BlastToSam

##Motivation

Convert a BLASTN-XML input to SAM

##Compilation

Requirements / Dependencies

java 1.8 http://www.oracle.com/technetwork/java/index.html (NOT the old java 1.7 or 1.6) . Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
GNU Make > 3.81
curl/wget
git
apache ant is only required to compile htsjdk
xsltproc http://xmlsoft.org/XSLT/xsltproc2.html

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make blast2sam

by default, the libraries are not included in the jar file, so you shouldn't move them (https://github.com/lindenb/jvarkit/issues/15#issuecomment-140099011 ). You can create a bigger but standalone executable jar by addinging standalone=yes on the command line:

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make blast2sam standalone=yes

The required libraries will be downloaded and installed in the dist directory.

edit 'local.mk' (optional)

The a file local.mk can be created edited to override/add some paths.

For example it can be used to set the HTTP proxy:

http.proxy.host=your.host.com
http.proxy.port=124567

##Synopsis

$ java -jar dist/blast2sam.jar  [options] (stdin|file)

Options

-o|--output (OUTPUT-FILE) Output file. Default:stdout.
-formatout|--formatout (FORMAT) output format : sam or bam. if stdout is used Default value : "sam".
-bam_compression_level|--bam_compression_level (LEVEL) BAM Compression level (0-9) Default value : "9".
-r|--REF (FASTA) indexed Fasta sequence
-p|--expect_size (VALUE) input is an interleaved list of sequences forward and reverse (paired-ends). 0: not interleaved Default value : "0".
-h|--help print help
-version|--version show version and exit

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/blast2sam/BlastToSam.java

Example

The following Makefile downloads a reference , generates some FASTQs, align them with blastn and convert it to SAM:

BLASTN=/commun/data/packages/ncbi/ncbi-blast-2.2.28+/bin/blastn
SAMTOOLS=/commun/data/packages/samtools-0.1.19
JVARKIT=/home/lindenb/src/jvarkit-git/dist/
SHELL=/bin/bash
.PHONY:all reads clean
all: out.sam



out.sam: ref.fa ref.fa.fai out.read1.fq out.read2.fq
	paste \
		<(cat out.read1.fq | paste - - - - | cut -f 1,2 ) \
		<(cat out.read2.fq | paste - - - - | cut -f 1,2 ) |\
	tr "\t" "\n" |\
	sed 's/^@/>/' |\
	${BLASTN} -subject ref.fa -dust no -outfmt 5 | \
	java -jar ${JVARKIT}/blast2sam.jar -r ref.fa -p 500  |\
	${SAMTOOLS}/samtools view -Sh -f 2 - > $@
	
reads: out.read1.fq out.read2.fq
out.read1.fq out.read2.fq: ref.fa ref.fa.fai
	${SAMTOOLS}/misc/wgsim  -d 100 -N 500 -1 50 -2 50   $< out.read1.fq out.read2.fq > /dev/null

ref.fa:
	curl -k -o $@ "https://raw.github.com/lindenb/genomehub/master/data/rotavirus/rf/rf.fa"

ref.fa.fai: ref.fa
	${SAMTOOLS}/samtools faidx $<

clean:
	rm -f ref.fa.fai ref.fa out.sam

Output

@HD	VN:1.4	SO:unsorted
@SQ	SN:RF01	LN:3302
@SQ	SN:RF02	LN:2687
@SQ	SN:RF03	LN:2592
@SQ	SN:RF04	LN:2362
@SQ	SN:RF05	LN:1579
@SQ	SN:RF06	LN:1356
@SQ	SN:RF07	LN:1074
@SQ	SN:RF08	LN:1059
@SQ	SN:RF09	LN:1062
@SQ	SN:RF10	LN:751
@SQ	SN:RF11	LN:666
@RG	ID:g1	LB:blast	DS:blast	SM:blast
@PG	ID:0	PN:blastn	VN:BLASTN_2.2.28+
@PG	ID:1	PN:com.github.lindenb.jvarkit.tools.blast2sam.BlastToSam	PP:0	VN:3365d9b714aa43d4fba44bfbf102a179a1f1573f	CL:-r ref.fa -p 500
RF01_445_573_0:0:0_0:0:0_0/1	83	RF01	524	40	50=	=	445	-30	GTGCCTTGGTACACCATATTTATTTACTGTTGAAGCTACTATAGTGAATA	JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ	BB:f:93.4528	BE:f:9.71473e-24	RG:Z:g1	NM:i:0	BS:f:50
RF01_445_573_0:0:0_0:0:0_0/2	163	RF01	445	40	50=	=	524	30	AATGCAGTTATGTTCTGGTTGGAAAAACATGAAAATGACGTTGCTGAAAA	JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ	BB:f:93.4528	BE:f:9.71473e-24	RG:Z:g1	NM:i:0	BS:f:50
RF01_1193_1294_1:0:0_1:0:0_1/1	83	RF01	1245	40	38=1X11=	=	1193	-3	CCATTACATGCATATTCTTTTTAGTCGAAAAAATTGTCATTCTACCAAAT	JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ	BB:f:87.9128	BE:f:4.51982e-22	RG:Z:g1	NM:i:0	BS:f:47
RF01_1193_1294_1:0:0_1:0:0_1/2	163	RF01	1193	40	4=1X45=	=	1245	3	CTGGATTACTATCAATGTCATCAGCGTCGAATGGTGAATCAAGACAACTA	JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ	BB:f:87.9128	BE:f:4.51982e-22	RG:Z:g1	NM:i:0	BS:f:47
RF01_638_718_1:0:0_0:0:0_2/1	83	RF01	669	40	50=	=	638	18	ATGACAGTACTATCAGTTCTCTCGCAATTAAATAATCTTCATGAGAAAAA	JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ	BB:f:93.4528	BE:f:9.71473e-24	RG:Z:g1	NM:i:0	BS:f:50
RF01_638_718_1:0:0_0:0:0_2/2	163	RF01	638	40	4=1X45=	=	669	-18	CAAAATCTTCAATTGAAATGCTGATGTCAGTTTTTTCTCATGAAGATTAT	JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ	BB:f:87.9128	BE:f:4.51982e-22	RG:Z:g1	NM:i:0	BS:f:47
RF01_1404_1584_0:0:0_2:0:0_3/1	99	RF01	1404	40	50=	=	1535	179	ATTTATCTTACCATATGAATATTTCATAGCACAACATGCTGTAGTTGAAA	JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ	BB:f:93.4528	BE:f:9.71473e-24	RG:Z:g1	NM:i:0	BS:f:50
RF01_1404_1584_0:0:0_2:0:0_3/2	147	RF01	1535	40	1S42=1X6=	=	1404	-179	NGACACGTCTGTATATAGTACCATAGAGTTATTAGATAAAAAGGGTGTAA	#JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ	BB:f:86.0662	BE:f:1.62562e-21	RG:Z:g1	NM:i:0	BS:f:46
RF01_284_373_0:0:0_1:0:0_5/1	99	RF01	284	40	50=	=	324	89	TAGTAAAATATGCAAAAGGTAAGCCGCTAGAAGCAGATTTGACAGTGAAT	JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ	BB:f:93.4528	BE:f:9.71473e-24	RG:Z:g1	NM:i:0	BS:f:50
RF01_284_373_0:0:0_1:0:0_5/2	147	RF01	324	40	8=1X41=	=	284	-89	AAAGTTCATATGTTATCTTGTTATTTTCATAATCCAACTCATTCACTGTC	JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ	BB:f:87.9128	BE:f:4.51982e-22	RG:Z:g1	NM:i:0	BS:f:47
RF01_1704_1823_1:0:0_0:0:0_7/1	83	RF01	1774	40	50=	=	1704	-21	ATTGAATTCGCTGCTTTCGTCTGCTTCTCTCCTGACGCTACAGCCCCATA	JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ	BB:f:93.4528	BE:f:9.71473e-24	RG:Z:g1	NM:i:0	BS:f:50
RF01_1704_1823_1:0:0_0:0:0_7/2	163	RF01	1704	40	5=1X44=	=	1774	21	ACAGAGGCAAATTAATCTAATGGATTCATACGTTCAAATACCAGATGGTA	JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ	BB:f:87.9128	BE:f:4.51982e-22	RG:Z:g1	NM:i:0	BS:f:47
RF01_689_741_1:0:0_1:0:0_8/1	83	RF01	692	40	19=1X30=	=	689	46	TGCCAGAGTCGATCTATTATAATATGACAGTACTATCAGTTCTCTCGCAA	JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ	BB:f:87.9128	BE:f:4.51982e-22	RG:Z:g1	NM:i:0	BS:f:47
RF01_689_741_1:0:0_1:0:0_8/2	163	RF01	689	40	30=1X19=	=	692	-46	TAATTGCGAGAGAACTGATAGTACTGTCATCTTCTAATAGATCGACTCTG	JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ	BB:f:87.9128	BE:f:4.51982e-22	RG:Z:g1	NM:i:0	BS:f:47
RF01_532_688_0:0:0_1:0:0_9/1	99	RF01	532	40	50=	=	639	156	ATAGTAGCTTCAACAGTAAATAAATATGGTGTACCAAGGCACAACGCGAA	JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ	BB:f:93.4528	BE:f:9.71473e-24	RG:Z:g1	NM:i:0	BS:f:50
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