elynx-seq 0.3.2 → 0.3.3
raw patch · 11 files changed
+140/−28 lines, 11 filesPVP ok
version bump matches the API change (PVP)
API changes (from Hackage documentation)
Files
- ChangeLog.md +5/−0
- README.md +27/−27
- data/AminoAcid.fasta +10/−0
- data/Erroneous.fasta +5/−0
- data/Nucleotide.fasta +6/−0
- data/NucleotideDifferentLength.fasta +22/−0
- data/NucleotideDifferentLengthTrimmed.fasta +14/−0
- data/NucleotideIUPAC.fasta +6/−0
- data/TranslateMitochondrialVertebrateDNA.fasta +26/−0
- data/TranslateMitochondrialVertebrateProtein.fasta +10/−0
- elynx-seq.cabal +9/−1
ChangeLog.md view
@@ -5,6 +5,11 @@ ## Unreleased changes +## Version 0.3.3++- Fix test suites.++ ## Version 0.3.2 - Remove llvm dependency.
README.md view
@@ -2,7 +2,7 @@ # The ELynx Suite -Version: 0.3.2.+Version: 0.3.3. Reproducible evolution made easy. <p align="center"><img src="https://travis-ci.org/dschrempf/elynx.svg?branch=master"/></p>@@ -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
+ data/AminoAcid.fasta view
@@ -0,0 +1,10 @@+>SEQUENCE_1+MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEGLVSVKVSDDF+TIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHKIPQFASRKQLSDAILKEAEE+KIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTLMGQFYVMDDKKTVEQVIAEKEKEFGGKIKI+VEFICFEVGEGLEKKTEDFAAEVAAQL+>SEQUENCE_2+SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQIATIGENLVVR+TIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHKIPQFASRKQLSDAILKEAEE+KIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTLMGQFYVMDDKKTVEQVIAEKEKEFGGKIKI+VEFICFEVGEGLEKKTEDFAAEVAAQL
+ data/Erroneous.fasta view
@@ -0,0 +1,5 @@+>Sequence_1+ACGT+>Sequence_2+ACGT+>Error
+ data/Nucleotide.fasta view
@@ -0,0 +1,6 @@+>SEQUENCE_1+AAAAAAAAAGCCCCCCCCCTGGGGGGGGGGTTTTTTTTTA+>SEQUENCE_2+GAAAAAAAAACCCCCCCCCCGGGGGGGGGGCTTTTTTTTT+>SEQUENCE_3+TTTAAAAAAACCCAAAACCCGGGCCCCGGGTTTTTTTAAA
+ data/NucleotideDifferentLength.fasta view
@@ -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
+ data/NucleotideDifferentLengthTrimmed.fasta view
@@ -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
+ data/NucleotideIUPAC.fasta view
@@ -0,0 +1,6 @@+>SEQUENCE_1+AAAAAAAAAGCCCCCCNCCTGGGGGGGGGGTTTTTTTTTA+>SEQUENCE_2+GAAAAAAAA-CCCCCCCCCCGGGGGGGGGGCTTTTTTTTT+>SEQUENCE_3+TTTAAAAAAACHCAAAACCCGGGCCCCGGGTTTTTTTAAA
+ data/TranslateMitochondrialVertebrateDNA.fasta view
@@ -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
+ data/TranslateMitochondrialVertebrateProtein.fasta view
@@ -0,0 +1,10 @@+>Ambystoma_andersoni+MNLSFFDQFMSPTMLGIPLILLAMTIPWLLYASPTDRWLNNRLTTLQAWFLASFTKQLML+PLSIKGYKWALPLTSLMIFLITMNLLGLLPYTFTPTTQLSLNLGLAVPFWLATVLIGLRN+QPTAALGHLLPEGTPTLLIPILIIIETISLFIRPLALGVRLTANLTAGHLLIQLISTAVF+VLMPMMPTTAIITAIVLFLLTLLEIAVAMIQAYVFVLLLSLYLQENT*+>Ambystoma_barbouri+MNLSFFDQFMSPTMLGIPLILLAMTIPWLLYVSPTDRWLNNRLTTLQTWFLATFTKQLML+PLNIKGHKWALSLSSLMVFLITMNLLGLLPYTFTPTTQLSLNLGLAVPFWLATVLIGLRN+QPTAALGHLLPEGTPTLLIPILIIIETISLFIRPLALGVRLTANLTAGHLLIQLISTAVF+VLMPMMPTTAIITAIVLFLLTLLEIAVAMIQAYVFVLLLSLYLQENT*
elynx-seq.cabal view
@@ -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 <https://github.com/dschrempf/elynx>. 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