Usage
-----
We support the use of **WGDI** to complete the work on the icon number.
.. toctree::
dotplot
collinearity
ks
blockinfo
correspondence
blockks
kspeaks
peaksfit
ksfigure
polyploidy_classification
ancestral_karyotype
ancestral_karyotype_repertoire
karyotype_mapping
karyotype
shared_fusions
fusion_positions_database
fusion_detetion
alignment
alignment_tree
retain
pindex
circos
**Common file**
* conf
The conf file contains parameters required for the corresponding operation, which are read when WGDI is performed.
Using ``wgdi -* ? > *.conf`` to get the configuration file in the current directory and modify it to run.
If you don't know which files are needed, you can view it through ``wgdi -* ?`` or ``wgdi -* help`` or ``wgdi -* example``. These three commands are equivalent.
In conf file: **gff1** , **lens1** , **genome1_name** and **gff2**, **lens2**, **genome2_name** represent the files of species 1 and 2 respectively.
We will no longer explain these in this documentation.
* gff
.. tabularcolumns:: column spec
====== ============ ======================================================
Column Information Explanation
1 Chr Chromosome number
2 Id Gene name
3 Strat The starting location of a gene
4 End The ending location of a gene
5 Direction Direction of a gene sequence
6 Order Order of each chromosome, starting from 1
7 Original Original id and not read
====== ============ ======================================================
* lens
.. tabularcolumns:: column spec
========= =========== =========================================
Column Information Explanation
1 Chr Chromosome number
2 Length Length of chromosome sequences
3 Number Number of chromosome genes
========= =========== =========================================
* blast
The protein-coding genes from each genome were compared against itself and other genomes using `BLASTP `_ (e-value < 10-5, and outfmt = 6) or other similar protein sequence searching software ( `MMseqs2 `_ , `DIAMOND `_ ).
* ancestor file
Required documents for karyotype evolution analysis
.. tabularcolumns:: column spec
========= =========== =============================================================
Column Information Explanation
1 Chr Chromosome number
2 Start Homologous regions of these protochromosomes in this genome
3 End Homologous regions of these protochromosomes in this genome
4 Color These protochromosomes with different colors
5 Subgenomes Subgenomes according to protochromosomes
========= =========== =============================================================
* Fusinon postions file
Required documents for shared fusion events
.. tabularcolumns:: column spec
========= =================== ===============================================================================
Column Information Explanation
1 Chr Chromosome number
2 Breakpoint The breakpoints of fusions, with multiple breakpoints listed on separate lines.
3 NumGeneSetsPerSide The number of genes within a single synteny block that spans across both sides of the fusion breakpoints.
4 Mark The unique marks of unique fusions
========= =================== ===============================================================================
**Tips**
* You can use ``wgdi -conf ? > total.conf`` generates a **total.conf** file with all parameters, and when you modify the parameters and run WGDI, WGDI will only read the parameters corresponding to the total.conf file to execute your command.
* When a folder runs WGDI, WGDI automatically generates results for you in the background, and you can exit the folder and go to the next folder to start working.
* WGDI performs the **conf** file for the current folder, so you can copy the **conf** file in bulk and make parameter modifications appied to the target folder.