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.
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.
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