Random scripts to deal with common fasta files, phylogenetic trees, tab-delimited lists and other fancy stuff. Such as split an alignment in defined positions, concatenate different fasta files, extract/remove sequences, reorder an alignment based on a tree, get the entropy on each position from an alignment, get the consensus sequence from an alignment, ...
Download and move the scripts to you prefered folder (e.g.;/usr/lobal/bin/) and start using them (you might have to make them executable: chmod +x *.py).
For fasta files manipulations (/fasta) :
alignmentConsensus.py: Creates a consensus of an aligned fasta file.
alignmentEntropy.py: Exports a table with the entropy and other values for every position of an aligned fasta file.
fastaConcat.py: From different fasta files, concatenates the sequences from identical sequence names.
fastaRevCom.py: Exports the reverse complement (or only reversed or only complement) fasta file.
fastaSplit.py: Takes an aligned fasta file and creates several fasta files cut at desired positions.
fastaStats.py: Prints to console certain statistics from a fasta file. Number of sequences, GC content, ...
multi2linefasta.py: From a fasta file where the sequences are saved in different sequences, exports a fasta file with each sequence in one line.
multi2line: Same script as multi2linefasta.py but written in bash.
sequenceSelect.py: From a fasta file, selects sequences from a given list or pattern and removes them or extracts them.
For phylogenetic tree manipulations (/phylogenetics):
fastaReorder.py: Orders the sequences of a fasta file by border of appearance in an phylogenetic tree.
findSeqs.py: From a phylogenetic tree and a fasta file, finds sequences that do not appear in either file.
treeCheckIntruders.py: From a phylogenetic tree and an attribute file, find sequences resolved within other attribute. Useful to identify badly placed sequences, long branch attraction artifacts and so on.
treeColourBranches.py: Based on a table, colours the branches of a phylogenetic tree, and goes inwards if the colours are monophyletic.
treeCountTips.py: Simply counts the number of tips of one or several phylogenetic trees.
treeLTT.py: Extract the Lineages Through Time curve from a time-calibrated tree. It also exports the highest posterior density to account for uncertainty and, if annotated, does the same for all annotated subclades.
treePruneList.py: Given a list of tips, prunes a phylogenetic tree of those tips.
treePruneOutliers.py: From a phylogenetic tree, finds and prunes branches which length is an outlier relative to the tree.
treeRemoveBranchLengths.py: Simply removes the branch lengths of a phylogenetic tree.
treeRoot.py: Given a list of tips, roots the tree in the last common ancestor of such tips.
treeRootOutgroup.py: Given a list of tips, creates an outgroup in the last common ancestor of such tips, rooting the tree with the outgroup.
treeStats.py: Prints to console certain statistics of a phylogenetic tree. Number of tips, nodes, branch lengths, ...
treeTipExtract.py: Exports the tip names of a phylogenetic tree to a list.
treeTipRename.py: Given a table, changes the tree tip names to the desire output.
How to cut, trim and concatenate a fasta file composed of two genes (/wrappers):
trimTwoGenes.sh
Remove reciprocal and identical hits from a pairwise comparison table (/others):
listRemoveReciprocals.py
For example how to create a constraint tree from a fasta file and a newick tree file containing the name of the groups (/phylogenetics):
checkConstrainTree.py: From a fasta file and a newick tree file, checks if every tree tip finds its sequences in the fasta file, and exports to a directory the list of sequence names found in the fasta file for every tree tip.
checkConstrainTaxa.sh: Checks each file from the previous directory, and exports a sumarised output. Be aware this script is highly dependent on the structure of your fasta sequence names...
buildConstrainTree.sh: Takes the original tree and the created directory with the sequence names to create the constraint tree to be used for phylogenetic analysis, with each group composed of a polytomy of all the sequences found in the fasta file.
Further details in the help of each script (script -h).
Please feel free to report bugs or suggestions. I'm creating these scripts as I need them, so they might also be targeted to my particular needs.