# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent kpvincent@bx.psu.edu # Date 1283348652 14400 # Node ID 09a684e9e0d42a3704e0093a15e54ad339da6329 # Parent 397241b761abe9a0cdad1f815e0a83328e3a665c Added BAM-to-SAM tool
--- /dev/null +++ b/test-data/bam_to_sam_out1.sam @@ -0,0 +1,10 @@ +HWI-EAS91_1_30788AAXX:1:1:1698:516 16 * 2735 25 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1398:854 16 * 3921 25 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1716:413 0 * 6040 25 36M * 0 0 GATCCAANNCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1634:211 0 * 9350 25 36M * 0 0 GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1513:715 16 * 9563 25 36M * 0 0 CTGACTACCACAACTAAACATCTATGCNNAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1310:991 16 * 10002 25 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTANNACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1711:249 16 * 10617 25 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1491:637 16 * 10864 25 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1630:59 16 * 12387 25 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1218:141 16 * 14062 25 36M * 0 0 ACAAAACTAACAACAAAAATAACACTCNNAATAAAC I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
--- /dev/null +++ b/tools/samtools/bam_to_sam.py @@ -0,0 +1,66 @@ +#!/usr/bin/env python +""" +Converts BAM data to sorted SAM data. +usage: bam_to_sam.py [options] + --input1: SAM file to be converted + --output1: output dataset in bam format +""" + +import optparse, os, sys, subprocess, tempfile, shutil +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +from bx.cookbook import doc_optparse +#from galaxy import util + +def stop_err( msg ): + sys.stderr.write( '%s\n' % msg ) + sys.exit() + +def __main__(): + #Parse Command Line + parser = optparse.OptionParser() + parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' ) + parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' ) + ( options, args ) = parser.parse_args() + + tmp_dir = tempfile.mkdtemp() + try: + # exit if input file empty + if os.path.getsize( options.input1 ) == 0: + raise Exception, 'Initial BAM file empty' + # Extract all alignments from the input BAM file to SAM format ( since no region is specified, all the alignments will be extracted ). + command = 'samtools view -o %s %s' % ( options.output1, options.input1 ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + tmp_stderr.close() + # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + if returncode != 0: + raise Exception, stderr + except Exception, e: + #clean up temp files + if os.path.exists( tmp_dir ): + shutil.rmtree( tmp_dir ) + stop_err( 'Error extracting alignments from (%s), %s' % ( options.input1, str( e ) ) ) + #clean up temp files + if os.path.exists( tmp_dir ): + shutil.rmtree( tmp_dir ) + # check that there are results in the output file + if os.path.getsize( options.output1 ) > 0: + sys.stdout.write( 'BAM file converted to SAM' ) + else: + stop_err( 'The output file is empty, there may be an error with your input file.' ) + +if __name__=="__main__": __main__()
--- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -286,6 +286,7 @@ <tool file="samtools/sam_bitwise_flag_filter.xml" /><tool file="samtools/sam2interval.xml" /><tool file="samtools/sam_to_bam.xml" /> + <tool file="samtools/bam_to_sam.xml" /><tool file="samtools/sam_merge.xml" /><tool file="samtools/sam_pileup.xml" /><tool file="samtools/pileup_parser.xml" />
--- /dev/null +++ b/tools/samtools/bam_to_sam.xml @@ -0,0 +1,37 @@ +<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.0"> + <description>converts BAM format to SAM format</description> + <command interpreter="python">bam_to_sam.py --input1=$input1 --output1=$output1</command> + <inputs> + <param name="input1" type="data" format="bam" label="BAM File to Convert" /> + </inputs> + <outputs> + <data name="output1" format="sam" /> + </outputs> + <tests> + <test> + <!-- + Bam-to-Sam command: + samtools view -o test-data/3.bam bam_to_sam_out1.sam + --> + <param name="input1" value="1.bam" ftype="bam" /> + <output name="output1" file="bam_to_sam_out1.sam" /> + </test> + <test> + <!-- + Bam-to-Sam command: + samtools view -o test-data/1.sam bam_to_sam_out2.sam + --> + <param name="input1" value="3.bam" ftype="bam" /> + <param name="output1" file="bam_to_sam_out2.sam" /> + </test> + </tests> + <help> + +**What it does** + +This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file. + +.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml + + </help> +</tool>
--- /dev/null +++ b/test-data/bam_to_sam_out2.sam @@ -0,0 +1,10 @@ +HWI-EAS91_1_30788AAXX:1:1:1095:605 0 chrM 23 25 36M * 0 0 AAGCAAGNNACTGAAAATGCCTAGATGAGTATTCTT IIIIIII""IIIIIIIIIIIIIIIEIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1650:1185 0 chrM 14956 25 36M * 0 0 ACCCCAGNNAACCCTCTCAGCACTCCCCCTCATATT IIIIIII""IIIIIIIIIIII6IIIIIIIII5I-II NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:799:192 16 chrM 8421 25 36M * 0 0 CCTGTAGCCCTAGCCGTGCGGCTAACCNNTAACATT II%::I<IIIIIEIII8IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1082:719 16 chrM 7191 25 36M * 0 0 TAAATTAACCCATACCAGCACCATAGANNCTCAAGA <III0EII3+3I29I>III8AIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1746:1180 16 chrM 12013 25 36M * 0 0 CCTAAGCTTCAAACTAGATTACTTCTCNNTAATTTT IIIIIIIIFIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:606:460 0 chrM 4552 25 36M * 0 0 TTAATTTNNATTATAATAACACTCACAATATTCATA IIIIIII""IIIIIIIIIIIIIIIIII?I6IIIII6 NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1059:362 16 chrM 7348 25 36M * 0 0 GGCCACCAATGATACTGAAGCTACGAGNNTACCGAT II/<)2IIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1483:1161 16 chrM 15080 25 36M * 0 0 TCCTGATCCTAGCACTCATCCCCACCCNNCACATAT HIIIIIFIIAIHIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1273:600 16 chrM 13855 25 36M * 0 0 GTATTAGACACCCATACCTCAGGATACNNCTCAGTA IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1190:1283 16 chrM 15338 25 36M * 0 0 TATATCGCACATTACCCTGGTCTTGTANNCCAGAAA EIII?-IIIIIAIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27