BOL: Related items

Five points for bioinformatics software/tools

Jitendra Narayan — Mon, 05 Aug 2013 04:12:32 -0500

In the bioinformatics sector we mostly spend time on computational analysis of huge amounts of data and try to make sense of it, biologically. But, most of the newbie bioinformaticians are faced with dilemma when they receive biological sequence data for the first time. They mostly found confusing over open source, user friendly GUI, and commercial bioinformatics software. Don’t be surprise this is true and also not an easy task to decide, because analytical step is the most crucial part and believe to be the biggest bottleneck in publishing paper in high impact journals. Through this blog I would like to address the pros and cons of both kind of software/tools and try to assist (Hmmm not really, It looks convince) you to make decision on your software selections.

The most common newbie questions are:

Should I try to use these free open source programs? Why are we not trying GUI software for computational analysis? Should I use commercial bioinformatics programs/software?”

1. Let’s be open

We generally think free and cheap are useless. But this concept is not applicable when we discuss open source software. Mostly, the bioinformatics software is developed by highly competitive biological programmers who believe in open sharing of knowledge. They come under Open Bioinformatics Foundation or O|B|F which is a non-profit, volunteer run organization focused on supporting open source programming in bioinformatics. The best part about open source tools/software is that they’re free to download the source code and read exactly what the program does. If you are so inclined, you can view all of the parts of the program and see the logical flow of the pipeline. In addition, open source makes an excellent learning tool for any beginning bioinformatician. Moreover, you can modify existing open source programs to deal with cutting-edge problems or to customize your pipeline. Apart from your computational and analysis work, most of the reviewer also prefers the open source based results so that they can validate the results if validation required.

2. Code headache

As a bioinformatician you are supposed to know the basics of programming languages, and if you are not good at it, then please learn it as soon as possible because you are not a bio-analyst but biological programmers. The open source programs usually lack dedicated service and support teams (often because they were the product of an overworked doc/postdoc!) so you are responsible for troubleshooting your own errors most of the time. We commonly receive the HELP email to support and assist to setup the pipeline; you can also find this kind of request on any QA forum. I personally believe this coding horror brings the biggest downside of open-source programs; where you need some programming skills in order to implement the program in your pipeline. But, if you are not able to fix the pipeline and modify the open source code according to your requirements them you should re-think on your bioinformatician name tag!!!

3. Dive into the codes

Some of the biologist turn bioinformatician says “if you can do the same thing with commercial software then why to get migraine with weird codes”, well this statement looks to me that guys are keen to learn swimming but still don’t like to get wet. If you are still using paid software and doing your work by customer support and clicking some of the well-designed GUI button then perhaps you are not interested in learning and trying new and challenging bioinformatics works. You are missing the basic flavour of bioinformatics. Let’s dive into the coding world, I am sure your will enjoy it. I recommend your to swim freely in code’s sea, and enjoy the journey; do not merely watch it from the outside.

4. Paid does not mean better

The bioinformatics company which are specializes in bioinformatics solutions develop well designed/packed, user friendly software by using a large number of specialised scientist, programmers and support staff. They also provide good services to accomplice your biological analysis work. This means that if you hit a ‘snag’ with your data, help is likely only a phone call away! These companies price their products competitively against the cost of a dedicated bioinformatician. You may be able to afford the program, but not the additional staff! Additionally, most of the functionality that you need in your analysis is already coded into the program. Need to plot a graph? Just click this button right here. It is that easy. But, as a bioinformatician this is not generally well encouraged approach in biological analysis work, because the software is not available to everyone and your data can’t be validated. Moreover, there is very less chances that anyone will repeat your work or love to do similar kind of research (because not all the labs in the world are rich like yours).

5. Take a caution

In biological analysis work, in which you deal GB/TB of data are having maximum chances of getting errors, so please be careful and always cross check your data before coming to any conclusion. Even an error in two line code can alter your entire analysis and display weird results. Some of the scientist blindly believes on commercial software, which is entirely wrong. Using proprietary tools does not absolve you of the need to actually read and research the type of analysis that you are doing. This is particularly true in the case of genome assembly and annotation.

At the end, I would like to tell only one think that open source solutions allows you to do more cutting edge analysis than the commercial tools. So let’s go for it.

Disclaimer:

This is my personal view. I have nothing to do with any company or open source community. The views expressed on these pages are mine alone and not those of my current/past employers. I do reserve the right to remove comments left by spammers or off-topic comments.

Linux for bioinformatician !!!

Rahul Nayak — Thu, 13 Mar 2014 16:59:26 -0500

Linux, free operating system for computers, provides several powerful admin tools and utilities which will help you to manage your systems effectively and handle huge amount of genomic/biological data with an ease. The field of bioinformatics relies heavily on Linux-based computers and software. Although most bioinformatics programs can be compiled to run. If you don’t know what these no so user-friendly tools are and how to use them, you could be spending lot of time trying to perform even the basic admin tasks. The focus of this linux series is to help you understand system admin as well as basic tools, which will help you to become an effective bioinformatician and computational biologist.

For knowledge about Linux and their importance amongst bioinformatician plesae read this article "An introduction to Linux for bioinformatics" by Paul Stothard.

Linux cheat sheet at http://bioinformaticsonline.com/file/view/87/linux-cheat-sheet

Please browse for futher useful linux pages on right hand side ...

Bioinformatics WalkIn at NII

Fri, 04 Sep 2015 21:48:15 -0500

ADVERTISEMENT OF WALK-IN-INTERVIEW

NAME OF THE POST : Bioinformatician (Part time 3 days in a week) (One Position only)

DURATION : One Year

NAME OF THE PROJECT : Next generation sequencing facility

EDUCATIONAL QUALIFICATIONS : At least a Masters degree in Bioinformatics and Bachelors degree in any stream of life sciences

REQUIREMENTS :

Around 5 years of experience and proven track record in next generation sequence data analysis (supported by publications in peer-reviewed journals), ability to analyze transcriptomics, Chip-seq, and small RNA –seq data.

: Should have the ability to analyze raw primary data generated by Illumina next generation sequencing platforms and create / troubleshoot custom analysis Pipelines.

Should have ability to handle all downstream secondary and tertiary data analysis using commercially available as well as open source softwares (transcriptomics, ChIP-seq, small RNA-seq)

Apart from these, the applicant should have knowledge of the following: Programming: Perl and Python. Operating system:

Linux and Windows. NGS Analysis tools: Maq, BWA, Bowtie, SAM tools, BEDTools, MACS, Galaxy, FastQC, Bismark, MEDIPS, Tophat, Cufflinks, AvadisNGS, CLC Genomics Workbench, Galaxy, BaseSpace, Trinity Statistics: Microsoft Excel and R. Database: MySQL Genome Browser: UCSC, Ensemble, IGV, IGB Motif Analysis Tools: MEME Suite, Transfac and RSAT Functional Annotation Tools: DAVID, GeneCodis, Gene Cards Networking Tools: Cytoscape

EMOLUMENTS : The incumbent will be paid a fee of Rs. 2000/- per sitting/ per day.

SCIENTIST NAME : Dr. Arnab Mukhopadhyay,

Staff Scientific V Next generation sequencing facility

SCIENTIST’S E-MAIL ID : arnab@nii.ac.in

WALK IN INTERVIEW ON : 18th September, 2015

REGISTRATION OF CANDIDATES: 10.30 AM to 11.00 AM

PLEASE NOTE- 1. CANDIDATE MAY FILL UP APPLICATION IN THE PRECRIBED FORMAT ALONG WITH NECESSARY DOCUMENTS FOR VERIFICATION. 2. APPLICATIONS CONTAINING INCOMPLETE INFORMATION SHALL NOT BE ENTERTAINED. 3. DATE OF PASSING THE EXAMINATIONS MUST BE INDICATED CLEARLY. 4. ONLY REGISTERED CANDIDATES WILL BE INTERVIEWED. 5. NO TA/DA WILL BE PAID FOR ATTENDING THE INTERVIEW PRESCRIBED FORM 1. NAME 2. FATHER’S NAME 3. MOTHER’S NAME 4. DATE OF BIRTH 5. SEX (MALE/FEMALE) 6. CATEGORY (SC/ ST/ OBC/ PH) 7. ADDRESS a. (CORRSPONDENCE) b. (PERMANENT) 8. E MAIL, TELEPHONE NO. & MOBILE No (if any) 9. ACADEMIC & PROFESSIONAL QUALIFICATIONS NAME OF EXAMINATION PASSED WITH SUBJECTS YEAR OF PASSING BOARD/ UNIVERSITY PERCENTAGE/ DIVISION REMARKS 10. PAST EXPERIENCE & PRESENT EMPLOYMENT, IF ANY 11. CANDIDATES SHOULD STATE CLEARLY WHETHER THEY HAVE BEEN AWARDED PH.D DEGREE OR THESIS HAS BEEN SUBMITTED. 12. HAVE YOU APPLIED FOR A POSITION EARLIER IN THE INSTITUTE? IF SO:- (1) THE DETAILS OF THE PROJECT AND PROJECT INVESTIGATOR (2) IF CALLED FOR INVERVIEW, RESULTS THEREOF

More at http://www1.nii.res.in/sites/default/files/walkininterview-18sept2015.pdf

Awesome bioinformatics pipelines !

Jitendra Prajapati — Wed, 30 Mar 2016 21:50:41 -0500

A curated list of awesome pipeline toolkits ...

https://github.com/pditommaso/awesome-pipeline

Address of the bookmark: https://github.com/pditommaso/awesome-pipeline

Tools and Method for Haplotype phasing !

Manisha Mishra — Fri, 04 Sep 2020 20:41:40 -0500

Huge amounts of genotype data are being produced with recent technological advances, both from increasingly comprehensive and inexpensive genome-wide SNP microarrays and from ever more accessible whole-genome and whole-exome sequencing methods. The vast amount of knowledge contained in these results, however, is best exploited through phased haplotypes, which classify the alleles co-located on the same chromosome. Since sequence and SNP array data normally take the form of unphased genotypes, one does not specifically observe which of the two parental chromosomes, or haplotypes, falls on a specific allele. Fortunately, new advances in both computational and laboratory methods promise improved determination of haplotype phase. Following are useful tools :

Arlequin: http://cmpg.unibe.ch/software/arlequin3/

BEAGLE: http://faculty.washington.edu/browning/beagle/beagle.html

fastPHASE: http://stephenslab.uchicago.edu/software.html

GENEHUNTER: http://linkage.rockefeller.edu/soft/gh/

The Genome Analysis Toolkit:

http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit

IMPUTE2: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html

MACH: http://www.sph.umich.edu/csg/abecasis/MACH/

MERLIN: http://www.sph.umich.edu/csg/abecasis/Merlin/

PHASE: http://stephenslab.uchicago.edu/software.html

PL-EM: http://www.people.fas.harvard.edu/~junliu/plem/

“Read-backed phasing” algorithm: http://www.broadinstitute.org/gsa/wiki/index.php/Read-backed_phasing_algorithm

SHAPE-IT: http://www.griv.org/shapeit/

Useful Bioinformatics Tools

Poonam Mahapatra — Mon, 29 Aug 2016 04:08:12 -0500

Collections of few handy tools for bioinformatician

http://molbiol-tools.ca/Convert.htm

Address of the bookmark: http://molbiol-tools.ca/Convert.htm

Harvest

Jit — Tue, 31 Jan 2017 10:57:56 -0600

Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.

Tools

Parsnp - Core-genome alignment and analysis
Gingr - Interactive visualization of alignments, trees and variants
HarvestTools - Archiving and postprocessing

Citation

Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biology, 15 (11), 1-15 [PDF]

Address of the bookmark: http://harvest.readthedocs.io/en/latest/index.html

WGS Celera Assembler version 8.3rc2

Jit — Mon, 10 Apr 2017 04:45:40 -0500

These are release notes for Celera Assembler version 8.3rc2, which was released on May 24, 2015.

This distribution package provides a stable, tested, documented version of the software. The distribution is usable on most Unix-like platforms, and some platforms have pre-compiled binary distributions ready for installation.

The source code package includes full source code (revision 4627), Makefiles, and scripts. A subset of the kmer package (http://kmer.sourceforge.net/, version r1994), used by some modules of Celera Assembler, is included. This distribution includes [http://samtools.sourceforge.net/ SAMtools], [http://www.cbcb.umd.edu/software/jellyfish/ Jellyfish 2.0], [https://github.com/pbjd/pbutgcns PBUTGCNS], [https://github.com/PacificBiosciences/pbdagcon PBDAGCON], [https://github.com/PacificBiosciences/BLASR BLASR], and parts of the [https://github.com/PacificBiosciences/FALCON/tree/v0.1.3 Falcon assembler].

Full documentation can be found online at http://wgs-assembler.sourceforge.net/.

Interesting scripts within it

urbe@urbo214b[bin] ls []
-rwxrwxr-x 1 urbe urbe 11K Apr 10 11:41 addCNSToStore
-rwxrwxr-x 1 urbe urbe 575K Apr 10 11:41 addReadsToUnitigs
-rwxrwxr-x 1 urbe urbe 128K Apr 10 11:41 analyzeBest
-rwxrwxr-x 1 urbe urbe 257K Apr 10 11:41 analyzePosMap
-rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 analyzeScaffolds
-rwxrwxr-x 1 urbe urbe 224K Apr 10 11:41 asmOutputFasta
-rwxrwxr-x 1 urbe urbe 448K Apr 10 11:41 asmOutputStatistics
-rwxrwxr-x 1 urbe urbe 2,4K Apr 10 11:41 asmToAGP.pl
-rwxrwxr-x 1 urbe urbe 7,6M Apr 10 11:41 blasr
-rwxrwxr-x 1 urbe urbe 1,6M Apr 10 11:41 bogart
-rwxrwxr-x 1 urbe urbe 183K Apr 10 11:41 bogus
-rwxrwxr-x 1 urbe urbe 272K Apr 10 11:41 bogusness
-rwxrwxr-x 1 urbe urbe 247K Apr 10 11:41 buildPosMap
-rwxrwxr-x 1 urbe urbe 213K Apr 10 11:41 buildRefContigs
-rwxrwxr-x 1 urbe urbe 990K Apr 10 11:41 buildUnitigs
-rwxrwxr-x 1 urbe urbe 18K Apr 10 11:41 ca2ace.pl
-rwxrwxr-x 1 urbe urbe 12K Apr 10 11:41 caqc_help.ini
-rwxrwxr-x 1 urbe urbe 61K Apr 10 11:41 caqc.pl
-rwxrwxr-x 1 urbe urbe 23K Apr 10 11:41 cat-corrects
-rwxrwxr-x 1 urbe urbe 24K Apr 10 11:41 cat-erates
-rwxrwxr-x 1 urbe urbe 1,9M Apr 10 11:41 cgw
-rwxrwxr-x 1 urbe urbe 1,4M Apr 10 11:41 cgwDump
-rwxrwxr-x 1 urbe urbe 204K Apr 10 11:41 chimChe
-rwxrwxr-x 1 urbe urbe 201K Apr 10 11:40 chimera
-rwxrwxr-x 1 urbe urbe 220K Apr 10 11:41 classifyMates
-rwxrwxr-x 1 urbe urbe 201K Apr 10 11:41 classifyMatesApply
-rwxrwxr-x 1 urbe urbe 215K Apr 10 11:41 classifyMatesPairwise
-rwxrwxr-x 1 urbe urbe 366K Apr 10 11:41 computeCoverageStat
-rwxrwxr-x 1 urbe urbe 9,8K Apr 10 11:41 convert-fasta-to-v2.pl
-rwxrwxr-x 1 urbe urbe 48K Apr 10 11:41 convertOverlap
-rwxrwxr-x 1 urbe urbe 119K Apr 10 11:41 convertSamToCA
-rwxrwxr-x 1 urbe urbe 20K Apr 10 11:41 convertToPBCNS
-rwxrwxr-x 1 urbe urbe 197K Apr 10 11:41 correct-frags
-rwxrwxr-x 1 urbe urbe 259K Apr 10 11:41 correct-olaps
-rwxrwxr-x 1 urbe urbe 520K Apr 10 11:41 correctPacBio
-rwxrwxr-x 1 urbe urbe 540K Apr 10 11:41 ctgcns
-rwxrwxr-x 1 urbe urbe 162K Apr 10 11:40 deduplicate
-rwxrwxr-x 1 urbe urbe 37K Apr 10 11:41 demotePosMap
-rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 dumpCloneMiddles
-rwxrwxr-x 1 urbe urbe 124K Apr 10 11:41 dumpPBRLayoutStore
-rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 dumpSingletons
-rwxrwxr-x 1 urbe urbe 171K Apr 10 11:41 erate-estimate
-rwxrwxr-x 1 urbe urbe 221K Apr 10 11:40 estimate-mer-threshold
-rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 extendClearRanges
-rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 extendClearRangesPartition
-rwxrwxr-x 1 urbe urbe 205K Apr 10 11:40 extractmessages
-rwxrwxr-x 1 urbe urbe 7,2M Apr 10 11:41 falcon_sense
-rwxrwxr-x 1 urbe urbe 9,8K Apr 10 11:41 fastaToCA
-rwxrwxr-x 1 urbe urbe 124K Apr 10 11:40 fastqAnalyze
-rwxrwxr-x 1 urbe urbe 137K Apr 10 11:40 fastqSample
-rwxrwxr-x 1 urbe urbe 62K Apr 10 11:40 fastqSimulate
-rwxrwxr-x 1 urbe urbe 121K Apr 10 11:40 fastqSimulate-sort
-rwxrwxr-x 1 urbe urbe 246K Apr 10 11:40 fastqToCA
-rwxrwxr-x 1 urbe urbe 140K Apr 10 11:41 filterOverlap
-rwxrwxr-x 1 urbe urbe 341K Apr 10 11:40 finalTrim
-rwxrwxr-x 1 urbe urbe 228K Apr 10 11:41 fixUnitigs
-rwxrwxr-x 1 urbe urbe 147K Apr 10 11:40 fragmentDepth
-rwxrwxr-x 1 urbe urbe 29K Apr 10 11:41 fragsInVars
-rwxrwxr-x 1 urbe urbe 545K Apr 10 11:41 frgs2clones
-rwxrwxr-x 1 urbe urbe 398K Apr 10 11:40 gatekeeper
-rwxrwxr-x 1 urbe urbe 139K Apr 10 11:40 gatekeeperbench
-rwxrwxr-x 1 urbe urbe 167K Apr 10 11:40 gkpStoreCreate
-rwxrwxr-x 1 urbe urbe 147K Apr 10 11:40 gkpStoreDumpFASTQ
-rwxrwxr-x 1 urbe urbe 184K Apr 10 11:41 greedyFragmentTiling
-rwxrwxr-x 1 urbe urbe 1,6K Apr 10 11:41 greedy_layout_to_IUM
-rwxrwxr-x 1 urbe urbe 142K Apr 10 11:40 initialTrim
-rwxrwxr-x 1 urbe urbe 967K Apr 10 11:41 jellyfish
-rwxrwxr-x 1 urbe urbe 219K Apr 10 11:41 markRepeatUnique
-rwxrwxr-x 1 urbe urbe 273K Apr 10 11:40 markUniqueUnique
-rwxrwxr-x 1 urbe urbe 114K Apr 10 11:40 mercy
-rwxrwxr-x 1 urbe urbe 3,8K Apr 10 11:41 mergeqc.pl
-rwxrwxr-x 1 urbe urbe 422K Apr 10 11:40 merTrim
-rwxrwxr-x 1 urbe urbe 125K Apr 10 11:40 merTrimApply
-rwxrwxr-x 1 urbe urbe 376K Apr 10 11:40 meryl
-rwxrwxr-x 1 urbe urbe 176K Apr 10 11:41 metagenomics_ovl_analyses
-rwxrwxr-x 1 urbe urbe 297K Apr 10 11:41 olap-from-seeds
-rwxrwxr-x 1 urbe urbe 275K Apr 10 11:41 outputLayout
-rwxrwxr-x 1 urbe urbe 229K Apr 10 11:41 overlapInCore
-rwxrwxr-x 1 urbe urbe 144K Apr 10 11:40 overlap_partition
-rwxrwxr-x 1 urbe urbe 179K Apr 10 11:41 overlapStats
-rwxrwxr-x 1 urbe urbe 179K Apr 10 11:41 overlapStore
-rwxrwxr-x 1 urbe urbe 153K Apr 10 11:41 overlapStoreBucketizer
-rwxrwxr-x 1 urbe urbe 175K Apr 10 11:41 overlapStoreBuild
-rwxrwxr-x 1 urbe urbe 33K Apr 10 11:41 overlapStoreIndexer
-rwxrwxr-x 1 urbe urbe 48K Apr 10 11:41 overlapStoreSorter
-rwxrwxr-x 1 urbe urbe 604K Apr 10 11:40 overmerry
lrwxrwxrwx 1 urbe urbe 4 Apr 10 11:41 pacBioToCA -> PBcR
-rwxrwxr-x 1 urbe urbe 131K Apr 10 11:41 PBcR
-rwxrwxr-x 1 urbe urbe 2,9M Apr 10 11:41 pbdagcon
-rwxrwxr-x 1 urbe urbe 1,9M Apr 10 11:41 pbutgcns
-rwxrwxr-x 1 urbe urbe 201K Apr 10 11:40 remove_fragment
-rwxrwxr-x 1 urbe urbe 153K Apr 10 11:40 removeMateOverlap
-rwxrwxr-x 1 urbe urbe 2,5K Apr 10 11:41 replaceUIDwithName-fastq
-rwxrwxr-x 1 urbe urbe 1,2K Apr 10 11:41 replaceUIDwithName-posmap
-rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 resolveSurrogates
-rwxrwxr-x 1 urbe urbe 139K Apr 10 11:41 rewriteCache
-rwxrwxr-x 1 urbe urbe 232K Apr 10 11:41 runCA
-rwxrwxr-x 1 urbe urbe 88K Apr 10 11:41 runCA-dedupe
-rwxrwxr-x 1 urbe urbe 14K Apr 10 11:41 runCA-overlapStoreBuild
-rwxrwxr-x 1 urbe urbe 3,6K Apr 10 11:41 run_greedy.csh
-rwxrwxr-x 1 urbe urbe 297K Apr 10 11:40 sffToCA
-rwxrwxr-x 1 urbe urbe 13K Apr 10 11:40 show-corrects
-rwxrwxr-x 1 urbe urbe 557K Apr 10 11:41 splitUnitigs
-rwxrwxr-x 1 urbe urbe 1,4M Apr 10 11:41 terminator
drwxrwxr-x 2 urbe urbe 4,0K Apr 10 11:41 TIGR
-rwxrwxr-x 1 urbe urbe 526K Apr 10 11:41 tigStore
-rwxrwxr-x 1 urbe urbe 35K Apr 10 11:41 tracearchiveToCA
-rwxrwxr-x 1 urbe urbe 35K Apr 10 11:41 tracedb-to-frg.pl
-rwxrwxr-x 1 urbe urbe 44K Apr 10 11:41 trimFastqByQVWindow
-rwxrwxr-x 1 urbe urbe 18K Apr 10 11:40 uidclient
-rwxrwxr-x 1 urbe urbe 589K Apr 10 11:41 unitigger
-rwxrwxr-x 1 urbe urbe 42K Apr 10 11:40 upgrade-v8-to-v9
-rwxrwxr-x 1 urbe urbe 42K Apr 10 11:40 upgrade-v9-to-v10
-rwxrwxr-x 1 urbe urbe 854 Apr 10 11:41 utg2fasta
-rwxrwxr-x 1 urbe urbe 731K Apr 10 11:41 utgcns
-rwxrwxr-x 1 urbe urbe 561K Apr 10 11:41 utgcnsfix

Address of the bookmark: http://wgs-assembler.sourceforge.net/wiki/index.php/Main_Page

Binding Site Prediction in Protein !

Poonam Mahapatra — Wed, 25 Apr 2018 04:35:57 -0500

The interaction between proteins and other molecules is fundamental to all biological functions. In this section we include tools that can assist in prediction of interaction sites on protein surface and tools for predicting the structure of the intermolecular complex formed between two or more molecules (docking).

Pockets Identification

CASTp

Automatic Identification of pockets and cavities in proteins structure, and quantitation of their volumes using Delaunay triangulation. Available also as PyMOL plugin

Pocket-Finder

Automatic identification of pockets and cavities in proteins structure, and quantitation of their volumes.

PocketPicker

Grid-based technique for the analysis of protein pockets. PocketPicker available as a plugin for PyMOL

Binding Site Prediction

ConSurf

Identification of functional regions in proteins by surface-mapping of phylogenetic information

CRESCENDO

Identification protein interaction sites. It uses sequence conservation patterns in homologous proteins to distinguish between residues that are conserved due to structural restraints from those due to functional restraints.

Ligand Binding Sites

3DLigandSite

The server utilizes protein-structure prediction to provide structural models of the binding site. Ligands bound to structures are superimposed onto the model and use to predict the binding site.

FINDSITE

A threading-based method for ligand-binding site prediction and functional annotation based on binding-site similarity across superimposed groups of threading templates.

LIGSITE^csc

Prediction of binding site by pocket identification using the Connolly surface and degree of conservation

metaPocketA meta server for ligand-binding site prediction. metaPocket use LIGSITE^csc, PASS, Q-SiteFinder and SURFNET

Installing python-numpy !

Jit — Mon, 07 May 2018 04:31:25 -0500

$ 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
0 upgraded, 73 newly installed, 0 to remove and 35 not upgraded.
Need to get 49,5 MB of archives.
After this operation, 271 MB of additional disk space will be used.
Do you want to continue? [Y/n] Y
Get:1 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-pymysql all 0.7.2-1ubuntu1 [56,4 kB]
Get:2 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-3 [574 kB]
Get:3 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 blt amd64 2.5.3+dfsg-3 [4.852 B]
Get:4 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 fonts-lyx all 2.1.4-2 [161 kB]
Get:5 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 fonts-mathjax all 2.6.1-1 [960 kB]
Get:6 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-decorator all 4.0.6-1 [9.326 B]
Get:7 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-ptyprocess all 0.5-1 [12,9 kB]
Get:8 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pexpect all 4.0.1-1 [40,5 kB]
Get:9 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-simplegeneric all 0.8.1-1 [11,5 kB]
Get:10 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 ipython all 2.4.1-1 [610 kB]
Get:11 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-highlight.js all 8.2+ds-4build1 [151 kB]
Get:12 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-highlight all 8.2+ds-4build1 [7.032 B]
Get:13 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-jquery-ui all 1.10.1+dfsg-1 [458 kB]
Get:14 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-marked all 0.3.2+dfsg-1 [12,7 kB]
Get:15 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-mathjax all 2.6.1-1 [5.601 kB]
Get:16 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libjs-underscore all 1.7.0~dfsg-1ubuntu1 [46,7 kB]
Get:17 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 ipython-notebook-common all 2.4.1-1 [712 kB]
Get:18 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-markupsafe amd64 0.23-2build2 [15,5 kB]
Get:19 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-jinja2 all 2.8-1 [109 kB]
Get:20 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-pycurl amd64 7.43.0-1ubuntu1 [43,3 kB]
Get:21 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-tornado amd64 4.2.1-1ubuntu3 [273 kB]
Get:22 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-zmq amd64 15.2.0-0ubuntu4 [200 kB]
Get:23 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 ipython-notebook all 2.4.1-1 [48,4 kB]
Get:24 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 isympy all 0.7.6.1-1 [82,5 kB]
Get:25 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libaec0 amd64 0.3.2-1 [18,0 kB]
Get:26 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libamd2.4.1 amd64 1:4.4.6-1 [21,3 kB]
Get:27 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libglpk36 amd64 4.57-1build3 [386 kB]
Get:28 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libgsl2 amd64 2.1+dfsg-2 [840 kB]
Get:29 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libsz2 amd64 0.3.2-1 [5.048 B]
Get:30 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libhdf5-10 amd64 1.8.16+docs-4ubuntu1 [995 kB]
Get:31 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-antlr all 2.7.7+dfsg-6ubuntu1 [19,0 kB]
Get:32 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-bs4 all 4.4.1-1 [64,2 kB]
Get:33 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-chardet all 2.3.0-2 [96,3 kB]
Get:34 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libdsdp-5.8gf amd64 5.8-9.1ubuntu2 [192 kB]
Get:35 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-cvxopt amd64 1.1.4-1.4 [1.344 kB]
Get:36 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-cycler all 0.9.0-1 [5.426 B]
Get:37 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-dateutil all 2.4.2-1 [42,5 kB]
Get:38 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-glade2 amd64 2.24.0-4ubuntu1 [9.078 B]
Get:39 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-gmpy amd64 1.17-1 [91,1 kB]
Get:40 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-html5lib all 0.999-4 [83,1 kB]
Get:41 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-pil amd64 3.1.2-0ubuntu1.1 [312 kB]
Get:42 http://be.archive.ubuntu.com/ubuntu xenial-updates/universe amd64 python-imaging all 3.1.2-0ubuntu1.1 [4.596 B]
Get:43 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-jdcal all 1.0-1build1 [7.702 B]
Get:44 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-joblib all 0.9.4-1 [74,6 kB]
Get:45 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-lxml amd64 3.5.0-1build1 [819 kB]
Get:46 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 ttf-bitstream-vera all 1.10-8 [352 kB]
Get:47 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-matplotlib-data all 1.5.1-1ubuntu1 [2.414 kB]
Get:48 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-pyparsing all 2.0.3+dfsg1-1ubuntu0.1 [35,4 kB]
Get:49 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-tz all 2014.10~dfsg1-0ubuntu2 [31,5 kB]
Get:50 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-numpy amd64 1:1.11.0-1ubuntu1 [1.763 kB]
Get:51 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-matplotlib amd64 1.5.1-1ubuntu1 [3.888 kB]
Get:52 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-mpmath all 0.19-3 [387 kB]
Get:53 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-nose all 1.3.7-1 [116 kB]
Get:54 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-numexpr amd64 2.4.3-1ubuntu1 [129 kB]
Get:55 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-openpyxl all 2.3.0-1 [193 kB]
Get:56 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pandas-lib amd64 0.17.1-3ubuntu2 [1.538 kB]
Get:57 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pandas all 0.17.1-3ubuntu2 [2.386 kB]
Get:58 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-patsy all 0.4.1-2 [169 kB]
Get:59 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-py all 1.4.31-1 [62,5 kB]
Get:60 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pyglet all 1.1.4.dfsg-3 [726 kB]
Get:61 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pytest all 2.8.7-4 [119 kB]
Get:62 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-simplejson amd64 3.8.1-1ubuntu2 [60,4 kB]
Get:63 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-sympy all 0.7.6.1-1 [2.252 kB]
Get:64 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-sympy-doc all 0.7.6.1-1 [4.774 kB]
Get:65 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-tables-lib amd64 3.2.2-2 [353 kB]
Get:66 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-tables-data all 3.2.2-2 [45,3 kB]
Get:67 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-tables all 3.2.2-2 [335 kB]
Get:68 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-tk amd64 2.7.12-1~16.04 [26,3 kB]
Get:69 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-xlrd all 0.9.4-1 [107 kB]
Get:70 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-xlwt all 0.7.5+debian1-1 [83,5 kB]
Get:71 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-scipy amd64 0.17.0-1 [8.733 kB]
Get:72 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-statsmodels-lib amd64 0.6.1-4 [173 kB]
Get:73 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-statsmodels all 0.6.1-4 [2.581 kB]
Fetched 49,5 MB in 0s (52,8 MB/s)
Extracting templates from packages: 100%
Selecting previously unselected package python-pymysql.
(Reading database ... 435155 files and directories currently installed.)
Preparing to unpack .../python-pymysql_0.7.2-1ubuntu1_all.deb ...
Unpacking python-pymysql (0.7.2-1ubuntu1) ...
Selecting previously unselected package tk8.6-blt2.5.
Preparing to unpack .../tk8.6-blt2.5_2.5.3+dfsg-3_amd64.deb ...
Unpacking tk8.6-blt2.5 (2.5.3+dfsg-3) ...
Selecting previously unselected package blt.
Preparing to unpack .../blt_2.5.3+dfsg-3_amd64.deb ...
Unpacking blt (2.5.3+dfsg-3) ...
Selecting previously unselected package fonts-lyx.
Preparing to unpack .../fonts-lyx_2.1.4-2_all.deb ...
Unpacking fonts-lyx (2.1.4-2) ...
Selecting previously unselected package fonts-mathjax.
Preparing to unpack .../fonts-mathjax_2.6.1-1_all.deb ...
Unpacking fonts-mathjax (2.6.1-1) ...
Selecting previously unselected package python-decorator.
Preparing to unpack .../python-decorator_4.0.6-1_all.deb ...
Unpacking python-decorator (4.0.6-1) ...
Selecting previously unselected package python-ptyprocess.
Preparing to unpack .../python-ptyprocess_0.5-1_all.deb ...
Unpacking python-ptyprocess (0.5-1) ...
Selecting previously unselected package python-pexpect.
Preparing to unpack .../python-pexpect_4.0.1-1_all.deb ...
Unpacking python-pexpect (4.0.1-1) ...
Selecting previously unselected package python-simplegeneric.
Preparing to unpack .../python-simplegeneric_0.8.1-1_all.deb ...
Unpacking python-simplegeneric (0.8.1-1) ...
Selecting previously unselected package ipython.
Preparing to unpack .../ipython_2.4.1-1_all.deb ...
Unpacking ipython (2.4.1-1) ...
Selecting previously unselected package libjs-highlight.js.
Preparing to unpack .../libjs-highlight.js_8.2+ds-4build1_all.deb ...
Unpacking libjs-highlight.js (8.2+ds-4build1) ...
Selecting previously unselected package libjs-highlight.
Preparing to unpack .../libjs-highlight_8.2+ds-4build1_all.deb ...
Unpacking libjs-highlight (8.2+ds-4build1) ...
Selecting previously unselected package libjs-jquery-ui.
Preparing to unpack .../libjs-jquery-ui_1.10.1+dfsg-1_all.deb ...
Unpacking libjs-jquery-ui (1.10.1+dfsg-1) ...
Selecting previously unselected package libjs-marked.
Preparing to unpack .../libjs-marked_0.3.2+dfsg-1_all.deb ...
Unpacking libjs-marked (0.3.2+dfsg-1) ...
Selecting previously unselected package libjs-mathjax.
Preparing to unpack .../libjs-mathjax_2.6.1-1_all.deb ...
Unpacking libjs-mathjax (2.6.1-1) ...
Selecting previously unselected package libjs-underscore.
Preparing to unpack .../libjs-underscore_1.7.0~dfsg-1ubuntu1_all.deb ...
Unpacking libjs-underscore (1.7.0~dfsg-1ubuntu1) ...
Selecting previously unselected package ipython-notebook-common.
Preparing to unpack .../ipython-notebook-common_2.4.1-1_all.deb ...
Unpacking ipython-notebook-common (2.4.1-1) ...
Selecting previously unselected package python-markupsafe.
Preparing to unpack .../python-markupsafe_0.23-2build2_amd64.deb ...
Unpacking python-markupsafe (0.23-2build2) ...
Selecting previously unselected package python-jinja2.
Preparing to unpack .../python-jinja2_2.8-1_all.deb ...
Unpacking python-jinja2 (2.8-1) ...
Selecting previously unselected package python-pycurl.
Preparing to unpack .../python-pycurl_7.43.0-1ubuntu1_amd64.deb ...
Unpacking python-pycurl (7.43.0-1ubuntu1) ...
Selecting previously unselected package python-tornado.
Preparing to unpack .../python-tornado_4.2.1-1ubuntu3_amd64.deb ...
Unpacking python-tornado (4.2.1-1ubuntu3) ...
Selecting previously unselected package python-zmq.
Preparing to unpack .../python-zmq_15.2.0-0ubuntu4_amd64.deb ...
Unpacking python-zmq (15.2.0-0ubuntu4) ...
Selecting previously unselected package ipython-notebook.
Preparing to unpack .../ipython-notebook_2.4.1-1_all.deb ...
Unpacking ipython-notebook (2.4.1-1) ...
Selecting previously unselected package isympy.
Preparing to unpack .../isympy_0.7.6.1-1_all.deb ...
Unpacking isympy (0.7.6.1-1) ...
Selecting previously unselected package libaec0:amd64.
Preparing to unpack .../libaec0_0.3.2-1_amd64.deb ...
Unpacking libaec0:amd64 (0.3.2-1) ...
Selecting previously unselected package libamd2.4.1:amd64.
Preparing to unpack .../libamd2.4.1_1%3a4.4.6-1_amd64.deb ...
Unpacking libamd2.4.1:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libglpk36:amd64.
Preparing to unpack .../libglpk36_4.57-1build3_amd64.deb ...
Unpacking libglpk36:amd64 (4.57-1build3) ...
Selecting previously unselected package libgsl2:amd64.
Preparing to unpack .../libgsl2_2.1+dfsg-2_amd64.deb ...
Unpacking libgsl2:amd64 (2.1+dfsg-2) ...
Selecting previously unselected package libsz2:amd64.
Preparing to unpack .../libsz2_0.3.2-1_amd64.deb ...
Unpacking libsz2:amd64 (0.3.2-1) ...
Selecting previously unselected package libhdf5-10:amd64.
Preparing to unpack .../libhdf5-10_1.8.16+docs-4ubuntu1_amd64.deb ...
Unpacking libhdf5-10:amd64 (1.8.16+docs-4ubuntu1) ...
Selecting previously unselected package python-antlr.
Preparing to unpack .../python-antlr_2.7.7+dfsg-6ubuntu1_all.deb ...
Unpacking python-antlr (2.7.7+dfsg-6ubuntu1) ...
Selecting previously unselected package python-bs4.
Preparing to unpack .../python-bs4_4.4.1-1_all.deb ...
Unpacking python-bs4 (4.4.1-1) ...
Selecting previously unselected package python-chardet.
Preparing to unpack .../python-chardet_2.3.0-2_all.deb ...
Unpacking python-chardet (2.3.0-2) ...
Selecting previously unselected package libdsdp-5.8gf.
Preparing to unpack .../libdsdp-5.8gf_5.8-9.1ubuntu2_amd64.deb ...
Unpacking libdsdp-5.8gf (5.8-9.1ubuntu2) ...
Selecting previously unselected package python-cvxopt.
Preparing to unpack .../python-cvxopt_1.1.4-1.4_amd64.deb ...
Unpacking python-cvxopt (1.1.4-1.4) ...
Selecting previously unselected package python-cycler.
Preparing to unpack .../python-cycler_0.9.0-1_all.deb ...
Unpacking python-cycler (0.9.0-1) ...
Selecting previously unselected package python-dateutil.
Preparing to unpack .../python-dateutil_2.4.2-1_all.deb ...
Unpacking python-dateutil (2.4.2-1) ...
Selecting previously unselected package python-glade2.
Preparing to unpack .../python-glade2_2.24.0-4ubuntu1_amd64.deb ...
Unpacking python-glade2 (2.24.0-4ubuntu1) ...
Selecting previously unselected package python-gmpy.
Preparing to unpack .../python-gmpy_1.17-1_amd64.deb ...
Unpacking python-gmpy (1.17-1) ...
Selecting previously unselected package python-html5lib.
Preparing to unpack .../python-html5lib_0.999-4_all.deb ...
Unpacking python-html5lib (0.999-4) ...
Selecting previously unselected package python-pil:amd64.
Preparing to unpack .../python-pil_3.1.2-0ubuntu1.1_amd64.deb ...
Unpacking python-pil:amd64 (3.1.2-0ubuntu1.1) ...
Selecting previously unselected package python-imaging.
Preparing to unpack .../python-imaging_3.1.2-0ubuntu1.1_all.deb ...
Unpacking python-imaging (3.1.2-0ubuntu1.1) ...
Selecting previously unselected package python-jdcal.
Preparing to unpack .../python-jdcal_1.0-1build1_all.deb ...
Unpacking python-jdcal (1.0-1build1) ...
Selecting previously unselected package python-joblib.
Preparing to unpack .../python-joblib_0.9.4-1_all.deb ...
Unpacking python-joblib (0.9.4-1) ...
Selecting previously unselected package python-lxml.
Preparing to unpack .../python-lxml_3.5.0-1build1_amd64.deb ...
Unpacking python-lxml (3.5.0-1build1) ...
Selecting previously unselected package ttf-bitstream-vera.
Preparing to unpack .../ttf-bitstream-vera_1.10-8_all.deb ...
Unpacking ttf-bitstream-vera (1.10-8) ...
Selecting previously unselected package python-matplotlib-data.
Preparing to unpack .../python-matplotlib-data_1.5.1-1ubuntu1_all.deb ...
Unpacking python-matplotlib-data (1.5.1-1ubuntu1) ...
Selecting previously unselected package python-pyparsing.
Preparing to unpack .../python-pyparsing_2.0.3+dfsg1-1ubuntu0.1_all.deb ...
Unpacking python-pyparsing (2.0.3+dfsg1-1ubuntu0.1) ...
Selecting previously unselected package python-tz.
Preparing to unpack .../python-tz_2014.10~dfsg1-0ubuntu2_all.deb ...
Unpacking python-tz (2014.10~dfsg1-0ubuntu2) ...
Selecting previously unselected package python-numpy.
Preparing to unpack .../python-numpy_1%3a1.11.0-1ubuntu1_amd64.deb ...
Unpacking python-numpy (1:1.11.0-1ubuntu1) ...
Selecting previously unselected package python-matplotlib.
Preparing to unpack .../python-matplotlib_1.5.1-1ubuntu1_amd64.deb ...
Unpacking python-matplotlib (1.5.1-1ubuntu1) ...
Selecting previously unselected package python-mpmath.
Preparing to unpack .../python-mpmath_0.19-3_all.deb ...
Unpacking python-mpmath (0.19-3) ...
Selecting previously unselected package python-nose.
Preparing to unpack .../python-nose_1.3.7-1_all.deb ...
Unpacking python-nose (1.3.7-1) ...
Selecting previously unselected package python-numexpr.
Preparing to unpack .../python-numexpr_2.4.3-1ubuntu1_amd64.deb ...
Unpacking python-numexpr (2.4.3-1ubuntu1) ...
Selecting previously unselected package python-openpyxl.
Preparing to unpack .../python-openpyxl_2.3.0-1_all.deb ...
Unpacking python-openpyxl (2.3.0-1) ...
Selecting previously unselected package python-pandas-lib.
Preparing to unpack .../python-pandas-lib_0.17.1-3ubuntu2_amd64.deb ...
Unpacking python-pandas-lib (0.17.1-3ubuntu2) ...
Selecting previously unselected package python-pandas.
Preparing to unpack .../python-pandas_0.17.1-3ubuntu2_all.deb ...
Unpacking python-pandas (0.17.1-3ubuntu2) ...
Selecting previously unselected package python-patsy.
Preparing to unpack .../python-patsy_0.4.1-2_all.deb ...
Unpacking python-patsy (0.4.1-2) ...
Selecting previously unselected package python-py.
Preparing to unpack .../python-py_1.4.31-1_all.deb ...
Unpacking python-py (1.4.31-1) ...
Selecting previously unselected package python-pyglet.
Preparing to unpack .../python-pyglet_1.1.4.dfsg-3_all.deb ...
Unpacking python-pyglet (1.1.4.dfsg-3) ...
Selecting previously unselected package python-pytest.
Preparing to unpack .../python-pytest_2.8.7-4_all.deb ...
Unpacking python-pytest (2.8.7-4) ...
Selecting previously unselected package python-simplejson.
Preparing to unpack .../python-simplejson_3.8.1-1ubuntu2_amd64.deb ...
Unpacking python-simplejson (3.8.1-1ubuntu2) ...
Selecting previously unselected package python-sympy.
Preparing to unpack .../python-sympy_0.7.6.1-1_all.deb ...
Unpacking python-sympy (0.7.6.1-1) ...
Selecting previously unselected package python-sympy-doc.
Preparing to unpack .../python-sympy-doc_0.7.6.1-1_all.deb ...
Unpacking python-sympy-doc (0.7.6.1-1) ...
Selecting previously unselected package python-tables-lib.
Preparing to unpack .../python-tables-lib_3.2.2-2_amd64.deb ...
Unpacking python-tables-lib (3.2.2-2) ...
Selecting previously unselected package python-tables-data.
Preparing to unpack .../python-tables-data_3.2.2-2_all.deb ...
Unpacking python-tables-data (3.2.2-2) ...
Selecting previously unselected package python-tables.
Preparing to unpack .../python-tables_3.2.2-2_all.deb ...
Unpacking python-tables (3.2.2-2) ...
Selecting previously unselected package python-tk.
Preparing to unpack .../python-tk_2.7.12-1~16.04_amd64.deb ...
Unpacking python-tk (2.7.12-1~16.04) ...
Selecting previously unselected package python-xlrd.
Preparing to unpack .../python-xlrd_0.9.4-1_all.deb ...
Unpacking python-xlrd (0.9.4-1) ...
Selecting previously unselected package python-xlwt.
Preparing to unpack .../python-xlwt_0.7.5+debian1-1_all.deb ...
Unpacking python-xlwt (0.7.5+debian1-1) ...
Selecting previously unselected package python-scipy.
Preparing to unpack .../python-scipy_0.17.0-1_amd64.deb ...
Unpacking python-scipy (0.17.0-1) ...
Selecting previously unselected package python-statsmodels-lib.
Preparing to unpack .../python-statsmodels-lib_0.6.1-4_amd64.deb ...
Unpacking python-statsmodels-lib (0.6.1-4) ...
Selecting previously unselected package python-statsmodels.
Preparing to unpack .../python-statsmodels_0.6.1-4_all.deb ...
Unpacking python-statsmodels (0.6.1-4) ...
Processing triggers for libc-bin (2.23-0ubuntu10) ...
Processing triggers for fontconfig (2.11.94-0ubuntu1.1) ...
Processing triggers for man-db (2.7.5-1) ...
Processing triggers for hicolor-icon-theme (0.15-0ubuntu1) ...
Processing triggers for gnome-menus (3.13.3-6ubuntu3.1) ...
Processing triggers for desktop-file-utils (0.22-1ubuntu5.1) ...
Processing triggers for mime-support (3.59ubuntu1) ...
Processing triggers for doc-base (0.10.7) ...
Processing 5 added doc-base files...
Setting up python-pymysql (0.7.2-1ubuntu1) ...
Setting up tk8.6-blt2.5 (2.5.3+dfsg-3) ...
Setting up blt (2.5.3+dfsg-3) ...
Setting up fonts-lyx (2.1.4-2) ...
Setting up fonts-mathjax (2.6.1-1) ...
Setting up python-decorator (4.0.6-1) ...
Setting up python-ptyprocess (0.5-1) ...
Setting up python-pexpect (4.0.1-1) ...
Setting up python-simplegeneric (0.8.1-1) ...
Setting up ipython (2.4.1-1) ...
Setting up libjs-highlight.js (8.2+ds-4build1) ...
Setting up libjs-highlight (8.2+ds-4build1) ...
Setting up libjs-jquery-ui (1.10.1+dfsg-1) ...
Setting up libjs-marked (0.3.2+dfsg-1) ...
Setting up libjs-mathjax (2.6.1-1) ...
Setting up libjs-underscore (1.7.0~dfsg-1ubuntu1) ...
Setting up ipython-notebook-common (2.4.1-1) ...
Setting up python-markupsafe (0.23-2build2) ...
Setting up python-jinja2 (2.8-1) ...
Setting up python-pycurl (7.43.0-1ubuntu1) ...
Setting up python-tornado (4.2.1-1ubuntu3) ...
Setting up python-zmq (15.2.0-0ubuntu4) ...
Setting up ipython-notebook (2.4.1-1) ...
Setting up isympy (0.7.6.1-1) ...
Setting up libaec0:amd64 (0.3.2-1) ...
Setting up libamd2.4.1:amd64 (1:4.4.6-1) ...
Setting up libglpk36:amd64 (4.57-1build3) ...
Setting up libgsl2:amd64 (2.1+dfsg-2) ...
Setting up libsz2:amd64 (0.3.2-1) ...
Setting up libhdf5-10:amd64 (1.8.16+docs-4ubuntu1) ...
Setting up python-antlr (2.7.7+dfsg-6ubuntu1) ...
Setting up python-bs4 (4.4.1-1) ...
Setting up python-chardet (2.3.0-2) ...
Setting up libdsdp-5.8gf (5.8-9.1ubuntu2) ...
Setting up python-cvxopt (1.1.4-1.4) ...
Setting up python-cycler (0.9.0-1) ...
Setting up python-dateutil (2.4.2-1) ...
Setting up python-glade2 (2.24.0-4ubuntu1) ...
Setting up python-gmpy (1.17-1) ...
Setting up python-html5lib (0.999-4) ...
Setting up python-pil:amd64 (3.1.2-0ubuntu1.1) ...
Setting up python-imaging (3.1.2-0ubuntu1.1) ...
Setting up python-jdcal (1.0-1build1) ...
Setting up python-joblib (0.9.4-1) ...
Setting up python-lxml (3.5.0-1build1) ...
Setting up ttf-bitstream-vera (1.10-8) ...
Setting up python-matplotlib-data (1.5.1-1ubuntu1) ...
Setting up python-pyparsing (2.0.3+dfsg1-1ubuntu0.1) ...
Setting up python-tz (2014.10~dfsg1-0ubuntu2) ...
Setting up python-numpy (1:1.11.0-1ubuntu1) ...
Setting up python-matplotlib (1.5.1-1ubuntu1) ...
Setting up python-mpmath (0.19-3) ...
Setting up python-nose (1.3.7-1) ...
Setting up python-numexpr (2.4.3-1ubuntu1) ...
Setting up python-openpyxl (2.3.0-1) ...
Setting up python-pandas-lib (0.17.1-3ubuntu2) ...
Setting up python-pandas (0.17.1-3ubuntu2) ...
Setting up python-patsy (0.4.1-2) ...
Setting up python-py (1.4.31-1) ...
Setting up python-pyglet (1.1.4.dfsg-3) ...
Setting up python-pytest (2.8.7-4) ...
Setting up python-simplejson (3.8.1-1ubuntu2) ...
Setting up python-sympy (0.7.6.1-1) ...
Setting up python-sympy-doc (0.7.6.1-1) ...
Setting up python-tables-lib (3.2.2-2) ...
Setting up python-tables-data (3.2.2-2) ...
Setting up python-tables (3.2.2-2) ...
Setting up python-tk (2.7.12-1~16.04) ...
Setting up python-xlrd (0.9.4-1) ...
Setting up python-xlwt (0.7.5+debian1-1) ...
Setting up python-scipy (0.17.0-1) ...
Setting up python-statsmodels-lib (0.6.1-4) ...
Setting up python-statsmodels (0.6.1-4) ...
Processing triggers for libc-bin (2.23-0ubuntu10) ...
➜ 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