Biostar139647

Convert alignment in Fasta/Clustal format to SAM/BAM file

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar biostar139647  [options] Files

Usage: biostar139647 [options] Files
  Options:
    --bamcompression
      Compression Level. 0: no compression. 9: max compression;
      Default: 5
    -F, --fullalignment
      by default heading/traling gaps are ignored ( as in read to reference 
      alignment). Use this option to treat them as meaningfull indels as in 
      full genome alignment. Optional
      Default: false
    -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 injected in the SAM/BAM IF not present in the alignment. 
      Note that not defining a reference will produce no Insertion.  Optional
      Default: chrUn
    -S, --refselection
      label of the reference, if present in the input alignment. Both 
      Insertion and Deletions variations can be computed. Optional
    --samoutputformat
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
    --version
      print version and exit

Keywords

• msa
• sam
• bam
• clustal

See also in Biostars

• https://www.biostars.org/p/139647

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar139647.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/biostar/Biostar139647Test.java

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 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

Example

$ 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    *