convert sam format to axt Format
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9.3 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 • 4.2k views
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does AXT supports INDELS (like SAM)?

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yes. it support indels

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

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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?

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

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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

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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]$
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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

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9.3 years ago

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

I must install jvarkit?

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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

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

make biostar170742
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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]$
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as it is described "ant-optional" is missing...

try googling please.

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

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