Mercurial > repos > artbio > cap3
diff newtests/cap3stdout.txt @ 1:a36a1acd5807 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 commit 3bb28761a3768b3b84616be41efc40683653da60
| author | artbio |
|---|---|
| date | Thu, 12 Oct 2023 23:17:38 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/newtests/cap3stdout.txt Thu Oct 12 23:17:38 2023 +0000 @@ -0,0 +1,299 @@ +Number of segment pairs = 342; number of pairwise comparisons = 14 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + +******************* Contig 1 ******************** +2+ + 9+ is in 2+ + 6+ is in 2+ +15+ + 1+ is in 15+ + 17+ is in 15+ +13+ +******************* Contig 2 ******************** +7+ + 10+ is in 7+ +******************* Contig 3 ******************** +11+ +4+ +******************* Contig 4 ******************** +18+ +12+ + +DETAILED DISPLAY OF CONTIGS +******************* Contig 1 ******************** + . : . : . : . : . : . : +2+ GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG +9+ GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG +15+ GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG + ____________________________________________________________ +consensus GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG + + . : . : . : . : . : . : +2+ GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG +9+ GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG +15+ GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG + ____________________________________________________________ +consensus GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG + + . : . : . : . : . : . : +2+ TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG +9+ TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG +6+ ACATCCTGG +15+ TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG + ____________________________________________________________ +consensus TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG + + . : . : . : . : . : . : +2+ GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC +9+ GTATGGTGGCTGTGGGC +6+ GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC +15+ GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC + ____________________________________________________________ +consensus GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC + + . : . : . : . : . : . : +2+ TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC +6+ TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC +15+ TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC + ____________________________________________________________ +consensus TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC + + . : . : . : . : . : . : +2+ ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA +6+ ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA +15+ ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA +17+ TACTCCTGCA + ____________________________________________________________ +consensus ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA + + . : . : . : . : . : . : +2+ ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTAC +6+ ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTAC +15+ ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT +1+ TTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT +17+ ACGTCCAGATTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT + ____________________________________________________________ +consensus ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT + + . : . : . : . : . : . : +15+ CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG +1+ CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG +17+ CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG + ____________________________________________________________ +consensus CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG + + . : . : . : . : . : . : +15+ TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA +1+ TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA +17+ TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA + ____________________________________________________________ +consensus TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA + + . : . : . : . : . : . : +15+ TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT +1+ TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT +17+ TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT + ____________________________________________________________ +consensus TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT + + . : . : . : . : . : . : +15+ CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA +1+ CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA +17+ CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA + ____________________________________________________________ +consensus CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA + + . : . : . : . : . : . : +15+ ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC +1+ ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC +17+ ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC + ____________________________________________________________ +consensus ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC + + . : . : . : . : . : . : +15+ CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC +1+ CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGT +17+ CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGT +13+ GTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC + ____________________________________________________________ +consensus CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC + + . : . : . : . : . : . : +15+ TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC +13+ TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC + ____________________________________________________________ +consensus TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC + + . : . : . : . : . : . : +15+ TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC +13+ TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC + ____________________________________________________________ +consensus TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC + + . : . : . : . : . : . : +15+ TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC +13+ TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC + ____________________________________________________________ +consensus TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC + + . : . : . : . : . : . : +15+ GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT +13+ GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT + ____________________________________________________________ +consensus GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT + + . : . : . : . : . : . : +15+ GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC +13+ GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC + ____________________________________________________________ +consensus GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC + + . : . : . : . : . : . : +15+ TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC +13+ TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC + ____________________________________________________________ +consensus TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC + + . : . : . : . : . : . : +15+ TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC +13+ TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC + ____________________________________________________________ +consensus TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC + + . : . : . : . : . : . : +15+ AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG +13+ AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG + ____________________________________________________________ +consensus AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG + + . : . : . : . : . : . : +15+ AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG +13+ AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG + ____________________________________________________________ +consensus AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG + + . : . : . : . : . : . : +15+ TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC +13+ TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC + ____________________________________________________________ +consensus TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC + +******************* Contig 2 ******************** + . : . : . : . : . : . : +7+ TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC +10+ TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC + ____________________________________________________________ +consensus TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC + + . : . : . : . : . : . : +7+ AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA +10+ AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA + ____________________________________________________________ +consensus AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA + + . : . : . : . : . : . : +7+ GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA +10+ GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA + ____________________________________________________________ +consensus GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA + + . : . : . : . : . : . : +7+ GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA +10+ GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA + ____________________________________________________________ +consensus GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA + + . : . : . : . : . : . : +7+ GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC +10+ GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC + ____________________________________________________________ +consensus GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC + + . : . : . : . : . : . : +7+ CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC +10+ CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC + ____________________________________________________________ +consensus CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC + + . : . : . : . : . : . : +7+ TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT +10+ TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT + ____________________________________________________________ +consensus TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT + + . : . : . : . : . : . : +7+ GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG +10+ GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG + ____________________________________________________________ +consensus GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG + + . : . : . : . : . : . : +7+ GATGAAGAGACAAGGCTTGGTTGTCAAAGAGGGAA +10+ GATGAAGAGACAAGGCTTAGTTGTCA + ____________________________________________________________ +consensus GATGAAGAGACAAGGCTTAGTTGTCAAAGAGGGAA + +******************* Contig 3 ******************** + . : . : . : . : . : . : +11+ AACGTAAAACAAACGACATGGATGCATCTAACCCTATTATTTCAAGCGATAGAAGCACTG +4+ ATAGAAGCACTG + ____________________________________________________________ +consensus AACGTAAAACAAACGACATGGATGCATCTAACCCTATTATTTCAAGCGATAGAAGCACTG + + . : . : . : . : . : . : +11+ TGAATCAGGTTTATGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG +4+ TGAATCAGGTTTACGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG + ____________________________________________________________ +consensus TGAATCAGGTTTACGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG + + . : . : . : . : . : . : +11+ AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG +4+ AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG + ____________________________________________________________ +consensus AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG + + . : . : . : . : . : . : +11+ AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG +4+ AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG + ____________________________________________________________ +consensus AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG + + . : . : . : . : . : . : +11+ TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT +4+ TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT + ____________________________________________________________ +consensus TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT + +******************* Contig 4 ******************** + . : . : . : . : . : . : +18+ TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA +12+ GGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA + ____________________________________________________________ +consensus TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA + + . : . : . : . : . : . : +18+ CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA +12+ CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA + ____________________________________________________________ +consensus CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA + + . : . : . : . : . : . : +18+ ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC +12+ ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC + ____________________________________________________________ +consensus ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC + + . : . : . : . : . : . : +18+ GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA +12+ GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA + ____________________________________________________________ +consensus GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA + + . : . : . : . : . : . : +18+ ACAGTTCTTGTTA +12+ ACAGTTCTTGTTA + ____________________________________________________________ +consensus ACAGTTCTTGTTA +