<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/140?offset=30 https://bioinformaticsonline.com/bookmarks/view/44179/python-mini-projects Mon, 16 Jan 2023 02:14:03 -0600 https://bioinformaticsonline.com/bookmarks/view/44179/python-mini-projects <![CDATA[Python Mini Projects !]]> There is a directory for each chapter of the book. Each directory contains a test.py program you can use with pytest to check that you have written the program correctly. I have included a short README to describe each exercise. If you have problems writing code (or if you would like to support this project!), the book contains details about the skills you need.

https://github.com/kyclark/tiny_python_projects

Address of the bookmark: https://github.com/kyclark/tiny_python_projects

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/12963/cosmos-our-workflow-management-system-for-ngs-data Wed, 23 Jul 2014 07:29:14 -0500 https://bioinformaticsonline.com/bookmarks/view/12963/cosmos-our-workflow-management-system-for-ngs-data <![CDATA[COSMOS, our workflow management system for NGS data]]> COSMOS, our Python-based management system for implementing large-scale parallel workflows focusing on, but not restricted to, large-scale short-read "NGS" sequencing data is open-access published via Advance Access in Bioinformatics (Gafni et al. 2014).  It is also available for download for non-commercial academic and research purposes at:

 http://cosmos.hms.harvard.edu/.

Address of the bookmark: https://cosmos.hms.harvard.edu/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/20471/bioinformatics-scripts Thu, 22 Jan 2015 22:29:39 -0600 https://bioinformaticsonline.com/bookmarks/view/20471/bioinformatics-scripts <![CDATA[Bioinformatics Scripts]]> Some of the useful bioinformatics scripts.

For example ... contig-stats.pl is a Perl script that will automatically describe features of a sequence assembly.

http://milkweedgenome.org/?q=scripts

Address of the bookmark: http://milkweedgenome.org/?q=scripts

]]> Jit https://bioinformaticsonline.com/bookmarks/view/30018/bipype Thu, 01 Dec 2016 08:47:38 -0600 https://bioinformaticsonline.com/bookmarks/view/30018/bipype <![CDATA[bipype]]> Bipype is a very useful program, which prepare a lot of types of bioinformatics analyses. There are three input options: amplicons, WGS (whole genome sequences) and metatranscriptomic data. If amplicons are input data, then bipype does reconstruction and pairs merging. After that biodiversity is searching. There are two types of searching depending on the amplicons types (ITS or 16S). If WGS are chosen, then bipype finds the SA coordinates of the input reads and generates alignments in the SAM format given single-end reads, aligns reads to reference sequence(s). All of these analyses will be shown with Krona program, which allows to show hierarchical data with pie charts.

Address of the bookmark: https://readthedocs.org/projects/bipype/

]]> Jit https://bioinformaticsonline.com/pages/view/36497/installing-python-numpy Mon, 07 May 2018 04:31:25 -0500 https://bioinformaticsonline.com/pages/view/36497/installing-python-numpy <![CDATA[Installing python-numpy !]]> $ sudo apt-get install python-numpy python-scipy python-matplotlib ipython ipython-notebook python-pandas python-sympy python-nose
[sudo] password for urbe:
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
bridge-utils containerd linux-headers-4.4.0-116 linux-headers-4.4.0-116-generic linux-headers-4.4.0-21 linux-headers-4.4.0-21-generic
linux-image-4.4.0-116-generic linux-image-4.4.0-21-generic linux-image-extra-4.4.0-116-generic linux-image-extra-4.4.0-21-generic
linux-signed-image-4.4.0-116-generic runc ubuntu-fan
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
blt fonts-lyx fonts-mathjax ipython-notebook-common isympy libaec0 libamd2.4.1 libdsdp-5.8gf libglpk36 libgsl2 libhdf5-10 libjs-highlight
libjs-highlight.js libjs-jquery-ui libjs-marked libjs-mathjax libjs-underscore libsz2 python-antlr python-bs4 python-chardet python-cvxopt
python-cycler python-dateutil python-decorator python-glade2 python-gmpy python-html5lib python-imaging python-jdcal python-jinja2 python-joblib
python-lxml python-markupsafe python-matplotlib-data python-mpmath python-numexpr python-openpyxl python-pandas-lib python-patsy python-pexpect
python-pil python-ptyprocess python-py python-pycurl python-pyglet python-pymysql python-pyparsing python-pytest python-simplegeneric
python-simplejson python-statsmodels python-statsmodels-lib python-sympy-doc python-tables python-tables-data python-tables-lib python-tk
python-tornado python-tz python-xlrd python-xlwt python-zmq tk8.6-blt2.5 ttf-bitstream-vera
Suggested packages:
blt-demo ipython-doc ipython-qtconsole python-pygments nodejs pandoc libiodbc2-dev libmysqlclient-dev gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info
| gsl-ref-html libjs-jquery-ui-docs fonts-mathjax-extras libjs-mathjax-doc python-gtk2-doc python-genshi python-jinja2-doc python-lxml-dbg
python-lxml-doc ffmpeg inkscape python-cairocffi python-configobj python-excelerator python-matplotlib-doc python-qt4 python-sip python-traits
python-wxgtk3.0 ttf-staypuft python-gmpy2 python-mpmath-doc python-coverage python-nose-doc python-numpy-dbg python-numpy-doc python-pandas-doc
python-patsy-doc python-pexpect-doc python-pil-doc python-pil-dbg subversion python-pytest-xdist libcurl4-gnutls-dev python-pycurl-dbg
python-pycurl-doc python-pymysql-doc python-mock python-scipy-doc python-statsmodels-doc python-tables-doc python-netcdf vitables tix
python-tk-dbg
The following NEW packages will be installed:
blt fonts-lyx fonts-mathjax ipython ipython-notebook ipython-notebook-common isympy libaec0 libamd2.4.1 libdsdp-5.8gf libglpk36 libgsl2
libhdf5-10 libjs-highlight libjs-highlight.js libjs-jquery-ui libjs-marked libjs-mathjax libjs-underscore libsz2 python-antlr python-bs4
python-chardet python-cvxopt python-cycler python-dateutil python-decorator python-glade2 python-gmpy python-html5lib python-imaging
python-jdcal python-jinja2 python-joblib python-lxml python-markupsafe python-matplotlib python-matplotlib-data python-mpmath python-nose
python-numexpr python-numpy python-openpyxl python-pandas python-pandas-lib python-patsy python-pexpect python-pil python-ptyprocess python-py
python-pycurl python-pyglet python-pymysql python-pyparsing python-pytest python-scipy python-simplegeneric python-simplejson python-statsmodels
python-statsmodels-lib python-sympy python-sympy-doc python-tables python-tables-data python-tables-lib python-tk python-tornado python-tz
python-xlrd python-xlwt python-zmq tk8.6-blt2.5 ttf-bitstream-vera
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➜ redundans git:(master) ✗ python2 redundans.py -v -i test/*_?.fq.gz -f test/contigs.fa -o test/run1
Options: Namespace(fasta='test/contigs.fa', fastq=['test/5000_1.fq.gz', 'test/5000_2.fq.gz', 'test/600_1.fq.gz', 'test/600_2.fq.gz'], identity=0.51, iters=2, joins=5, limit=0.2, linkratio=0.7, log=', mode 'w' at 0x7f85d1de31e0>, longreads=[], mapq=10, mem=16, minLength=200, nocleaning=True, nogapclosing=True, norearrangements=False, noreduction=True, noscaffolding=True, outdir='test/run1', overlap=0.8, reference='', resume=False, threads=4, tmp='/tmp', usebwa=False, verbose=True)

##################################################
[Mon May 7 11:29:18 2018] Reduction...
#file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]
/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
test/run1/contigs.fa 163897 245 66377 40.50 221 90.20 94.854 0 97520 59.50 24 9.80

##################################################
[Mon May 7 11:29:29 2018] Estimating parameters of libraries...
Aligning 19504 mates per library...
Insert size statistics Mates orientation stats
FastQ files read length median mean stdev FF FR RF RR
test/5000_1.fq.gz test/5000_2.fq.gz 50 4998 4990.20 721.47 0 4674 0 0
test/600_1.fq.gz test/600_2.fq.gz 100 599 598.63 47.68 0 10000 0 0

##################################################
[Mon May 7 11:29:29 2018] Scaffolding...
iteration 1.1: test/run1/contigs.reduced.fa 24 97520 39.355 17 94157 7321 2195 0 29603
19505 pairs. 17302 passed filtering [88.71%]. 1627 in different contigs [8.34%].
1526 pairs. 558 in different contigs [36.57%].
iteration 1.2: test/run1/_sspace.1.1.fa 3 97626 39.344 3 97626 87536 6063 821 87536
19505 pairs. 17607 passed filtering [90.27%]. 182 in different contigs [0.93%].
1077 pairs. 124 in different contigs [11.51%].
iteration 2.1: test/run1/_sspace.1.2.fa 3 97626 39.344 3 97626 87536 6063 821 87536
19505 pairs. 15112 passed filtering [77.48%]. 1295 in different contigs [6.64%].
3417 pairs. 396 in different contigs [11.59%].
iteration 2.2: test/run1/_sspace.2.1.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
19505 pairs. 15152 passed filtering [77.68%]. 0 in different contigs [0.00%].
3398 pairs. 0 in different contigs [0.00%].

##################################################
[Mon May 7 11:29:34 2018] Gap closing...
iteration 1.1: test/run1/scaffolds.fa 1 99133 39.344 1 99133 99133 99133 2328 99133

##################################################
[Mon May 7 11:29:35 2018] Final reduction...
#file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]
[WARNING] Nothing reduced!
test/run1/scaffolds.filled.fa 99390 1 0 0.00 0 0.00 0.000 0 99390 100.00 1 100.00

##################################################
[Mon May 7 11:29:35 2018] Reporting statistics...
#fname contigs bases GC [%] contigs >1kb bases in contigs >1kb N50 N90 Ns longest
test/contigs.fa 245 163897 40.298 24 117391 3975 233 0 29603
test/run1/contigs.fa 245 163897 40.298 24 117391 3975 233 0 29603
test/run1/contigs.reduced.fa 24 97520 39.355 17 94157 7321 2195 0 29603
test/run1/_sspace.1.1.fa 3 97626 39.344 3 97626 87536 6063 821 87536
test/run1/_sspace.1.2.fa 3 97626 39.344 3 97626 87536 6063 821 87536
test/run1/_sspace.2.1.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/_sspace.2.2.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/scaffolds.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/_gapcloser.1.1.fa 1 99390 39.689 1 99390 99390 99390 2 99390
test/run1/scaffolds.filled.fa 1 99390 39.689 1 99390 99390 99390 2 99390
test/run1/scaffolds.reduced.fa 1 99390 39.689 1 99390 99390 99390 2 99390

##################################################
[Mon May 7 11:29:35 2018] Cleaning-up...
#Time elapsed: 0:00:17.376924

]]> Jit https://bioinformaticsonline.com/blog/view/37627/setting-python-version-as-default-on-linux Tue, 04 Sep 2018 10:15:47 -0500 https://bioinformaticsonline.com/blog/view/37627/setting-python-version-as-default-on-linux <![CDATA[Setting python version as default on Linux]]> If you have a later version than 2.6 you'll need to set 2.6 as the default Python. Later versions would be 2.7 and 3.1; see what you have by typing

python -V

at the terminal. For purposes of this example we'll assume you have 3.1 installed. You'll next need to execute the following commands:

 

sudo apt-get install python2.6 idle-python2.6
sudo update-alternatives --install /usr/bin/python python /usr/bin/python3.1 1
sudo update-alternatives --install /usr/bin/python python /usr/bin/python2.6 10
sudo update-alternatives --config python

This last command will allow you to choose which version of python to use by default. If you have done everything above correctly, python2.6 should already be set as the default. If it is not, choose it to be the default. From now on, running python should start version 2.6.

Undoing These Changes

In some cases (e.g., installing or updating certain packages), you'll get an error message if you've run the commands above. To update these packages, you'll have to temporarily undo these changes. Here's how to do that:

sudo update-alternatives --remove-all python
sudo ln -s python3.1 /usr/bin/python

Once you're done updating these packages, execute the commands at the top to set python2.6 as the default again.

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/40834/nucleus-python-and-c-code-for-reading-and-writing-genomics-data Sun, 02 Feb 2020 08:14:19 -0600 https://bioinformaticsonline.com/bookmarks/view/40834/nucleus-python-and-c-code-for-reading-and-writing-genomics-data <![CDATA[Nucleus: Python and C++ code for reading and writing genomics data.]]> Nucleus is a library of Python and C++ code designed to make it easy to read, write and analyze data in common genomics file formats like SAM and VCF. In addition, Nucleus enables painless integration with the TensorFlow machine learning framework, as anywhere a genomics file is consumed or produced, a TensorFlow tfrecords file may be used instead.

Address of the bookmark: https://github.com/google/nucleus

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42923/flanker Sat, 27 Feb 2021 22:04:53 -0600 https://bioinformaticsonline.com/bookmarks/view/42923/flanker <![CDATA[Flanker]]> Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of mobile genetic elements (MGEs) without prior knowledge of their structure. Flanker can be flexibly parameterised to finetune outputs by characterising upstream and downstream regions separately and investigating variable lengths of flanking sequence.

image

Address of the bookmark: https://github.com/wtmatlock/flanker

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/34567/jobtree-based-python-wrapper-to-run-the-genome-simulation-tool-suite-evolver Fri, 08 Dec 2017 16:26:32 -0600 https://bioinformaticsonline.com/bookmarks/view/34567/jobtree-based-python-wrapper-to-run-the-genome-simulation-tool-suite-evolver <![CDATA[jobTree based python wrapper to run the genome simulation tool suite Evolver]]> evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation as it runs including text and image files. Also included are convenience scripts to: check on a running simulation and see detailed status and logging information; extract fasta sequence files from the leaf nodes of a completed simulation; extract pairwise multiple alignment files (.maf) from leaf and branch nodes from a completed simulation and with the help of mafJoin, join them together into a single maf covering the entire simulation.

Address of the bookmark: https://github.com/dentearl/evolverSimControl

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40099/contiguator Fri, 04 Oct 2019 01:27:58 -0500 https://bioinformaticsonline.com/bookmarks/view/40099/contiguator <![CDATA[CONTIGuator !]]> CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome assembly process and to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT).

 

Address of the bookmark: https://sourceforge.net/projects/contiguator/

]]> BioStar