ssi-analysis-result-parsers 0.0.1__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (21) hide show
  1. ssi_analysis_result_parsers/Legionella_parser.py +88 -0
  2. ssi_analysis_result_parsers/__init__.py +1 -0
  3. ssi_analysis_result_parsers/_modidx.py +38 -0
  4. ssi_analysis_result_parsers/blast_parser.py +178 -0
  5. ssi_analysis_result_parsers/config/config.default.env +24 -0
  6. ssi_analysis_result_parsers/config/config.default.yaml +9 -0
  7. ssi_analysis_result_parsers/core.py +252 -0
  8. ssi_analysis_result_parsers/hello_world.py +61 -0
  9. ssi_analysis_result_parsers/some_string.py +27 -0
  10. ssi_analysis_result_parsers-0.0.1.dist-info/METADATA +109 -0
  11. ssi_analysis_result_parsers-0.0.1.dist-info/RECORD +21 -0
  12. ssi_analysis_result_parsers-0.0.1.dist-info/WHEEL +5 -0
  13. ssi_analysis_result_parsers-0.0.1.dist-info/entry_points.txt +7 -0
  14. ssi_analysis_result_parsers-0.0.1.dist-info/licenses/LICENSE +8 -0
  15. ssi_analysis_result_parsers-0.0.1.dist-info/top_level.txt +8 -0
  16. test_input/.DS_Store +0 -0
  17. test_input/Legionella/lag-1_blast.tsv +1 -0
  18. test_input/Legionella/test.sbt.tsv +2 -0
  19. test_input/blast_parser/allele_matches_test.tsv +536 -0
  20. test_input/blast_parser/gene_presence_absence_test.tsv +3 -0
  21. test_output/output_with_sample_name.tsv +2 -0
test_input/blast_parser/gene_presence_absence_test.tsv ADDED
@@ -0,0 +1,3 @@
1
+ asd contig_1 98.732 473 473 1 473 8288 7816 CGCTGTTGGTATTAGTCGTATTAATGTGGCGACTTACCAGTCTGTTTCCGGGACTGGCAAAAAAGCCATCAGCGAACTGGTTGCTCAGGTAGGCGATCTTTTAAATGGGAGACCAGCTAATGTTCAAGTCTATCCTCAGCAAATTGCTTTTAATGCGCTTCCTCATATTGATCAGTTCGAAGACAATGGTTATACCCGGGAAGAGATGAAGATGGTCTGGGAAACCCGCAAGATTATGGAAGATGACAGCATTATGGTTAACCCTACAGCCGTCAGGGTTCCCGTTATTTATGGGCATTCTGAAGCGGTTCATCTGGAATTAAAAAAGCCTTTGACGGCTGACGATGCTCGCGCGCTTTTGGCAAAGGCACCCGGCGTTACTGTAGTGGATAATCTTTCTAAAGCAAGTTATCCCACAGCAATTAAGAATGCAGTCGGGCATGATGATGTTTTTGTAGGGCGCATAAGGCAGG 0.0 841
2
+ proA contig_2 97.284 405 405 1 405 11341 10937 TATGAAAACGCCTACTGGGACGGCAAGCAAATGACCTTTGGTGATGGTGACACCATGATGTATCCTTTGGTTTCTCTAGGTGTAGGTGGTCATGAAGTTAGCCATGGATTCACTGAACAACATTCTGGACTTGAATATTTCGGTCAGTCTGGTGGCATGAATGAGTCGTTTTCAGATATGGCTGCTCAAGCTGCTGAATATTATTCAGTTGGAAAAAACAGCTGGCAGATCGGCCCGGAAATAATGAAAGAAGACAGTGGTTATGACGCATTGCGTTACATGGATAAACCAAGCCGTGATGGTATGTCTATTGATGTAGCTGATGATTATTATGGCGGGTTAGATGTTCATTACTCCAGTGGAGTGTATAACCATTTATTCTACATATTAGCTAATCAACCTAAT 0.0 688
3
+ pilE contig_3 82.835 405 405 1 405 11341 10937 TATGAAAACGCCTACTGGGACGGCAAGCAAATGACCTTTGGTGATGGTGACACCATGATGTATCCTTTGGTTTCTCTAGGTGTAGGTGGTCATGAAGTTAGCCATGGATTCACTGAACAACATTCTGGACTTGAATATTTCGGTCAGTCTGGTGGCATGAATGAGTCGTTTTCAGATATGGCTGCTCAAGCTGCTGAATATTATTCAGTTGGAAAAAACAGCTGGCAGATCGGCCCGGAAATAATGAAAGAAGACAGTGGTTATGACGCATTGCGTTACATGGATAAACCAAGCCGTGATGGTATGTCTATTGATGTAGCTGATGATTATTATGGCGGGTTAGATGTTCATTACTCCAGTGGAGTGTATAACCATTTATTCTACATATTAGCTAATCAACCTAAT 0.0 688
test_output/output_with_sample_name.tsv ADDED
@@ -0,0 +1,2 @@
1
+ sample_name a b new: b c
2
+ sample1 1 2 5 7