Convert alignment in Fasta/Clustal format to SAM/BAM file
Usage: biostar139647 [options] Files
Options:
--bamcompression
Compression Level.
Default: 5
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --output
Output file. Optional . Default: stdout
-R, --refname
reference name. Optional
Default: chrUn
--samoutputformat
Sam output format.
Default: SAM
Possible Values: [BAM, SAM, CRAM]
--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 biostar139647
The java jar file will be installed in the dist
directory.
The project is licensed under the MIT license.
Should you cite biostar139647 ? 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
$ curl -sL "https://raw.githubusercontent.com/suryasaha/Pred_cutoff/60a6f980c9940dfb6e381c5394918f27cb14564f/data/Xylella-RpoH.aln" |\
java -jardist/biostar139647.jar
@HD VN:1.4 SO:unsorted
@SQ SN:chrUn LN:42
@PG ID:0 VN:3a0c4ccb05e7492382e00328ac60951f215d9400 CL:(empty) PN:Biostar139647
1 0 chrUn 1 60 42M * 0 0 CATACTTGGTCATCGGTCGTGTCCTTGAAAGTGACTTGTTAA *
2 0 chrUn 1 60 42M * 0 0 TCTCTGAACCCCCTTGAAACCCCTACACTCAGCCATATATGC *
3 0 chrUn 1 60 42M * 0 0 TACCTTCGGGTCCTTGAAAATAGCGTCGCCGTGCTTATCTGT *
4 0 chrUn 1 60 5M2D35M * 0 0 TTGACAGCCGCTTGAGCAGGCGTCGGTCATCCCCACATTC *
5 0 chrUn 1 60 18M1D9M1D13M * 0 0 ATGCCTGGGTGGCTTGAAAGCTGGCGGCTTGCCCACATAC *
6 0 chrUn 1 60 20M1D21M * 0 0 TCAGTTTTATCGCTTGATATTCACTGAGACTGGCCACACAT *
$ curl -sL "https://raw.github.com/biopython/biopython/master/Tests/Clustalw/opuntia.aln" 2> /dev/null | java -jar dist-1.128/biostar139647.jar
@HD VN:1.4 SO:unsorted
@SQ SN:chrUn LN:156
@PG ID:0 VN:3a0c4ccb05e7492382e00328ac60951f215d9400 CL:(empty) PN:Biostar139647
gi|6273285|gb|AF191659.1|AF191 0 chrUn 1 60 56M10D90M * 0 0 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATAATATATTTCA
AATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGTACCAGA*
gi|6273284|gb|AF191658.1|AF191 0 chrUn 1 60 58M8D90M * 0 0 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATAATATATTT
CAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA *
gi|6273289|gb|AF191663.1|AF191 0 chrUn 1 60 60M6D90M * 0 0 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATAATATAT
TTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTATACCAGA *
gi|6273291|gb|AF191665.1|AF191 0 chrUn 1 60 156M * 0 0 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTT
CAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA *
gi|6273287|gb|AF191661.1|AF191 0 chrUn 1 60 56M10D90M * 0 0 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATAATATATTTCA
AATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA*
gi|6273286|gb|AF191660.1|AF191 0 chrUn 1 60 56M10D90M * 0 0 TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATAATATATTTAT
AATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA*
gi|6273290|gb|AF191664.1|AF191 0 chrUn 1 60 60M6D90M * 0 0 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATAATATAT
TTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA *