Here is a collection my smart shell and perl scripts. Feel free to download and use my solutions. All software distributed through this page is free for non-commercial use and copying.
- blastgrep – This utility allows you to grep for pattern matches but on query-basis in BLAST reports. So, if you would like to find all queries that has found a sequence which description matches the pattern “photosystem”, you type “blastgrep -i blast_report_file -e ‘photosystem’ -o query” and you get a list of which queries that have such matches. Tested on BLAST 2.2.23, and should work on all other versions of BLAST 2.
Download (version 1.0.2)
- extract_wanted_gi – A perl script to cut out sequences that fulfil certain e-value and score criteria from a hmmsearch output file. Not tested with HMMER3 (yet).
- excel_ready_from_fasta – A perl script to convert a FASTA-file into a tabulated list of GI, accession ID and organism data, which makes Excel (and other table-handling softwares) happy.
- prepare_silva_for_metaxa.sh – A shell scripts that prepares a SILVA SSURef release FASTA-file into a database for use with Metaxa, see this post for more info.
- You may have to right-click the links to download the files.
- After download, move the files to a place where your unix-like system finds executables (like /usr/local/bin). Personally I have added a directory called “bin” in my home folder to my PATH and usually to put scripts and things there.
- When the file is in place, move into that directory and type:
chmod 744 name_of_the_downloaded_file
where “name_of_the_downloaded_file” should be replaced with the name of the downloaded file, e.g. “blastgrep”
- From now on, you should be able to call the script from anywhere in your system, just as a usual Linux/Unix command.
- For most of my scripts and programs, help and instruction for usage can be found by using the -h flag.
Comments, questions, beers, pizzas, cakes, fruit pies, job positions and other types of feedback to my e-mail address:firstname.lastname [at] microbiology.se (and my name is, as usual, Johan Bengtsson).