# HG changeset patch
# User rnateam
# Date 1445026414 14400
# Node ID ae4d5733272f8b3efc7c8ff869ff9b50f420b334
# Parent 7439ffbd894308e3711cce9c40606006a40bcd88
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta commit 03f3cc2000e6ce876a3cb44c55c3fe878a2e7ce3-dirty
diff -r 7439ffbd8943 -r ae4d5733272f splitFasta.py
--- a/splitFasta.py Wed Jul 08 06:23:46 2015 -0400
+++ b/splitFasta.py Fri Oct 16 16:13:34 2015 -0400
@@ -1,14 +1,13 @@
-import sys, os
+#!/usr/bin/env python
+import os
+import sys
+from Bio import SeqIO
+
if __name__ == "__main__":
- #assuming perfect input, read every two lines
inpath = sys.argv[1]
- file_contents = open(inpath, 'r').readlines()
- os.makedirs('splits')
- inname = os.path.basename(inpath)
- for i in range(0, len(file_contents), 2):
- headline = file_contents[i]
- outname = headline[1:headline.index(' ')]+'.fa'
- outfile = open(os.path.join('splits',outname), 'w')
- outfile.write(file_contents[i])
- outfile.write(file_contents[i+1])
- outfile.close()
+ os.mkdir('splits')
+ with open(inpath, 'r') as handle:
+ for record in SeqIO.parse(handle, 'fasta'):
+ header = os.path.join('splits', record.id + '.fasta')
+ with open(header, 'w') as handle2:
+ SeqIO.write([record], handle2, 'fasta')
diff -r 7439ffbd8943 -r ae4d5733272f splitFasta.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/splitFasta.xml Fri Oct 16 16:13:34 2015 -0400
@@ -0,0 +1,44 @@
+
+ files into a collection
+
+ biopython
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+ @ARTICLE{bgruening_galaxytools,
+ Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},
+ keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
+ title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
+ url = {https://github.com/bgruening/galaxytools}
+ }
+
+
+
diff -r 7439ffbd8943 -r ae4d5733272f splitfasta.xml
--- a/splitfasta.xml Wed Jul 08 06:23:46 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
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- outputFormat == 'collection'
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- outputFormat == 'separate'
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- @ARTICLE{bgruening_galaxytools,
- Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},
- keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
- title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
- url = {https://github.com/bgruening/galaxytools}
- }
-
-
-
-
diff -r 7439ffbd8943 -r ae4d5733272f test-data/ID1_result1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ID1_result1.fasta Fri Oct 16 16:13:34 2015 -0400
@@ -0,0 +1,2 @@
+>ID1 desc
+GATACA
diff -r 7439ffbd8943 -r ae4d5733272f test-data/ID2_result1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ID2_result1.fasta Fri Oct 16 16:13:34 2015 -0400
@@ -0,0 +1,2 @@
+>ID2 desc
+GATACAGATACAGATACAGATACAGATACA
diff -r 7439ffbd8943 -r ae4d5733272f test-data/ID3_result1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ID3_result1.fasta Fri Oct 16 16:13:34 2015 -0400
@@ -0,0 +1,3 @@
+>ID3 desc
+GATACAGATACAGATACAGATACAGATACAGATACAGATACAGATACAGATACAGATACA
+GATACA
diff -r 7439ffbd8943 -r ae4d5733272f test-data/test.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.fasta Fri Oct 16 16:13:34 2015 -0400
@@ -0,0 +1,11 @@
+>ID1 desc
+GATACA
+
+
+>ID2 desc
+GATACAGATACA
+GATACAGA
+TACAGATACA
+>ID3 desc
+GATACAGATACAGATACAGATACAGATACAGATACAGATACAGATACAGATACAGA
+TACAGATACA
diff -r 7439ffbd8943 -r ae4d5733272f tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri Oct 16 16:13:34 2015 -0400
@@ -0,0 +1,6 @@
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