Looping a command through Powershell

Question

I recently had to change from the Linux UI to Windows to run some of my analysis for my Science work.

I'm running a program called Blast on Linux and I use it to run multiple files at a time.

The command I use on Linux is this:

for f in *.log; do blastn -query $f -db dbname -out $f.out -outfmt 6 -evalue 0.000001 &done

Upon which, the program will take all the files with *.log, run the command, then create output files named *.out

However, I've 0 idea on how to convert that into a Powershell command.

I'm currently running it one by one but I have hundred of files.

This is the base command in Powershell.

blastn.exe -query .\filename_log -db ..\dbname -out filename.out -outfmt 6 -evalue 0.00001

I'm considering the following, but it's not working because I am still woefully not sure of how to make it do something. =____=

Get-ChildItem "C:\pathway\Genomes\" -Filter *.log | Foreach-Object { $content = Get-Content $_.FullName
$content | Where-Object {$_ -do blastn.exe -query .\filename_log -db ..\dbname -out filename.out -outfmt 6 -evalue 0.00001'} | Set-Content ($_.BaseName + '.out') }

If creating such a command is not possible, would it be possible to create a script for this?

Basically the same ls *.log | %{$_.Name} | %{blastn.exe -query $_ -db dbname -out $_.out -outfmt 6 -evalue 0.000001} — Larry Song
– Larry Song, Commented Jun 21, 2019 at 5:07
@LarrySong Using %_.out will look for a property in the object with the name out instead of appending it to the end of the $_ result — Drew
– Drew, Commented Jun 21, 2019 at 5:13

Nirav Mistry · Accepted Answer · 2019-06-21 05:55:07Z

0

Try this :

$FileList = Get-ChildItem "C:\\pathway\\Genomes\\"  -Filter "*.log" # GETTING THE LIST OF .LOG FILES

$FileList | %{ # FOR EACH LOOP ON ALL .LOG FILE

    blastn.exe -query .\filename_log -db ..\dbname -out filename.out -outfmt 6 -evalue 0.00001 | Set-Content $_.BaseName.out
    # YOUR COMMAND | SET-CONTENT FILENAME # TO SAVE COMMAND OUTPUT IN FILE
    # $_ IS FOR LOOP VARIABLE AND BASENAME IS FILENAME WITHOUT EXTENSION
}

edited Jun 21, 2019 at 5:55

answered Jun 21, 2019 at 5:36

Nirav Mistry

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