Description:

This notebook goes through the plotting of CRISPR loci

Before running this notebook:

run the Setup notebook

User-defined variables



In [62]:

    
# directory where you want the spacer blasting to be done
## CHANGE THIS!
workDir = "/home/nyoungb2/t/CLdb_Ecoli/loci_plots/"

Init



In [63]:

    
import os
from IPython.display import Image



In [64]:

    
if not os.path.isdir(workDir):
    os.makedirs(workDir)



In [65]:

    
# checking that CLdb is in $PATH & ~/.CLdb config file is set up
!CLdb --config-params









    



#-- Config params --#
DATABASE = /home/nyoungb2/t/CLdb_Ecoli/CLdb.sqlite

Plotting loci

As with arrayBlast, plotLoci has subcommands of it's own



In [66]:

    
!CLdb -- plotLoci -h









    



Usage:
    plotLoci [options] subcommand -- [subcommand_options]

  Options:
    --list
        List all subcommands.

    --perldoc
        Get perldoc of subcommand.

    -v Verbose output
    -h This help message

  For more information:
    CLdb --perldoc -- plotLoci



In [67]:

    
!CLdb -- plotLoci --list









    



format_dna_segs_colors
make_comparison
make_dna_segs
make_xlims
order_by_tree
prune_tree
rotate_tree
run

Basics on how a plot is made

Note: some steps are optional (like mapping loci plots to a tree)

Make a table of spacer/DR sequence locations & other info.
- A 'dna_segs' table
[optional] order the table by a tree file
[optional] add color info to the table
Make a table of the range limits for each locus.
- ie., the start & stop positions of each plot
- An 'xlims' table
[optional] order the table by a tree file.
Make a comparison file to compare sequence similarity among loci.
- A 'compare' table
Feed all of the tables into an R script for making the figure.

Making the plot

dna_segs table



In [68]:

    
# making table
!cd $workDir; \
    CLdb -- plotLoci -- make_dna_segs > dna_segs.txt
    
# checking output
!cd $workDir; \
    echo; \
    head -n 5 dna_segs.txt









    



WARNING: no ITEP db provided! All genes will have col value of '1'!
WARNING: no matching entries in leaders table! Leaders not added to dna_segs table!
...Found multiple loci for 1 or more taxa. Adding loci_ids to names in dna_segs table!

name	start	end	strand	col	lty	lwd	pch	cex	gene_type	taxon_name	locus_id	feat	feat_id	subtype	dna_segs_id
12	2876425	2876457	1	29	1	0.5	8	1	blocks	Escherichia_coli_K-12_MG1655	A	spacer	12	I-E	Escherichia_coli_K-12_MG1655__A
7	2876118	2876150	1	31	1	0.5	8	1	blocks	Escherichia_coli_K-12_MG1655	A	spacer	7	I-E	Escherichia_coli_K-12_MG1655__A
11	2876364	2876396	1	24	1	0.5	8	1	blocks	Escherichia_coli_K-12_MG1655	A	spacer	11	I-E	Escherichia_coli_K-12_MG1655__A
9	2876241	2876274	1	3	1	0.5	8	1	blocks	Escherichia_coli_K-12_MG1655	A	spacer	9	I-E	Escherichia_coli_K-12_MG1655__A

Adding coloring info



In [84]:

    
# making table
!cd $workDir; \
    CLdb -- plotLoci -- format_dna_segs_colors < dna_segs.txt > dna_segs_col.txt
    
# checking output
!cd $workDir; \
    echo; \
    head -n 5 dna_segs_col.txt









    



name	start	end	strand	col	lty	lwd	pch	cex	gene_type	taxon_name	locus_id	feat	feat_id	subtype	dna_segs_id
1	2875723	2875752	1	#000000	1	0.1	8	1	blocks	Escherichia_coli_K-12_MG1655	A	directrepeat	1	I-E	Escherichia_coli_K-12_MG1655__A
13	2876457	2876486	1	#000000	1	0.1	8	1	blocks	Escherichia_coli_K-12_MG1655	A	directrepeat	13	I-E	Escherichia_coli_K-12_MG1655__A
4	2875906	2875935	1	#000000	1	0.1	8	1	blocks	Escherichia_coli_K-12_MG1655	A	directrepeat	4	I-E	Escherichia_coli_K-12_MG1655__A
2	2875784	2875813	1	#000000	1	0.1	8	1	blocks	Escherichia_coli_K-12_MG1655	A	directrepeat	2	I-E	Escherichia_coli_K-12_MG1655__A

xlims table



In [69]:

    
# making table
!cd $workDir; \
    CLdb -- plotLoci -- make_xlims > xlims.txt
    
# checking output
!cd $workDir; \
    echo; \
    head -n 5 xlims.txt









    



...Found multiple loci for 1 or more taxa. Adding leaves to the tree! Adding loci_ids to leaves & xlims table!

start	end	taxon_name	locus_id	subtype	dna_segs_id
3665521	3691424	Escherichia_coli_O157_H7	G	I-E	Escherichia_coli_O157_H7__G
3665829	3691513	Escherichia_coli_O157_H7	H	I-E	Escherichia_coli_O157_H7__H
2880811	2903063	Escherichia_coli_K-12_W3110	F	I-E	Escherichia_coli_K-12_W3110__F
2876357	2885875	Escherichia_coli_K-12_W3110	E	I-E	Escherichia_coli_K-12_W3110__E



In [85]:

    
# making table
!cd $workDir; \
    CLdb -- plotLoci -- make_comparison < dna_segs_col.txt









    



...WARNING: no ITEP db provided ('-i')! No blastp information will be included!
### Getting spacer clusters ###
start1	end1	start2	end2	col	dna_segs_id1	dna_segs_id2	feat	feat_id	sfeat_id

making figure



In [86]:

    
!cd $workDir; \
    CLdb -- plotLoci -- run \
    -d dna_segs_col.txt \
    -x xlims.txt \
    -f png \
    -o all_loci









    



Loci plot written: "all_loci"
null device 
          1



In [87]:

    
pngFile = os.path.join(workDir, 'all_loci.png')
Image(filename=pngFile)









    Out[87]:

Notes:

For some CRISPRs, many non-CAS genes are intervieing between the CRISPR array and CAS genes.
Genes could be colored by annotation or gene cluster.
Comparisons could be shown between spacers, genes, or both.



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