diff --git a/ChangeLog.md b/ChangeLog.md --- a/ChangeLog.md +++ b/ChangeLog.md @@ -5,6 +5,11 @@ ## Unreleased changes +## Version 0.3.3 + +- Fix test suites. + + ## Version 0.3.2 - Remove llvm dependency. diff --git a/README.md b/README.md --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ # The ELynx Suite -Version: 0.3.2. +Version: 0.3.3. Reproducible evolution made easy.

@@ -90,9 +90,9 @@ slynx --help | head -n -16 - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] COMMAND @@ -136,9 +136,9 @@ slynx concatenate --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE Concatenate sequences found in input files. @@ -157,9 +157,9 @@ slynx examine --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: slynx examine (-a|--alphabet NAME) INPUT-FILE [--per-site] Examine sequences. If data is a multi sequence alignment, additionally analyze columns. @@ -179,9 +179,9 @@ slynx filter-rows --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: slynx filter-rows (-a|--alphabet NAME) INPUT-FILE [--longer-than LENGTH] [--shorter-than LENGTH] [--standard-characters] @@ -202,9 +202,9 @@ slynx filter-columns --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE [--standard-chars DOUBLE] @@ -226,9 +226,9 @@ slynx simulate --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL] [-m|--mixture-model MODEL] [-e|--edm-file NAME] @@ -305,9 +305,9 @@ slynx sub-sample --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: slynx sub-sample (-a|--alphabet NAME) INPUT-FILE (-n|--number-of-sites INT) @@ -335,9 +335,9 @@ slynx translate --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: slynx translate (-a|--alphabet NAME) INPUT-FILE (-r|--reading-frame INT) (-u|--universal-code CODE) @@ -360,9 +360,9 @@ tlynx --help | head -n -16 - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] COMMAND @@ -399,9 +399,9 @@ tlynx compare --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect] [-f|--newick-format FORMAT] NAMES @@ -428,9 +428,9 @@ tlynx examine --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT] Compute summary statistics of phylogenetic trees. @@ -452,9 +452,9 @@ tlynx simulate --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: tlynx simulate [-t|--nTrees INT] [-n|--nLeaves INT] [-H|--height DOUBLE] [-M|--condition-on-mrca] [-l|--lambda DOUBLE] @@ -491,9 +491,9 @@ elynx --help | head -n -16 - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: elynx COMMAND Validate and redo past ELynx analyses diff --git a/data/AminoAcid.fasta b/data/AminoAcid.fasta new file mode 100644 --- /dev/null +++ b/data/AminoAcid.fasta @@ -0,0 +1,10 @@ +>SEQUENCE_1 +MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEGLVSVKVSDDF +TIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHKIPQFASRKQLSDAILKEAEE +KIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTLMGQFYVMDDKKTVEQVIAEKEKEFGGKIKI +VEFICFEVGEGLEKKTEDFAAEVAAQL +>SEQUENCE_2 +SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQIATIGENLVVR +TIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHKIPQFASRKQLSDAILKEAEE +KIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTLMGQFYVMDDKKTVEQVIAEKEKEFGGKIKI +VEFICFEVGEGLEKKTEDFAAEVAAQL diff --git a/data/Erroneous.fasta b/data/Erroneous.fasta new file mode 100644 --- /dev/null +++ b/data/Erroneous.fasta @@ -0,0 +1,5 @@ +>Sequence_1 +ACGT +>Sequence_2 +ACGT +>Error diff --git a/data/Nucleotide.fasta b/data/Nucleotide.fasta new file mode 100644 --- /dev/null +++ b/data/Nucleotide.fasta @@ -0,0 +1,6 @@ +>SEQUENCE_1 +AAAAAAAAAGCCCCCCCCCTGGGGGGGGGGTTTTTTTTTA +>SEQUENCE_2 +GAAAAAAAAACCCCCCCCCCGGGGGGGGGGCTTTTTTTTT +>SEQUENCE_3 +TTTAAAAAAACCCAAAACCCGGGCCCCGGGTTTTTTTAAA diff --git a/data/NucleotideDifferentLength.fasta b/data/NucleotideDifferentLength.fasta new file mode 100644 --- /dev/null +++ b/data/NucleotideDifferentLength.fasta @@ -0,0 +1,22 @@ +>SEQUENCE_1 +AAAAAAACCCCCCCCCTGGGGGGGGGGTTTTTTTTTA +>SEQUENCE_2 +GAAAAA +>SEQUENCE_3 +ATTTAAAAAAACCCAAAACCCGGGCCCCGGGTTTTTTTA +>SEQUENCE_4 +AAAAAAACCCCCCCCCTGGGGGGGGGGTTTTTTTTTA +>SEQUENCE_5 +GAAAAAACCCGGGGGGGGGGCTTTTTTTTT +>SEQUENCE_6 +TTTAAAAAAACCCAAAACCCGGGCCCCGGGTTTTTTTA +>SEQUENCE_7 +AAAAAAACCCCCCCCCTGGGGGGGGGGTTTTTTTTTA +>SEQUENCE_8 +AAAACCCGGGGGGGGGGCTTTTTTTTT +>SEQUENCE_9 +TTTTTTTA +>SEQUENCE_10 +TTTTTTTACG +>SEQUENCE_11 +TTTTTTTAC diff --git a/data/NucleotideDifferentLengthTrimmed.fasta b/data/NucleotideDifferentLengthTrimmed.fasta new file mode 100644 --- /dev/null +++ b/data/NucleotideDifferentLengthTrimmed.fasta @@ -0,0 +1,14 @@ +>SEQUENCE_1 +AAAAAAACCCCCCCCCTGGGGGGGGGGTTTTTTTTTA +>SEQUENCE_3 +ATTTAAAAAAACCCAAAACCCGGGCCCCGGGTTTTTTTA +>SEQUENCE_4 +AAAAAAACCCCCCCCCTGGGGGGGGGGTTTTTTTTTA +>SEQUENCE_5 +GAAAAAACCCGGGGGGGGGGCTTTTTTTTT +>SEQUENCE_6 +TTTAAAAAAACCCAAAACCCGGGCCCCGGGTTTTTTTA +>SEQUENCE_7 +AAAAAAACCCCCCCCCTGGGGGGGGGGTTTTTTTTTA +>SEQUENCE_8 +AAAACCCGGGGGGGGGGCTTTTTTTTT diff --git a/data/NucleotideIUPAC.fasta b/data/NucleotideIUPAC.fasta new file mode 100644 --- /dev/null +++ b/data/NucleotideIUPAC.fasta @@ -0,0 +1,6 @@ +>SEQUENCE_1 +AAAAAAAAAGCCCCCCNCCTGGGGGGGGGGTTTTTTTTTA +>SEQUENCE_2 +GAAAAAAAA-CCCCCCCCCCGGGGGGGGGGCTTTTTTTTT +>SEQUENCE_3 +TTTAAAAAAACHCAAAACCCGGGCCCCGGGTTTTTTTAAA diff --git a/data/TranslateMitochondrialVertebrateDNA.fasta b/data/TranslateMitochondrialVertebrateDNA.fasta new file mode 100644 --- /dev/null +++ b/data/TranslateMitochondrialVertebrateDNA.fasta @@ -0,0 +1,26 @@ +>Ambystoma_andersoni +ATGAACCTAAGCTTTTTTGACCAATTCATAAGCCCAACTATGTTAGGTATCCCATTAATT +TTACTAGCAATAACTATCCCATGATTATTATATGCTTCACCAACAGATCGATGATTAAAC +AACCGCCTTACCACCCTGCAAGCGTGATTTTTAGCTTCCTTTACAAAGCAACTAATACTT +CCTCTCAGCATTAAAGGGTATAAATGAGCTTTACCATTGACTTCCCTAATAATCTTTTTA +ATTACAATGAATTTATTAGGGTTATTACCTTATACTTTTACCCCTACAACTCAACTTTCA +TTAAACTTAGGATTAGCTGTTCCATTCTGACTAGCTACAGTACTAATTGGATTACGAAAT +CAACCAACTGCAGCATTAGGACACTTACTTCCTGAAGGCACCCCAACACTATTAATTCCA +ATTTTAATTATTATTGAAACAATTAGCTTATTTATTCGCCCATTAGCTTTAGGAGTTCGT +CTTACTGCTAACCTTACAGCTGGCCATCTTCTTATTCAACTTATCTCTACAGCAGTATTT +GTTTTAATACCTATAATACCAACAACAGCTATTATTACTGCTATTGTATTATTTCTTTTA +ACTCTTTTAGAAATTGCCGTAGCAATAATTCAAGCTTATGTCTTTGTACTTCTATTAAGT +CTTTATCTTCAAGAAAACACATAA +>Ambystoma_barbouri +ATGAACCTAAGCTTTTTTGACCAATTTATAAGCCCCACAATATTAGGTATTCCACTAATT +TTATTAGCAATAACCATTCCATGGCTATTATATGTTTCACCAACAGACCGCTGATTAAAT +AATCGCCTTACTACCCTACAAACATGATTTCTAGCCACCTTTACAAAACAACTAATGCTA +CCGCTAAATATCAAAGGACATAAATGAGCCTTATCACTAAGCTCATTAATAGTTTTTCTA +ATTACAATAAACTTACTTGGATTATTACCTTATACCTTTACCCCAACAACACAACTTTCA +CTAAATTTAGGGTTGGCTGTTCCGTTCTGATTGGCAACAGTGTTAATCGGCCTACGAAAT +CAACCAACTGCAGCCCTTGGACACCTTCTTCCAGAAGGCACCCCAACACTGCTAATCCCA +ATTTTAATTATTATCGAAACAATTAGTTTATTTATTCGACCACTAGCCCTAGGAGTCCGT +TTAACTGCAAATCTCACAGCAGGCCACCTACTTATTCAACTTATTTCTACAGCAGTCTTT +GTATTAATACCAATAATACCAACAACAGCTATTATTACTGCTATTGTTTTATTTCTACTA +ACCCTTTTAGAAATTGCTGTAGCAATAATTCAAGCTTATGTTTTTGTCCTTCTTTTAAGC +CTCTATCTTCAAGAGAATACATAA diff --git a/data/TranslateMitochondrialVertebrateProtein.fasta b/data/TranslateMitochondrialVertebrateProtein.fasta new file mode 100644 --- /dev/null +++ b/data/TranslateMitochondrialVertebrateProtein.fasta @@ -0,0 +1,10 @@ +>Ambystoma_andersoni +MNLSFFDQFMSPTMLGIPLILLAMTIPWLLYASPTDRWLNNRLTTLQAWFLASFTKQLML +PLSIKGYKWALPLTSLMIFLITMNLLGLLPYTFTPTTQLSLNLGLAVPFWLATVLIGLRN +QPTAALGHLLPEGTPTLLIPILIIIETISLFIRPLALGVRLTANLTAGHLLIQLISTAVF +VLMPMMPTTAIITAIVLFLLTLLEIAVAMIQAYVFVLLLSLYLQENT* +>Ambystoma_barbouri +MNLSFFDQFMSPTMLGIPLILLAMTIPWLLYVSPTDRWLNNRLTTLQTWFLATFTKQLML +PLNIKGHKWALSLSSLMVFLITMNLLGLLPYTFTPTTQLSLNLGLAVPFWLATVLIGLRN +QPTAALGHLLPEGTPTLLIPILIIIETISLFIRPLALGVRLTANLTAGHLLIQLISTAVF +VLMPMMPTTAIITAIVLFLLTLLEIAVAMIQAYVFVLLLSLYLQENT* diff --git a/elynx-seq.cabal b/elynx-seq.cabal --- a/elynx-seq.cabal +++ b/elynx-seq.cabal @@ -1,6 +1,6 @@ cabal-version: 2.2 name: elynx-seq -version: 0.3.2 +version: 0.3.3 synopsis: Handle molecular sequences description: Examine, modify, and simulate molecular sequences in a reproducible way. Please see the README on GitHub at . category: Bioinformatics @@ -16,6 +16,14 @@ extra-source-files: README.md ChangeLog.md + data/AminoAcid.fasta + data/Erroneous.fasta + data/NucleotideDifferentLength.fasta + data/NucleotideDifferentLengthTrimmed.fasta + data/Nucleotide.fasta + data/NucleotideIUPAC.fasta + data/TranslateMitochondrialVertebrateDNA.fasta + data/TranslateMitochondrialVertebrateProtein.fasta source-repository head type: git