Seqs data of this repo and the BacMet-Scan_v1.1.pl forked from BacMet version 2, but I have modified it according to myself.
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add function that can run diamond (v0.9.10) search of BacMet-Scan_v1.1, that can run faster for blastp.
when you run
perl ./BacMet-Scan_v1.1.pl -h, you will find -diamond option, others no change, so that you can run it good for you.Also, I had provided a database of diamond v0.9.10 at BacMet2_EXP, BacMet2_EXP directory, you can use it directly without make database by diamond makedb.
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make a new mapping.txt for BacMet v2 adjust to BacMet-Scan_v1.1.pl, because version 2 is different from v1.1 about BacMet. More see the mapping.txt.
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fixed some bug of BacMet-Scan_v1.1.pl.
# for help
perl ./BacMet-Scan_v1.1.pl -h
# then you can see the help informations, like this
Usage: BacMet-Scan -i <input file> -o <output files base>
Options:
-i <input file> : the path to the input file containing non-paired sequences to scan
-1 <input file> : if using paired-end input, the path to the input file containing the first reads to scan
-2 <input file> : if using paired-end input, the path to the input file containing the second reads to scan
-o <output> : the base name of the BacMet-Scan output files (if not specified, BacMet-Scan will write to stdout)
-d <database> : the database to use, either EXP, PRE, or a path to a specific database directory, default 'PRE'
Software options:
=================
-blast : uses BLAST for searching BacMet (default)
-blastall : uses the old BLAST engine for searching BacMet
-blat : uses BLAT for searching BacMet
-pblat : uses Parallel BLAT (pblat) for searching BacMet
-vmatch : uses VMATCH for searching BacMet
-fixst : uses FIXST for searching BacMet
-diamond : uses diamond (v0.9.10) for searching BacMet
-cpu <value> : number of CPUs to use (if possible), default = 1
-r <file> : use this file (output from the tool above that generated the file)
for input instead of performing the actual search
-protein : input sequence file is in protein format (nucleotides are assumed by default)
Filtering options:
=================
-e <value> : E-value cutoff, default = 1
-l <value> : Length cutoff, default = 30
-p <value> : Percent identity cutoff, default = 90
-s <value> : Score per length cutoff, not used by default (tool dependent!)
Output options:
=================
-table : outputs a BacMet-Scan report in table format (default)
-report : outputs the BLAST/BLAT/VMATCH/FIXST report
-counts : outputs a list of counts for each gene
-matrix : outputs a list of counts for each gene, without the gene names, suitable for matrix format
-toplist : outputs a list of encountered genes, sorted by abundance
-all : outputs all possible BacMet-Scan output
-columns : selects what columns to output to the BacMet-Scan output table
comma-separated list with the following possible items:
query,subject,gene,description,organism,location,compound,identity,length,evalue,score
default is: query,subject,gene,identity,length
can also be specified as 'all' to get all columns
-v : be verbose (print messages during the BacMet-Scan process)
-h : displays short usage information
-help : displays this help message
-bugs : displays the bug fixes and known bugs in this version
-license : displays licensing information
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# example
perl ./BacMet-Scan_v1.1.pl -i ecoli_protein.fa -o ecoli_bacmet -d ./BacMet2_PRE -diamond -protein -cpu 10 -e 1e-5 -p 80 -all -columns all
for more example, see test directory.
See bacmet_class_summary.py and ar_class_barplot.R. Example,
# summary
python3 bacmet_class_summary.py ecoli_bacmet.table > bacmet_class_count.txt
# barplot
Rscript ar_class_barplot.R bacmet_class_count.txt bacmet_class_count
# will make bacmet_class_count.pdf and bacmet_class_count.png of BacMet barplot output (only top 50 to plot)
AR barplot can see test_args_bacmet_count.pdf(png) at ./test directory. Like this:
Copyright (C) 2013-2014 Johan Bengtsson-Palme & Chandan Pal.
More see license file.