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input directory #32
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Hi @Ahmed-Shibl, this is currently not implemented. I guess it should not be too hard to do but I'm not sure when I will have time to do it. There are some things to consider, e.g. taking all files or just those with specific suffixes, automatically generating the name from the file name (requires the filenames to be sensible and not contain spaces or other illegal characters)... I used a for loop to write my proteomes to an options file for trees of 100+ proteomes in the past. So in your case you could run this in your folder: for i in *.pep.fa *.faa
do
name=$(basename $i .pep.fa)
name=$(basename $name .faa)
echo --proteome \"$name\"=\"$i\"
done >bcgTree.options This will create a
Then run |
Hey, To generate such file, you could use basic unix commands, |
@iimog |
Is there a way to use a folder containing the proteomes to be analyzed as input instead of adding each one individually in the command line:
bcgTree.pl --proteome bac1=bacterium1.pep.fa --proteome bac2=bacterium2.faa --proteome bac3=bacterium3.pep.fa --proteome bac4=bacterium4.faa
I want to generate a tree for ~30 proteomes using the command line..
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