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Description:

jcvi 1.4.22

JCVI: A Versatile Toolkit for Comparative Genomics Analysis

Collection of Python libraries to parse bioinformatics files, or perform
computation related to assembly, annotation, and comparative genomics.

Authors
Haibao Tang (tanghaibao)

Vivek Krishnakumar (vivekkrish)

Xingtan Zhang (tangerzhang)

Won Cheol Yim (wyim-pgl)

Email
tanghaibao@gmail.com

License
BSD

How to cite

[!TIP]
JCVI is now published in iMeta!
Tang et al. (2024) JCVI: A Versatile Toolkit for Comparative Genomics
Analysis. iMeta

Contents
Following modules are available as generic Bioinformatics handling
methods.

algorithms

Linear programming solver with SCIP and GLPK.
Supermap: find set of non-overlapping anchors in BLAST or NUCMER output.
Longest or heaviest increasing subsequence.
Matrix operations.

apps

GenBank entrez accession, Phytozome, Ensembl and SRA downloader.
Calculate (non)synonymous substitution rate between gene pairs.
Basic phylogenetic tree construction using PHYLIP, PhyML, or RAxML, and viualization.
Wrapper for BLAST+, LASTZ, LAST, BWA, BOWTIE2, CLC, CDHIT, CAP3, etc.

formats
Currently supports .ace format (phrap, cap3, etc.), .agp
(goldenpath), .bed format, .blast output, .btab format,
.coords format (nucmer output), .fasta format, .fastq
format, .fpc format, .gff format, obo format (ontology),
.psl format (UCSC blat, GMAP, etc.), .posmap format (Celera
assembler output), .sam format (read mapping), .contig
format (TIGR assembly format), etc.

graphics

BLAST or synteny dot plot.
Histogram using R and ASCII art.
Paint regions on set of chromosomes.
Macro-synteny and micro-synteny plots.

utils

Grouper can be used as disjoint set data structure.
range contains common range operations, like overlap
and chaining.
Miscellaneous cookbook recipes, iterators decorators,
table utilities.

Then there are modules that contain domain-specific methods.

assembly

K-mer histogram analysis.
Preparation and validation of tiling path for clone-based assemblies.
Scaffolding through ALLMAPS, optical map and genetic map.
Pre-assembly and post-assembly QC procedures.

annotation

Training of ab initio gene predictors.
Calculate gene, exon and intron statistics.
Wrapper for PASA and EVM.
Launch multiple MAKER processes.

compara

C-score based BLAST filter.
Synteny scan (de-novo) and lift over (find nearby anchors).
Ancestral genome reconstruction using Sankoff's and PAR method.
Ortholog and tandem gene duplicates finder.

Applications
Please visit wiki for
full-fledged applications.
Dependencies
Following are a list of third-party python packages that are used by
some routines in the library. These dependencies are not mandatory
since they are only used by a few modules.

Biopython
numpy
matplotlib

There are other Python modules here and there in various scripts. The
best way is to install them via pip install when you see
ImportError.
Installation
The easiest way is to install it via PyPI:
pip install jcvi

To install the development version:
pip install git+git://github.com/tanghaibao/jcvi.git

Alternatively, if you want to install manually:
cd ~/code # or any directory of your choice
git clone git://github.com/tanghaibao/jcvi.git
pip install -e .

In addition, a few module might ask for locations of external programs,
if the extended cannot be found in your PATH. The external programs
that are often used are:

Kent tools
BEDTOOLS
EMBOSS

Most of the scripts in this package contains multiple actions. To use
the fasta example:
Usage:
python -m jcvi.formats.fasta ACTION

Available ACTIONs:
clean | Remove irregular chars in FASTA seqs
diff | Check if two fasta records contain same information
extract | Given fasta file and seq id, retrieve the sequence in fasta format
fastq | Combine fasta and qual to create fastq file
filter | Filter the records by size
format | Trim accession id to the first space or switch id based on 2-column mapping file
fromtab | Convert 2-column sequence file to FASTA format
gaps | Print out a list of gap sizes within sequences
gc | Plot G+C content distribution
identical | Given 2 fasta files, find all exactly identical records
ids | Generate a list of headers
info | Run `sequence_info` on fasta files
ispcr | Reformat paired primers into isPcr query format
join | Concatenate a list of seqs and add gaps in between
longestorf | Find longest orf for CDS fasta
pair | Sort paired reads to .pairs, rest to .fragments
pairinplace | Starting from fragment.fasta, find if adjacent records can form pairs
pool | Pool a bunch of fastafiles together and add prefix
qual | Generate dummy .qual file based on FASTA file
random | Randomly take some records
sequin | Generate a gapped fasta file for sequin submission
simulate | Simulate random fasta file for testing
some | Include or exclude a list of records (also performs on .qual file if available)
sort | Sort the records by IDs, sizes, etc.
summary | Report the real no of bases and N's in fasta files
tidy | Normalize gap sizes and remove small components in fasta
translate | Translate CDS to proteins
trim | Given a cross_match screened fasta, trim the sequence
trimsplit | Split sequences at lower-cased letters
uniq | Remove records that are the same

Then you need to use one action, you can just do:
python -m jcvi.formats.fasta extract

This will tell you the options and arguments it expects.
Feel free to check out other scripts in the package, it is not just
for FASTA.
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