanktofasta-6b5153d02ac2/genbanktofasta.xml
--- a/genbanktofasta-6b5153d02ac2/genbanktofasta.xml Tue Nov 04 17:27:17 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-
-
-
- to Fasta format
-
-
-
- python
-
-
-
- genbanktofasta.py $input $output
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-================
-GenBank to Fasta
-================
-
------------
-Description
------------
-
- | This tool converts a GenBank file to FASTA nucleotides format.
- | Reference: http://www.warwick.ac.uk/go/peter_cock/python/genbank2fasta/
-
-.. image:: image.jpg
-
-
-
-
diff -r ddbc12fc8885 -r ea16c9e1196a genbanktofasta-6b5153d02ac2/repository_dependencies.xml
--- a/genbanktofasta-6b5153d02ac2/repository_dependencies.xml Tue Nov 04 17:27:17 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-
-
-
-
diff -r ddbc12fc8885 -r ea16c9e1196a genbanktofasta-6b5153d02ac2/static/.DS_Store
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