Windows Command Prompt FINDSTR

[GSviral]

Hello,

I am currently working with the latest BLAST+ package configured to be a local BLAST nt database using Windows command prompt.

I have set up the database to run BLAST which works without any bother.

Subsequently, I wanted to create a new BLAST database using the makeblastdb command. My input FASTA file is the GenBank viral database.

When I attempt to create the database the command runs however it reaches an error - "FASTA Reader - No residues found". Through forum searching I have deduced that this is due to there being an empty record in the FASTA file eg:

>gi|xxxx|
AGGATGCTAGCT

>gi|xxxx|

>gi|yyyyy|
AGACCGATGACT

My question is - is there a command on Windows command prompt that can automatically remove these empty headers and output a modified FASTA without them? I know of the FINDSTR command however I can't seem to get it to do what I want as I am not as familiar with command prompt on Windows compared to command line on Linux.

If I were running Linux this would be no bother as this problem has been documented however the alternative Linux computer I am using simply will not carry out the makeblastdb command as it comes up with a segmentation fault right away, even when I type makeblastdb -help.

Thanks for any help given.

[WhatsOEver]

Why not modifying the file on the linux machine and transferring it to windows?
Alternatively, you can simply install cygwin on your windows computer which provides grep/sed/awk on default which should be sufficient to solve your problem.

[maubp]

You could use a scripting language like Perl or Python for this

[Brian Bushnell]

You can also get rid of those with reformat:

java -Xmx1g -cp path/to/bbmap/current jgi.ReformatReads in=file.fasta out=filtered.fasta minlen=1