Mercurial > repos > abims-sbr > pogs
comparison test-data/pogs.output @ 6:b19ed7395dcc draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
| author | abims-sbr |
|---|---|
| date | Wed, 17 Jan 2018 08:54:30 -0500 |
| parents | dad7053ba20e |
| children |
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| 5:dad7053ba20e | 6:b19ed7395dcc |
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| 1 *** pogs.py *** | |
| 1 | 2 |
| 2 Number of locus before removeRedondancy = 11 | 3 Building of orthogroups based on pairs of genes obtained by pairwise comparisons between pairs of species. |
| 4 Genes are gathered in orthogroups based on the principle of transitivity between genes pairs. | |
| 3 | 5 |
| 6 Parsing input files ... | |
| 7 Creating Orthogroups ... | |
| 4 | 8 |
| 5 Number of locus = 11 | 9 Summary before paralogous filtering : |
| 6 | 10 |
| 11 2 sps 3 sps 4 sps | |
| 12 2 seqs 1394 0 0 | |
| 13 3 seqs 0 163 0 | |
| 14 4 seqs 0 26 33 | |
| 15 5 seqs 0 3 17 | |
| 16 6 seqs 0 0 17 | |
| 17 7 seqs 0 0 7 | |
| 18 8 seqs 0 0 2 | |
| 19 11 seqs 0 0 1 | |
| 20 13 seqs 0 0 1 | |
| 7 | 21 |
| 8 NUMBER OF REMAINING LOCUS AFTER INTRA LOCUS TREATMENT [PARALOGS NAIVE FILTERING] = 11 | 22 Writing orthogroups with paralogs files ... |
| 9 NUMBER OF REMAINING LOCUS AFTER 2ND TREATMENT [INTER LOCUS] = 11 | |
| 10 | 23 |
| 24 Filtering paralogous sequences and writing final orthogroups files ... | |
| 25 (Dropping Orthogroups with less than 3 species) | |
| 11 | 26 |
| 12 REMOVAL OF LOCUS WITH LESS THAN 2 SEQUENCES | 27 Summary after paralogous filtering : |
| 13 | 28 |
| 14 Number of species in the locus : 4 | 29 3 sps 4 sps |
| 15 Number of locus : 0 | 30 3 seqs 192 0 |
| 31 4 seqs 0 78 | |
| 16 | 32 |
| 17 Number of species in the locus : 3 | 33 270 orthogroups have been infered from 6 pairwise comparisons by RBH |
| 18 Number of locus : 1 | |
| 19 | 34 |
| 20 Number of species in the locus : 2 | |
| 21 Number of locus : 10 | |
| 22 |