# HG changeset patch
# User sanbi-uwc
# Date 1457679729 18000
# Node ID d51c5af7a8fe8fb30515e4764713d789f381dfbb
# Parent 905996402f3c677596c27e88a9f327f104739411
planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
diff -r 905996402f3c -r d51c5af7a8fe novo_align.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/novo_align.py Fri Mar 11 02:02:09 2016 -0500
@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+import argparse
+from subprocess import check_call, CalledProcessError, Popen
+import shlex
+import os
+import logging
+log = logging.getLogger( __name__ )
+
+def novo_align(output_filename, index_filename, fwd_file, rev_file ):
+ #novoalign -c 8 -k -d /cip0/research/ajayi/RNA-seq_Analysis_Project_Case_Study/reference/Homo_Sapiens/out/TB_H37Rv.nix
+ # -f X165_820L8_.R1_val_1.fq X165_820L8_.R2_val_2.fq -i PE 250,100
+ # -o SAM '@RG\tID:readgroup\tPU:platform unit\tLB:library' | samtools view -bS - > `pwd`/out/X165_820L8.bam
+ #output_filename = path.join(output_directory, fwd_file.split(".")[0] + ".bam")
+ param = r'@RG\tID:RG\tSM:$i\tPL:ILLUMINA'
+ cmdline_str = "novoalign -c 8 -k -d {} -f {} {} -i PE 250, 100 -o SAM '{}' | samtools view -bS - > {}".format(
+ index_filename,
+ fwd_file,
+ rev_file,
+ param,
+ output_filename)
+ #cmdline = newSplit(cmdline_str)
+
+ os.system(cmdline_str)
+ #try:
+ #check_call(cmdline)
+ #except CalledProcessError:
+ # print("Error running the nova-align", file=sys.stderr)
+
+def newSplit(value):
+ lex = shlex.shlex(value)
+ lex.quotes = '"'
+ lex.whitespace_split = True
+ lex.commenters = ''
+ return list(lex)
+
+def main():
+ parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool")
+ parser.add_argument('output_filename')
+ parser.add_argument('--index_filename')
+ parser.add_argument('--forward_filename')
+ parser.add_argument('--reverse_filename')
+ args = parser.parse_args()
+
+ #a dirty way of referencing the file
+ index_file_path = args.index_filename + "/" + args.index_filename.split("/")[-1]
+
+ novo_align(args.output_filename, index_file_path, args.forward_filename, args.reverse_filename)
+
+if __name__ == "__main__": main()
diff -r 905996402f3c -r d51c5af7a8fe novo_align.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/novo_align.xml Fri Mar 11 02:02:09 2016 -0500
@@ -0,0 +1,32 @@
+
+
+ Tool to run the Novo Align mapping tool
+
+ samtools
+
+
+
+
+
+
+ novo_align.py '${out_file}' --index_file ${index1.fields.path} --forward_file ${fastq_input1} --reverse_file ${fastq_input2}
+
+
+
+
+
+
+
+
+
+
+
+ Help!
+
+
+
+
+
+
+
+
diff -r 905996402f3c -r d51c5af7a8fe novo_sort.py
--- a/novo_sort.py Thu Mar 10 15:53:44 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-#!/usr/bin/env python
-
-from __future__ import print_function
-import argparse
-from subprocess import check_call, CalledProcessError
-from json import load, dump, dumps
-from os import environ, mkdir, makedirs, path
-from os.path import isdir, exists
-import shlex
-import sys
-import logging
-log = logging.getLogger( __name__ )
-
-def novo_sort( bam_filename ):
- #novosort -c 8 -m 8G -s-f $i > $i".sorted"; done
- cmdline_str = "novosort -c 8 -m 8G -s -f {}".format( bam_filename )
- cmdline = newSplit(cmdline_str)
- try:
- check_call(cmdline)
- except CalledProcessError:
- print("Error running the nova-align", file=sys.stderr)
-
-def newSplit(value):
- lex = shlex.shlex(value)
- lex.quotes = '"'
- lex.whitespace_split = True
- lex.commenters = ''
- return list(lex)
-
-def main():
- parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool")
- parser.add_argument('output_filename')
- parser.add_argument('--bam_filename')
- args = parser.parse_args()
-
- novo_sort(args.bam_filename)
-
-if __name__ == "__main__": main()
diff -r 905996402f3c -r d51c5af7a8fe novo_sort.xml
--- a/novo_sort.xml Thu Mar 10 15:53:44 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-
-
- Tool to run the Novo Sort mapping tool
-
- samtools
-
-
-
-
-
-
- novo_sort.py '${out_file}' --bam_filename ${input1}
-
-
-
-
-
-
-
- Help!
-
-
-
-
-
-
-
-