convert sam format to axt Format

Question

[midox]

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

[Pierre Lindenbaum]

does AXT supports INDELS (like SAM)?

[midox]

yes. it support indels

[Pierre Lindenbaum]

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

[midox]

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?

[midox]

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

[Pierre Lindenbaum]

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

[midox]

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]$

[Pierre Lindenbaum]

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

[midox]

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

have you another solution to run samtoaxt.java?

Thanks

Answer 1

[Pierre Lindenbaum]

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
(...)

[midox]

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

I must install jvarkit?

[Pierre Lindenbaum]

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

[midox]

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

there are errors.

[m@rainman biostar]$ javac Biostar170742.java

[Pierre Lindenbaum]

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

make biostar170742

[midox]

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]$

[Pierre Lindenbaum]

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

try googling please.

[Pierre Lindenbaum]

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