jvarkit
SAM4WebLogo
Sequence logo for different alleles or generated from SAM/BAM
Usage
Usage: sam4weblogo [options] Files
Options:
-c, --clipped, --clip
Use Clipped Bases
Default: false
-q, --fastq
[20180812]print fastq-like format. Was :
https://github.com/lindenb/jvarkit/issues/109
Default: false
-fqp, --fqp
[20180813] fastq padding quality character
Default: -
-fqu, --fqu
[20180813] fastq unknown quality character
Default: !
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
* -r, --region, --interval
Region to observe: chrom:start-end
-o, --output
Output file. Optional . Default: stdout
-readFilter, --readFilter
[20171201](moved to jexl)A JEXL Expression that will be used to filter
out some sam-records (see
https://software.broadinstitute.org/gatk/documentation/article.php?id=1255).
An expression should return a boolean value (true=exclude, false=keep
the read). An empty expression keeps everything. The variable 'record'
is the current observed read, an instance of SAMRecord (https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html).
Default: 'Accept all' (Empty expression)
--version
print version and exit
Keywords
- sam
- bam
- visualization
- logo
See also in Biostars
Compilation
Requirements / Dependencies
- java compiler SDK 11. Please check that this java is in the
${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
Download and Compile
$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew sam4weblogo
The java jar file will be installed in the dist directory.
Source code
Unit Tests
Contribute
- Issue Tracker: http://github.com/lindenb/jvarkit/issues
- Source Code: http://github.com/lindenb/jvarkit
License
The project is licensed under the MIT license.
Citing
Should you cite sam4weblogo ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030
Motivation
“Sequence logo ( http://weblogo.berkeley.edu/logo.cgi ) for different alleles or generated from SAM/BAM” http://www.biostars.org/p/73021
Example
$ java -jar dist/sam4weblogo.jar -r seq1:80-110 sorted.bam 2> /dev/null | head -n 50
>B7_593:4:106:316:452/1
TGTTG--------------------------
>B7_593:4:106:316:452a/1
TGTTG--------------------------
>B7_593:4:106:316:452b/1
TGTTG--------------------------
>B7_589:8:113:968:19/2
TGGGG--------------------------
>B7_589:8:113:968:19a/2
TGGGG--------------------------
>B7_589:8:113:968:19b/2
TGGGG--------------------------
>EAS54_65:3:321:311:983/1
TGTGGG-------------------------
>EAS54_65:3:321:311:983a/1
TGTGGG-------------------------
>EAS54_65:3:321:311:983b/1
TGTGGG-------------------------
>B7_591:6:155:12:674/2
TGTGGGGG-----------------------
>B7_591:6:155:12:674a/2
TGTGGGGG-----------------------
>B7_591:6:155:12:674b/2
TGTGGGGG-----------------------
>EAS219_FC30151:7:51:1429:1043/2
TGTGGGGGGCGCCG-----------------
>EAS219_FC30151:7:51:1429:1043a/2
TGTGGGGGGCGCCG-----------------
>EAS219_FC30151:7:51:1429:1043b/2
TGTGGGGGGCGCCG-----------------
>B7_591:5:42:540:501/1
TGTGGGGGCCGCAGTG---------------
>EAS192_3:5:223:142:410/1
TGGGGGGGGCGCAGT----------------
>B7_591:5:42:540:501a/1
TGTGGGGGCCGCAGTG---------------
>EAS192_3:5:223:142:410a/1
TGGGGGGGGCGCAGT----------------
>B7_591:5:42:540:501b/1
TGTGGGGGCCGCAGTG---------------
>EAS192_3:5:223:142:410b/1
TGGGGGGGGCGCAGT----------------
fastq-like output
$ java -jar dist/sam4weblogo.jar -r 'RF01:100-130' src/test/resources/S1.bam -q -c
@RF01_44_622_1:0:0_1:0:0_3a/1
TATTCTTCCAATAG-----------------
+
22222222222222
@RF01_44_499_0:0:0_3:0:0_7b/2
TATTCTTCCAATAG-----------------
+
22222222222222
@RF01_67_565_0:0:0_2:0:0_67/2
TATTCTTCCAATAGTGAATTAGAGAATAGAT
+
2222222222222222222222222222222
@RF01_94_620_1:0:0_2:0:0_15/2
TATTCTTCCAATAGTGAATTAGAGAATAGAT
+
2222222222222222222222222222222
@RF01_102_665_1:0:0_1:0:0_71/1
--TTCTTCCAATAGTGAATTAGAGAATAGAT
+
22222222222222222222222222222
@RF01_110_504_2:0:0_1:0:0_5d/2
----------ATAGTGAATTAGATAATAGAT
+
222222222222222222222
@RF01_121_598_1:0:0_3:0:0_6e/2
---------------------GAGAATAGAT
+
2222222222
See also
- https://www.biostars.org/p/103052/
- http://www.sciencedirect.com/science/article/pii/S1874778715300210