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توضیحات

ویژگی	مقدار
سیستم عامل	-
نام فایل	abeona-0.45.0
نام	abeona
نسخه کتابخانه	0.45.0
نگهدارنده	['Warren W. Kretzschmar']
ایمیل نگهدارنده	['warrenk@kth.se']
نویسنده	Warren W. Kretzschmar
ایمیل نویسنده	warrenk@kth.se
آدرس صفحه اصلی	https://github.com/winni2k/abeona
آدرس اینترنتی	https://pypi.org/project/abeona/
مجوز	Apache-2.0

abeona ====== .. image:: https://travis-ci.org/winni2k/abeona.svg?branch=master :alt: Travis-CI Build Status :target: https://travis-ci.org/winni2k/abeona .. image:: https://img.shields.io/github/commits-since/winni2k/abeona/v0.45.0.svg :alt: Commits since latest release :target: https://github.com/winni2k/abeona/compare/v0.45.0...master .. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :alt: freedom :target: http://bioconda.github.io/recipes/abeona/README.html abeona v0.45.0 A simple transcriptome assembler based on kallisto and Cortex graphs. Abeona consists of the following stages: 1. Assembly of reads into a De Bruijn graph 2. Pruning of tips and low-coverage unitigs 3. Partitioning of the De Bruijn graph into subgraphs 4. Generation of candidate transcripts by simple path traversal 5. Filtering of candidate transcripts by kallisto Installation ------------ The easiest way to install abeona is into a `conda <https://conda.io/miniconda.html>`_ environment. After activating the conda environment, run: .. code-block:: bash conda install abeona -c conda-forge -c bioconda Usage ----- The principal command is ``abeona assemble``. This command assembles transcripts from cleaned short-read RNA-seq reads in FASTA or FASTQ format. A description of command arguments is available with the command: .. code-block:: bash abeona assemble --help Specifying input read data ~~~~~~~~~~~~~~~~~~~~~~~~~~ Abeona is designed to be run on reads from one biological sample at a time. Abeona uses sequencing reads in two stages: for De Bruijn-graph construction, and for candidate transcript filtering with kallisto. The first stage accepts paired-end, single-end, or both types of reads through the ``--fastx-*`` arguments. The reads for the second stage are specified with the ``--kallisto-fastx-*`` arguments. Kallisto only accepts single-end or paired-end reads, so input to this stage is also restricted in that manner. Toy Example ----------- .. code-block:: bash # Let's create a FASTA consisting of sub-reads from two transcripts: AAAAACCC and AAAAAGGG $ for s in AAAAACC AAAAAGG AAAACCC AAAAGGG; do for i in $(seq 1 3); do echo -e ">_\n$s" >> input.fa; done; done # Now feed the fasta to the graph assembly step with --fastx-single and to the kallisto filtering # step with --kallisto-fastx-single. $ abeona assemble -k 5 -m 4 --fastx-single input.fa --kallisto-fastx-single \ input.fa --kallisto-fragment-length 7 --kallisto-sd 1 -o test --no-links N E X T F L O W ~ version 0.31.1 Launching `assemble.nf` [determined_allen] - revision: 11c20ed355 [bootstrap_samples:100, fastx_forward:null, fastx_reverse:null, fastx_single:/Users/winni/tmp/input.fa, initial_contigs:null, jobs:2, kallisto_fastx_forward:null, kallisto_fastx_reverse:null, kallisto_fastx_single:/Users/winni/tmp/input.fa, kallisto_fragment_length:7.0, kallisto_sd:1.0, kmer_size:5, max_paths_per_subgraph:0, memory:4, merge_candidates_before_kallisto:false, min_tip_length:0, min_unitig_coverage:4, out_dir:test, quiet:false, resume:false, mccortex:mccortex 5, mccortex_args:--sort --force -m 4G] [warm up] executor > local [26/119d41] Submitted process > fullCortexGraph [fc/585605] Submitted process > cleanCortexGraph [dd/40b5fc] Submitted process > pruneCortexGraphOfTips [36/f63343] Submitted process > traverseCortexSubgraphs [23/6d9033] Submitted process > candidateTranscripts (1) [d5/05d417] Submitted process > buildKallistoIndices (1) [ac/e36d53] Submitted process > kallistoQuant (1) [ec/2b258d] Submitted process > filter_transcripts (1) [49/d4c7e3] Submitted process > concatTranscripts # View the resulting assembled transcripts $ zcat test/all_transcripts/transcripts.fa.gz >g0_p0 prop_bs_est_counts_ge_1=0.98 AAAAAGGG >g0_p1 prop_bs_est_counts_ge_1=1.0 AAAAACCC Development ----------- :: conda env create -f environment.yml my-dev-env conda activate my-dev-env make test License ------- Abeona is distributed under the terms of the `Apache License, Version 2.0 <https://choosealicense.com/licenses/apache-2.0>`_. Citing ------ If you use abeona in your research, please cite: Akhter S, Kretzschmar WW, Nordal V, Delhomme N, Street NR, Nilsson O, Emanuelsson O, Sundström JF. Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies. Front. Plant Sci. 9, 1–18 (2018). Changelog --------- Version 0.45.0 ~~~~~~~~~~~~~~ :Date: XXX New features ............ **abeona assemble** * Mccortex is now used for pruning by default * The command line argument ``--prune-tips-with-mccortex`` is now deprecated. Instead use ``--no-prune-tips-with-mccortex``. * New iterative pruning strategy ``--prune-tips-iteratively``. Version 0.44.0 ~~~~~~~~~~~~~~ :Date: 2019-03-26 This version skips commits made for the 0.43.0 tag. New features ............ * Reads that share kmers with subgraphs that are skipped are now reported in the ``unassembled_reads`` directory. Version 0.42.0 ~~~~~~~~~~~~~~ :Date: 2018-12-17 Interface Changes ................. * Cleanup now deletes all directories in output dir except for ``all_transcripts/transcripts.fa.gz`` * Cleanup is now on by default * Cleanup can be turned off with ``--no-cleanup`` flag * ``all_transcripts/transcripts.fa.gz`` is unzipped and stored as ``transcripts.fa`` to conform to the convention set by Trinity and Oases for output file names Version 0.41.0 ~~~~~~~~~~~~~~ :Date: 2018-12-13 Interface changes ................. * Remove ``--kallisto-fastx-*`` arguments. Being able to separately specify reads to graph building and kallisto has not been all that useful, and it increases the complexity of the code. * Add default value of ``--kmer-size`` for ``--min-tip-length``. Fixes ..... * There are several ways in which kallisto can fail due to no reads pseudoaligning to a subgraph's candidate transcripts. When this happens, abeona now catches the error and silently ignores the subgraph. Version 0.40.0 ~~~~~~~~~~~~~~ :Date: 2018-11-17 New features ............ * Add ``--no-links`` argument to turn off link use in candidate transcript creation * Add ``--max-junctions`` argument to allow fast skipping of subgraphs with too many junctions Fixes ..... * Properly assign reads to all subgraphs to which they are assignable * Solve high-mem use problem by creating links only on assigned reads Version 0.36.0 ~~~~~~~~~~~~~~ :Date: 2018-10-25 New features ............ * Graph traversal now uses links Fixes ..... * Lots of improvements to ``abeona reads`` to improve memory and filehandle use Version 0.33.0 ~~~~~~~~~~~~~~ :Date: 2018-10-17 New features ............ * Use kmer mapping (``abeona reads``) to assign reads to subgraphs before quantification of candidate transcripts with kallisto Fixes ..... * Add missing conda dependency ``seqtk`` to ``environment.yml`` for travis CI

نیازمندی

مقدار	نام
>=0.45.6	cortexpy
-	pandas
-	progressbar2
-	pysam

نحوه نصب

نصب پکیج whl abeona-0.45.0:

pip install abeona-0.45.0.whl

نصب پکیج tar.gz abeona-0.45.0:

pip install abeona-0.45.0.tar.gz