convert sam format to axt Format

Entering edit mode

9.5 years ago

midox ▴ 290

hello,
I would like to convert my sam file (.sam) to another type is .axt format.
i used BWA for alignement but the output of this tool is .sam format.
Can you help me?
Thanks

alignment sam axtformat • 4.4k views

ADD COMMENT • link 9.5 years ago by midox ▴ 290

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does AXT supports INDELS (like SAM)?

ADD REPLY • link 9.5 years ago by Pierre Lindenbaum 166k

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yes. it support indels

ADD REPLY • link 9.5 years ago by midox ▴ 290

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so, how does it look likes with indels, I cannot find an example

ADD REPLY • link updated 5.6 years ago by Ram 45k • written 9.5 years ago by Pierre Lindenbaum 166k

Entering edit mode

this is an example:

14 NODE_98_length_11049_ID_45456 4251 4311 Read_10 8190 8248 - 3854
aaatgtattccgataggccattttacatttggagggacggttgaaag---tggacagaggaaaa
aaatgtattccgatagg----tttacatttggagg-acggttgaaagacttggacagaggaaaa

so how convert .sam output to .axt?

ADD REPLY • link updated 5.6 years ago by Ram 45k • written 9.5 years ago by midox ▴ 290

Entering edit mode

i cant install ant in my server!!! have you solution?

ADD REPLY • link 9.5 years ago by midox ▴ 290

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you don't need to be root to install ant, just download and put it anywhere: https://ant.apache.org/bindownload.cgi

ADD REPLY • link updated 5.6 years ago by Ram 45k • written 9.5 years ago by Pierre Lindenbaum 166k

Entering edit mode

I installed apache.

but no run to biostar170742.

[mk@rainman jvarkit]$ /home/mk/apache-ant-1.9.6/bin/ant -version
Apache Ant version 1.7.1 compiled on August 24 2010
[mk@rainman jvarkit]$ make biostar170742
echo "Compiling htsjdk with ${JAVA_HOME} = "
Compiling htsjdk with  =
echo "Compiling htsjdk library for java. Requires  apache ANT. If it fails here, it's a not a problem with jvarkit."
Compiling htsjdk library for java. Requires  apache ANT. If it fails here, it's a not a problem with jvarkit.
echo "And ${JAVA_HOME}/bin/javac should be >=1.8"
And /bin/javac should be >=1.8
(cd /home/mk/jvarkit/htsjdk-2.0.1 && ant )
Buildfile: build.xml

write-version-property:

BUILD FAILED
/home/mk/jvarkit/htsjdk-2.0.1/build.xml:64: Problem: failed to create task or type propertyfile
Cause: the class org.apache.tools.ant.taskdefs.optional.PropertyFile was not found.
        This looks like one of Ant's optional components.
Action: Check that the appropriate optional JAR exists in
        -/usr/share/ant/lib
        -/home/mk/.ant/lib
        -a directory added on the command line with the -lib argument

Do not panic, this is a common problem.
The commonest cause is a missing JAR.

This is not a bug; it is a configuration problem

Total time: 0 seconds
make: *** [/home/mk/jvarkit/htsjdk-2.0.1/dist/htsjdk-2.0.1.jar] Erreur 1
[mk@rainman jvarkit]$

ADD REPLY • link updated 5.6 years ago by Ram 45k • written 9.5 years ago by midox ▴ 290

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https://ant.apache.org/manual/install.html#optionalTasks

ADD REPLY • link 9.5 years ago by Pierre Lindenbaum 166k

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thank you but I cant install apache. I don't know the problem

have you another solution to run samtoaxt.java?

Thanks

ADD REPLY • link updated 5.6 years ago by Ram 45k • written 9.5 years ago by midox ▴ 290

Entering edit mode

9.5 years ago

Pierre Lindenbaum 166k

I quickly wrote a converter https://github.com/lindenb/jvarkit/wiki/Biostar170742

$ java -jar dist-2.0.1/biostar170742.jar \
    -R ref.fa \
    S1.bam

0 rotavirus 1 70 rotavirus_1_317_5:0:0_7:0:0_2de/1 + 60
GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGCAGATGGTAAGCTCTATTATT
GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAATATGGCGTCAACTCAGCAGATGGTCAGCTCTAATATT

1 rotavirus 1 70 rotavirus_1_535_4:0:0_4:0:0_1a6/2 + 60
GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGCAGATGGTAAGCTCTATTATT
GGCTTTTACTGCTTTTCAGTGGTTGCTTCTCAAGATGGAGTGTACTCATCAGATGGTAAGCTCTATTATT

2 rotavirus 1 70 rotavirus_1_543_5:0:0_11:0:0_390/2 + 60
GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGCAGATGGTAAGCTCTATTATT
GGCTTTTAATGCTTTTCATTTGATGCTGCTCAAGATGGAGTCTACACAGCAGATGGTCAGCTCTATTATT

3 rotavirus 1 70 rotavirus_1_578_3:0:0_7:0:0_7c/1 + 60
GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGCAGATGGTAAGCTCTATTATT
GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTCCTGAGCAGCTGGTAAGCTCTATTATT
(...)

ADD COMMENT • link updated 5.6 years ago by Ram 45k • written 9.5 years ago by Pierre Lindenbaum 166k

Entering edit mode

thank you pierre but I can't run this code.

I must install jvarkit?

ADD REPLY • link updated 5.6 years ago by Ram 45k • written 9.5 years ago by midox ▴ 290

Entering edit mode

yes https://github.com/lindenb/jvarkit/wiki/Compilation

ADD REPLY • link 9.5 years ago by Pierre Lindenbaum 166k

Entering edit mode

I installed the tool. but I can't run Biostar70742.java

there are errors.

[m@rainman biostar]$ javac Biostar170742.java

	Biostar170742.java:29: package com.github.lindenb.jvarkit.util.picard does not exist
	import com.github.lindenb.jvarkit.util.picard.GenomicSequence;
	^
	Biostar170742.java:30: package com.github.lindenb.jvarkit.util.picard does not exist
	import com.github.lindenb.jvarkit.util.picard.SAMSequenceDictionaryProgress;
	^
	Biostar170742.java:32: package htsjdk.samtools does not exist
	import htsjdk.samtools.Cigar;
	^
	Biostar170742.java:33: package htsjdk.samtools does not exist
	import htsjdk.samtools.CigarElement;
	^
	Biostar170742.java:34: package htsjdk.samtools does not exist
	import htsjdk.samtools.CigarOperator;
	^
	Biostar170742.java:35: package htsjdk.samtools does not exist
	import htsjdk.samtools.SAMRecord;
	^
	Biostar170742.java:36: package htsjdk.samtools does not exist
	import htsjdk.samtools.SAMRecordIterator;
	^
	Biostar170742.java:37: package htsjdk.samtools does not exist
	import htsjdk.samtools.SamReader;
	^
	Biostar170742.java:38: package htsjdk.samtools.reference does not exist
	import htsjdk.samtools.reference.IndexedFastaSequenceFile;
	^
	Biostar170742.java:39: package htsjdk.samtools.util does not exist
	import htsjdk.samtools.util.CloserUtil;
	^
	Biostar170742.java:42: cannot find symbol
	symbol: class AbstractBiostar170742
	public class Biostar170742 extends AbstractBiostar170742
	^
	Biostar170742.java:44: package org.slf4j does not exist
	private static final org.slf4j.Logger LOG = com.github.lindenb.jvarkit.util.log.Logging.getLog(Biostar170742.class);
	^
	Biostar170742.java:44: package com.github.lindenb.jvarkit.util.log does not exist
	private static final org.slf4j.Logger LOG = com.github.lindenb.jvarkit.util.log.Logging.getLog(Biostar170742.class);
	^
	Biostar170742.java:51: cannot find symbol
	symbol : variable super
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	if(super.faidx==null)
	^
	Biostar170742.java:53: cannot find symbol
	symbol : method wrapException(java.lang.String)
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	return wrapException("Reference sequence was not defined");
	^
	Biostar170742.java:56: cannot find symbol
	symbol : class SamReader
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	SamReader sfr=null;
	^
	Biostar170742.java:57: cannot find symbol
	symbol : class SAMRecordIterator
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	SAMRecordIterator iter=null;
	^
	Biostar170742.java:58: cannot find symbol
	symbol : class GenomicSequence
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	GenomicSequence genomicSequence = null;
	^
	Biostar170742.java:59: cannot find symbol
	symbol : class IndexedFastaSequenceFile
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	IndexedFastaSequenceFile indexedFastaSequenceFile= null;
	^
	Biostar170742.java:62: cannot find symbol
	symbol : class IndexedFastaSequenceFile
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	indexedFastaSequenceFile = new IndexedFastaSequenceFile(super.faidx);
	^
	Biostar170742.java:62: cannot find symbol
	symbol : variable super
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	indexedFastaSequenceFile = new IndexedFastaSequenceFile(super.faidx);
	^
	Biostar170742.java:64: cannot find symbol
	symbol : method openSamReader(java.lang.String)
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	sfr = openSamReader(inputName);
	^
	Biostar170742.java:65: cannot find symbol
	symbol : variable super
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	out = super.openFileOrStdoutAsPrintStream();
	^
	Biostar170742.java:69: cannot find symbol
	symbol : class SAMSequenceDictionaryProgress
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(sfr.getFileHeader());
	^
	Biostar170742.java:69: cannot find symbol
	symbol : class SAMSequenceDictionaryProgress
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(sfr.getFileHeader());
	^
	Biostar170742.java:73: cannot find symbol
	symbol : class SAMRecord
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	final SAMRecord rec= progress.watch(iter.next());
	^
	Biostar170742.java:75: cannot find symbol
	symbol : class Cigar
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	final Cigar cigar = rec.getCigar();
	^
	Biostar170742.java:82: cannot find symbol
	symbol : class GenomicSequence
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	genomicSequence = new GenomicSequence(indexedFastaSequenceFile, rec.getReferenceName());
	^
	Biostar170742.java:89: cannot find symbol
	symbol : class CigarElement
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	for(final CigarElement ce: cigar.getCigarElements())
	^
	Biostar170742.java:91: cannot find symbol
	symbol : class CigarOperator
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	final CigarOperator op = ce.getOperator();
	^
	Biostar170742.java:92: cannot find symbol
	symbol : variable CigarOperator
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	if(op.equals(CigarOperator.S))
	^
	Biostar170742.java:94: operator + cannot be applied to int,CigarElement.getLength
	readpos+=ce.getLength();
	^
	Biostar170742.java:94: inconvertible types
	found : <nulltype>
	required: int
	readpos+=ce.getLength();
	^
	Biostar170742.java:97: cannot find symbol
	symbol : variable CigarOperator
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	if(op.equals(CigarOperator.H))
	^
	Biostar170742.java:163: cannot find symbol
	symbol : variable RETURN_OK
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	return RETURN_OK;
	^
	Biostar170742.java:167: cannot find symbol
	symbol : method wrapException(java.lang.Exception)
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	return wrapException(err);
	^
	Biostar170742.java:171: cannot find symbol
	symbol : variable CloserUtil
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	CloserUtil.close(out);
	^
	Biostar170742.java:172: cannot find symbol
	symbol : variable CloserUtil
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	CloserUtil.close(iter);
	^
	Biostar170742.java:173: cannot find symbol
	symbol : variable CloserUtil
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	CloserUtil.close(sfr);
	^
	Biostar170742.java:174: cannot find symbol
	symbol : variable CloserUtil
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	CloserUtil.close(indexedFastaSequenceFile);
	^
	Biostar170742.java:49: method does not override or implement a method from a supertype
	@Override
	^
	Biostar170742.java:180: cannot find symbol
	symbol : method instanceMain(java.lang.String[])
	location: class com.github.lindenb.jvarkit.tools.biostar.Biostar170742
	new Biostar170742().instanceMain(args);
	^
	42 errors

view raw biostars-170828.log hosted with ❤ by GitHub

ADD REPLY • link updated 5.6 years ago by Ram 45k • written 9.5 years ago by midox ▴ 290

Entering edit mode

you didn't follow the instructions: https://github.com/lindenb/jvarkit/wiki/Biostar170742

make biostar170742

ADD REPLY • link updated 5.6 years ago by Ram 45k • written 9.5 years ago by Pierre Lindenbaum 166k

Entering edit mode

same problem BUILD Failed.

[mk@rainman jvarkit]$ make biostar170742
echo "Compiling htsjdk with ${JAVA_HOME} = "
Compiling htsjdk with  =
echo "Compiling htsjdk library for java. Requires  apache ANT. If it fails here, it's a not a problem with jvarkit."
Compiling htsjdk library for java. Requires  apache ANT. If it fails here, it's a not a problem with jvarkit.
echo "And ${JAVA_HOME}/bin/javac should be >=1.8"
And /bin/javac should be >=1.8
(cd /home/mk/jvarkit/htsjdk-2.0.1 && ant )
Buildfile: build.xml

write-version-property:

BUILD FAILED
/home/mk/jvarkit/htsjdk-2.0.1/build.xml:64: Problem: failed to create task or type propertyfile
Cause: the class org.apache.tools.ant.taskdefs.optional.PropertyFile was not found.
        This looks like one of Ant's optional components.
Action: Check that the appropriate optional JAR exists in
        -/usr/share/ant/lib
        -/home/mk/.ant/lib
        -a directory added on the command line with the -lib argument

Do not panic, this is a common problem.
The commonest cause is a missing JAR.

This is not a bug; it is a configuration problem

Total time: 0 seconds
make: *** [/home/mk/jvarkit/htsjdk-2.0.1/dist/htsjdk-2.0.1.jar] Erreur 1
[mk@rainman jvarkit]$

ADD REPLY • link updated 5.6 years ago by Ram 45k • written 9.5 years ago by midox ▴ 290

Entering edit mode

as it is described "ant-optional" is missing...

try googling please.

ADD REPLY • link updated 5.6 years ago by Ram 45k • written 9.5 years ago by Pierre Lindenbaum 166k

Entering edit mode

forgot to put the read positions: udpated the source https://github.com/lindenb/jvarkit/commit/84dfac8015be3ae66cdb15b25618022198b8f106

ADD REPLY • link 9.5 years ago by Pierre Lindenbaum 166k