pegi3s/omegamap

Sponsored OSS

By i3S

Updated 5 months ago

omegaMap (https://github.com/danny-wilson/omegaMap/) docker image.

Image
Data Science
Machine Learning & AI

709

This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles)

(Please note that the original software licenses still apply)

This image facilitates the usage of omegaMap, a program for detecting natural selection and recombination in DNA or RNA sequences. It provides a single command analyze which creates the analysis model (i.e. the configuration file), runs omegaMap and finally runs the summarize utility from omegaMap.

Using the omegaMap image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/omegamap analyze /data/input.fasta /data 25000

In this command, you should replace:

  • /your/data/dir to point to the directory that contains the FASTA file you want to analyze.
  • input.fasta to the actual name of your input file.
  • data to the actual name of the directory where output files will be created.
  • 25000 to the actual number of iterations you want

Two files will be created: input.fasta.result and input.fasta.summary.

Test data

To test the previous command, you can copy and paste the following sample data, which consists of aligned sequences obtained from here, into the input.fasta file:

>AF264073.1 Drosophila capricorni alcohol dehydrogenase (Adh) gene, partial cds
AACTTGGTGATCCTCGATCGTATTGATAATCCTGCTGCCATTGCTGAACTGAAGGCAATCAATCCCAAGG
TGACAGTTACCTTCTTCCCCTACGATGTGACCACATCCTTGGCCGAGACCTCCAAATTGCTGAAAACCAT
TTTCGCTCAACTGAAGACTGTCGATGTTCTGATCAATGGAGCTGGCATTCTGGACGATCATCAGATTGAA
CGCACCATTGCCGTCAATTTCACCGGCCTGGTCAATACCACAACCGCAATTTTGGACTTCTGGGACAAGC
GTAAGGGTGGTCCAGGTGGTGTGATCTGCAACATTGGATCGGTGACTGGTTTCAATGCCATCTACCAGGT
GCCCGTCTACTCGGCATCGAAGGCAGCTGTCGTCAGCTTCACTCAGTCCATTGCC
>AF264074.1 Drosophila equinoxialis alcohol dehydrogenase (Adh) gene, partial cds
AACTTGGTGATCCTGGATCGTATTGACAATCCTGCTGCCATCGCTGAACTGAAGGCAATCAATCCCAAAG
TAACAGTTACTTTCTATCCCTATGATGTTACCACACCCTTGACAGAGACTACCAAATTGTTGAAGACCAT
TTTCGCCCAATTGAAGACTGTCGATGTTCTAATCAATGGAGCTGGTATTTTGGATGATCATCAGATTGAG
CGAACCATTGCCGTGAACTTCACTGGTTTGGTCAATACCACCACAGCTATTTTGGACTTCTGGGATAAGC
GCAAGGGTGGACCAGGTGGTGTCATCTGCAACATTGGCTCTGTGACCGGTTTCAATGCCATCTATCAGGT
CCCTGTCTATTCTGCATCAAAAGCACGTGTTGTTAGCTTCACTCAATCCATTGCC
>AF264075.1 Drosophila fumipennis alcohol dehydrogenase (Adh) gene, partial cds
AACTTGGTGGTCCTGGATCGTATTGACAATCCTGCTGCCATTGCTGAACTGAAGGCAATCAATCCCAAGG
TGACAGTTACCTTCTATCCCTATGATGTGACCGTACCCTTGGCGGAGACCACCAAATTGCTAAAGACCAT
TTTCGATCAACTCAAGACTGTCGATGTTCTGATCAATGGTGCTGGCATTCTAGATGATCATCAGATCGAG
CGTACCATTGCTGTGAAATTCACTGGTCTGGTCAATACTACAACGGCCATTCTGGACTTCTGGAACAAGC
GTAAGGGTGGTCCAGGTGGTGTGATCTGCAATATTGGCTCGGTGACTGGTTTTAATGCCATCTACCAGGT
GCCTGTCTATAGTGCATCAAAGGAGGATGTTGTTAGCTTCACTCAATGTATTGCC
>AF264076.1 Drosophila insularis alcohol dehydrogenase (Adh) gene, partial cds
AACTTGGTGGTCCTGGATCGTATTGACAATCCTGCTGCCATTGCTGAACTGAAGGCAATCAATCCCAAGG
TGACAGTTACTTTCTATCCCTATGATGTTACCACACCCTTGACAGAGACCACCAAATTGTTGAAGACCAT
TTTCGCCCAATTGAAGACCGTCGATGTTCTGATCAATGGAGCTGGCATTTTGGATGACCATCAGATTGAG
CGCACCATTGCTGTGAATTTCACTGGTCTGGTCAATACCACGACAGCCATTTTGGACTTCTGGGACAAGC
GTAAGGGTGGTCCAGGTGGTGTCATCTGCAACATTGGCTCTGTGACCGGTTTCAATGCCATCTATCAGGT
GCCTGTCTATAGTGCATCAAAGGAGGATGTTGTTAGCTTCACTCAATGTATTGCC
>AF264077.1 Drosophila nebulosa alcohol dehydrogenase (Adh) gene, partial cds
AACTTGGTGATCCTCGATCGCATTGACAAGCCTGCTGCCATGGCGGAACTGAAGGCAATCAATCCCAAAG
TGATAGTTACCTTCTATCCCTATGATGTTACCACACCCATTACGGAGACCACCAAATTGCTAAAGACCAT
TTTCGCTCAACTAAAGACCGTTGATGTGCTGATCAATGGTGCTGGCATTTTGGATGATCATCAGATTGAG
CGCACCATTGCCGTTAACTTTACTGGTTTGGTTAATACCACCACGGCCATTTTGGACTTCTGGGACAAGC
GTAAGGGTGGTCCAGGTGGTGTTATTTGCAACATTGGTTCGGTGACTGGCTTCAATGCCATTTACCAAGT
GCCCGTCTATTCCGGCATCGAGGCAGCAGTTGTTAGCTTCACTCAATCGATTGCC
>AF264078.1 Drosophila paulistorum alcohol dehydrogenase (Adh) gene, partial cds
AACTTGGTGATCCTCGATCGCATTGACAAGCCTGCTGCCATGGCGGAACTGAAGGCAATCAATCCCAAAG
TGATAGTTACTTTCTATCCCTATGATGTGACCACACCCTTGACAGAGACTACCAAATTGTTGAAGACCAT
TTTCGCCCAATTGAAGACTGTCGATGTTCTGATCAATGGAGCTGGCATTTTGGATGATCATCAGATTGAG
CGAACCATTGCCGTGAACTTCACTGGTTTGGTCAAAACCACCACAGCCATTTTGGACTTCTGGGATAAGC
GTAAGGGTGGACCAGGTGGTATTATCTGCAACATAGGATCGGTGACTGGTTTCAATGCCATGTACCAGGT
CCCCGTCTACTCGGCATCGAAAGCAGCTGTCGTCAGCTTCACTCAGTCCATTGCC
>AF264079.1 Drosophila pavlovskiana alcohol dehydrogenase (Adh) gene, partial cds
AACTTGGTGATCCTGGATCGTATTGACAATCCTGCTGCCATTGCTGAACTGAAGGCAATGAATCCCAAAG
TGACAGTTACTTTCTATCCCTATGATGTTACCACACCCTTGACAGAGACTACCAAATTGTTGAAGACCAT
TTTCGCCCAATTGAAGACTGTCGATGTTCTGATCAATGGAGCTGGCATTTTGGATGCTCATCAGATTGAG
CGAACCATTGCCGTGAACTTCACTGGTTTGGTCAATACCACCACAGCCATTTTGGACTTCTGGGATAAGC
GTAAGGGTGGACCAGGTGGTGTTATCTGCAACATTGGCTCTGTGACCGGTTTCAATGCCATCTATCAGGT
CCCTGTCTATTCTGCATCGAAAGCAGCTGTTGTTAGCTTCACTCAATCCATTGCC
>AF264080.1 Drosophila sucinea alcohol dehydrogenase (Adh) gene, partial cds
AACTTGGTGATCCTCGATCGTATTGATAATCCTGATGCCATTGCTGAACTGAAGGCAATCAATCCCAAGG
TGACAGTTACCTTCTTCCCCTACGATGTGACCACATCCTTGGCCGAGACCACCAAATTGCTGATAACCAT
TTTCGCTCAACTGATGACTGTCGTTCTGCTGATCAATGGAGCTGGCATTCTGGACGATCATCAGATTGAA
CGCACCATTGCCGTGAAATTCACCGGCCTGGTCAATACCATCAACGCAATTTTGGACATCTGGGACAAGC
GTAAGGGTGGACCAGGTGGTGTGATCTGCAACATTGGATCGGTGACTGGTTTCAATGCCATGTACCAGGT
CCCCGTCTACTCGGCATCGAAAGCAGCTGTCGTCAGCTTCACTCAGTCCATTGCC
>AF264081.1 Drosophila tropicalis alcohol dehydrogenase (Adh) gene, partial cds
AACCTGGTGATCCTGGATCGTATTGACAATCCTGCTGCCATTGCTGAGCTGAAGGCAATCAATCCCAAAG
TGACAGTTTACTTCTATCCCTACGATGTTACCGCACCCGTTGCAGAGACTACCAAATTGTTGAAGACCAT
TTTCGCTCAATTGAAAACTGTCGATGTTCTGATCAACGGAGCTGGCATTTTGGATGATCATCAGATTGAG
CGTACCATTGCTGTGAACTTCACTGGTTTGGTCAACACCACCACAGCCATTTTGGACTTCTGGGATAAGC
GCAAGGGTGGTCCAGGCGGTGTCATCTGCAACATTGGCTCCGTGACCGGTTTCAATGCGATCTATCAGGT
GGCTGTATATTCCGGCACGAAAGCAGGTGTGGTCAACTTCACTCAATCCATTGCC
>AF264082.1 Drosophila willistoni alcohol dehydrogenase (Adh) gene, partial cds
AACTTGGTGATCCTGGATCGTATTGACAAACCTGCTGCCATTGCTGAACTGAAGGCAATCAATCCCAAAG
TGACAGTTACCTTCTATCCCTATGATGTTACCACACCCTTGACAGAGACTACCAATTTGTTGAAGACCAT
TTTCGCCCAATTGAAGACTGTCGATGTCCTGATCAATGGAGCTGGCATTTTGGATGATCATCAGATCGAG
CGTACCATTGCTGTGAACTTCACTGGTTTGGTCAATACCACCACAGCCATTTTGGACTTCTGGGATAAGC
GTAAGGGTGGACCAGGTGGCGTCATCTGCAACATTGGCTCTGTGACCGGTTTCAATGCCATCTACCAGGT
CCCTGTCTATTCCGCATCCAAAGCAGCTGTTGTTAGCTTCACTCAATCCATTGCC

Docker Pull Command

docker pull pegi3s/omegamap