Question: convert sam format to axt Format
0
gravatar for midox
5.1 years ago by
midox260
Tunisia
midox260 wrote:

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

sam alignment axtformat • 1.8k views
ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by midox260

does AXT supports INDELS (like SAM)?

ADD REPLYlink written 5.1 years ago by Pierre Lindenbaum133k

yes. it support indels

ADD REPLYlink written 5.1 years ago by midox260

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

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.1 years ago by Pierre Lindenbaum133k

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 REPLYlink modified 13 months ago by _r_am32k • written 5.1 years ago by midox260

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

ADD REPLYlink written 5.1 years ago by midox260

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

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.1 years ago by Pierre Lindenbaum133k

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 REPLYlink modified 13 months ago by _r_am32k • written 5.1 years ago by midox260

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

ADD REPLYlink written 5.1 years ago by Pierre Lindenbaum133k

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

have you another solution to run samtoaxt.java?

Thanks

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.1 years ago by midox260
2
gravatar for Pierre Lindenbaum
5.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum133k wrote:

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 COMMENTlink modified 13 months ago by _r_am32k • written 5.1 years ago by Pierre Lindenbaum133k

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

I must install jvarkit?

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.1 years ago by midox260

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

ADD REPLYlink written 5.1 years ago by Pierre Lindenbaum133k

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

there are errors.

[m@rainman biostar]$ javac Biostar170742.java

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.1 years ago by midox260

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

make biostar170742
ADD REPLYlink modified 13 months ago by _r_am32k • written 5.1 years ago by Pierre Lindenbaum133k

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 REPLYlink modified 13 months ago by _r_am32k • written 5.1 years ago by midox260

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

try googling please.

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.1 years ago by Pierre Lindenbaum133k

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

ADD REPLYlink written 5.1 years ago by Pierre Lindenbaum133k
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