Python read file tree

BaseTree Tree class, depending on the file format. Parse and return exactly one tree from the given file or handle. If the file contains zero or multiple trees, a ValueError is raised. This is useful if you know a file contains just one tree, to load that tree object directly rather than through parse and next , and as a safety check to ensure the input file does in fact contain exactly one phylogenetic tree at the top level.

See examples of this in the unit tests for Phylo in the Biopython source code. Write a sequence of Tree objects to the given file or handle. Passing a single Tree object instead of a list or iterable will also work see, Phylo is friendly. Given two files or handles and two formats, both supported by Bio.

Phylo , convert the first file from the first format to the second format, writing the output to the second file. Within the Phylo module are parsers and writers for specific file formats, conforming to the basic top-level API and sometimes adding additional features. See the PhyloXML page for details. NewickIO: A port of the parser in Bio.

Trees to support the Newick a. NexusIO: Wrappers around Bio. Nexus to support the Nexus tree format. Requires RDFlib. The Nexus format actually contains several sub-formats for different kinds of data; to represent trees, Nexus provides a block containing some metadata and one or more Newick trees another kind of Nexus block can represent alignments; this is handled in AlignIO.

So to parse a complete Nexus file with all block types handled, use Bio. Nexus directly, and to extract just the trees, use Bio. The basic objects are defined in Bio. To support additional information stored in specific file formats, sub-modules within Tree offer additional classes that inherit from BaseTree classes.

Each sub-class of BaseTree. Tree or Node has a class method to promote an object from the basic type to the format-specific one. These sub-class objects can generally be treated as instances of the basic type without any explicit conversion. This site uses Akismet to reduce spam. Learn how your comment data is processed. Creating a list of files in directory and sub directories using os. Related Posts. Table of Contents. Improve Article. Save Article. Like Article.

Opening and Closing a file "MyFile. Program to show various ways to. To show difference between read and readline. Writing data to a file. Reading form a file.

Attention geek! Strengthen your foundations with the Python Programming Foundation Course and learn the basics. Previous Open a File in Python. Next Writing to file in Python. Recommended Articles. Article Contributed By :. Easy Normal Medium Hard Expert. Writing code in comment? Please use ide. Edit: Added bonus! Nice tool, do you have a quick example on how to use criteria in order to exclude folder names?

This is exactly what I was looking for. Thank you so much! List directory tree structure in Python? More features Now GNU tree gives us a couple of useful features that I'd like to have with this function: prints the subject directory name first does so automatically, ours does not prints the count of n directories, m files option to limit recursion, -L level option to limit to just directories, -d Also, when there is a huge tree, it is useful to limit the iteration e.

Comments are welcome! Community Bot 1 1 1 silver badge. This was exactly what I needed in my code, and taught me some new Python tricks! Otherwise if a folder doesn't have a directory for the last file, the tree won't be drawn correctly. I see no such guarantee in the API for iterdir. Please provide a reference on how iterdir orders or is guaranteed to provide the desired ordering. Show 3 more comments. A solution without your indentation: for path, dirs, files in os.

Ignoring the dirs list prevents the overlapping you mention. Intra Intra 1, 3 3 gold badges 18 18 silver badges 23 23 bronze badges. FrancescoMantovani "path" is the variable containing the directory you want to print, i. Used different loops so the one not showing files doesn't check if it has to on each iteration. Hope it helps someone else as dhobbs answer helped me.

Thanks a lot. Defaults to False. PaulDong 7 7 silver badges 19 19 bronze badges. I feel this answer doesn't contribute to the already accepted answer. The only thing you are providing is additional fluff code to turn off features or not in the response. Your feeling is right, jason-heine. The accepted answer is good enough, but some people asked how to do this fluff stuff and I wanted to give something to them.