Sequence logo for different alleles or generated from SAM/BAM
Usage: java -jar dist/sam4weblogo.jar [options] Files
Usage: sam4weblogo [options] Files
Options:
-c, --clipped, --clip
Use Clipped Bases
Default: false
--format, -F
output format.
Default: fasta
Possible Values: [fasta, fastq, tabular]
-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. A source of intervals. The following suffixes are
recognized: vcf, vcf.gz bed, bed.gz, gtf, gff, gff.gz, gtf.gz.Otherwise
it could be an empty string (no interval) or a list of plain interval
separated by '[ \t\n;,]'
Default: (unspecified)
--naming
How to print a Read. A format 'a la C-printf'. %% :% , %n:read name, %s:
read bases, %q: read quals, %f : read flags,%m: mapq, %c: contig, %b:
start, %B: unclipped start, %e: end, %E: unclipped end,%I: read group
id, %N: sample name,%S: SAM String.
Default: %n (%f) %N
--no-insert
Do not show insertions
Default: false
-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)
-R, --reference
For Reading CRAM. Indexed fasta Reference file. This file must be
indexed with samtools faidx and with picard CreateSequenceDictionary
--version
print version and exit
${PATH}
. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew sam4weblogo
The java jar file will be installed in the dist
directory.
20130524
The project is licensed under the MIT license.
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
“Sequence logo ( http://weblogo.berkeley.edu/logo.cgi ) for different alleles or generated from SAM/BAM” http://www.biostars.org/p/73021
On October 14th, I tried to implement the insertions. I haven’t tested this feature in depth.
$ 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----------------
$ java -jar dist/sam4weblogo.jar -r 'RF01:100-130' src/test/resources/S1.bam --format fastq -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
$ java -jar /home/lindenb/src/jvarkit-git/dist/sam4weblogo.jar -r 'chr4:15648762-15648862' src/test/resources/retrocopy01.bwa.bam --format tabular -c
CTTGAACCCAGGAGGGGGAGGTGCCAGGGAGCCGAGATCATGCCACTGCACCCCAGCCTGGGCAACAAACCAAACCTCCATCC-C-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1111:24870:51570/1
CTTGAACCCAGGAGGCAGAGGTGGCAGTGAGCAGAAAACAAGCCACTGCACCCCAGCCGGGGAAAAAAAACAAGACCCCATCTaA-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1107:19532:10468/1
CTTGAACCCAGGAGGCAGAGGTTGCAGTGAGCCGAGATCATGCCACTGCACTCCAGCCTGGGCAACAAAGCAAGACTCCATCT-C-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:2121:23043:26536/2
ctggacCCCAGGAGGCAGAGGTTGCAGGTACCCGAAATAATGCCCCTGCCCCCCAGCCTGGGCAACAAAGCAAGACCCCATCT-A-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1212:10642:64966/2
-------------GGCAGAGGTTGCAGTGAGCCGAGATCATGCCACTGCACTCCAGCCTGGGCAACAAAGCAAGACTCCATCT-CaAAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1119:27661:8095/2
--------------------------------CGAGATCATGCCACTGCACTCCAGCCTGGGCAACAAAGCAAGACTCCATCT-C-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:2224:26189:58778/2
-------------------------------------------CACTGCACTCCAGCCTGGGCAACAAAGCAAGACTCCATCT-C-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:2103:11972:45611/1
ctggacccaaggaggcagaggttgaagggagcagaaacaaggccacggccccCCAGCCTGGGAAACAAAGCAAACCCCAATCT-A-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:2121:29701:6108/1
---------------------------------------------------------CTGGGCAACAAAGCAAGACTCCATCT-C-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1114:11992:43044/1
---------------------------------------------------------CTGGGCAACAAAGCAAGACTCCATCT-CaAAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:2109:9019:23477/2
----------------------------------------------------------------ACAAAGCAAGACTCCATCT-CaAAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:2110:15706:60765/2
---------------------------------------------------------------------GCAAGACTCCATCT-C-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1218:27600:65793/1
-------------------------------------------------------------------------GACNCCATCT-C-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1209:1326:20805/1
-----------------------------------------------------------------------------CCATCT-C-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:2201:25895:8095/2
gggccgatggtgaaaagtggcagggcgcaacaaaaaatgcccgtcacaccaaccgggggcaaaaaaaaaaaaccccaaccaaa-a-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1102:32319:57829/2
-----------------------------------------------------agcagggaaaacaaaccaaaacacaacata-a-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1106:29437:72033/1
--------------------------------------------------------------------------------------AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1109:27813:4104/1
------------------------------------------ccacgaccccaccacggaaaaaaaaaaaaaacacaaaaaaa-a-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1112:17137:65951/1
tttaaaccaagacgccagacgtccaagatatacgactacccgccactgcaaaaccacctgtgcacaaacacacaaataaaact-a-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1117:10693:25042/2
------------------------------------------------------caccagggaaaaaaaaaaaaactcaaaaa-a-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1118:24962:18502/1
ttgacaccagaagcaaaagttaaaagtcaaccgaaatcagcaaaataatctacaacgtaggaaaaagccaaagtctcattcta-a-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1119:15432:30791/1
tgaaagacggggggcagaggttgcaagagcccaaaaacatgccccggcacccaaacgtgggcaacaaagaaaaacccaatcaa-a-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1123:1590:53891/1
----------------------------------------------------------------------------------a-a-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1215:26585:67586/1
--------------------------------------------------------------------------------------AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1216:18142:49900/1
---------------------------------------atgccactgaacccaagccagggcaaaaaagaaaaaaccaatcc-a-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1219:25043:11048/2
-------------------------------------------------------------------aaaaaaacacaaaaaa-a-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:2113:14215:55086/1
aataaacccaaaagaaaaagtgcgcagtaggccaaaatcaagcaaatgaaatcaagccggggaaaaaaacaaagaccccacat-a-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:2113:14418:23618/1
-------------------------------------------aaccgaaacccaacccagaaaaaaaaaaaaaacacaaaca-a-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:2120:21420:20629/2
--------------------------------------aaagcacagacaaaacaaccagacaaacaaaaaaaaaacaaaaaa-a-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:2212:28564:14301/1
tacgaaccagggaggctcgggctgaggaagccgaacttcattcctcccaccgcaagactggcaaataaatcaagtcccaattt-a-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:2216:20324:64685/1
--------------------------------------------accaccccccacccgggccacaaaaaaaaaaccaaaaaa-a-AAAAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:2216:23429:26607/1
---------------------------------------------------------------------------------------AAAAAAAAAAAGAGAA X2:1:H7T57CCXY:8:2124:1306:6249/1
----------------------------------------------------------------------------------------AAAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1222:16579:28488/1
-----------------------------------------------------------------------------------------AAAAAAAAAAAAAA X2:1:H7T57CCXY:8:1222:17513:27890/1
-------------------------------------------------------------------------------------------AAAAAAAAAAAA X2:1:H7T57CCXY:8:2109:14316:7902/1
-------------------------------------------------------------------------------------------------AAAAAA X2:1:H7T57CCXY:8:2108:14357:62329/1
--------------------------------------------------------------------------------------------------AAAAA X2:1:H7T57CCXY:8:1124:18223:49162/1