samandmac / phylobuild Goto Github PK

So I've encountered two problems with users who use macOS:

• SED error when running PhyloGenes
• The "if" condition in the loop for some reason isn't working, even though that comparison should

To bypass these issues I recommend these solutions, respectively:

• Download gnu-sed brew install gnu-sed and replace all the "sed" in PhyloGenes.sh with "gsed".
• Comment out lines 189 - 196 in PhyloGenes.sh - this ignores deletion of files in the PhyloGenes folder. From here, run each part of the if condition manually:

blastn -query /Users/you/Documents/PhyloTree-main/PhyloGenes/GeneListX.txt -subject /Users/you/Documents/PhyloTree-main/Tree_Genomes/$W.fasta -qcov_hsp_perc 80 -perc_identity 70 -outfmt "6 qseqid pident" | gsed 's/^\(.\{0\}\)/\1>/' | awk '!seen[$0]++' | sort -k 2n  > Z_Last_File.txt #X in GeneListX.txt should be the number of genomes. E.g. if you have 88 strains, you should use GeneList88.txt

head Z_Last_File.txt | awk '{print $1}' > Z_Ortho_Names.txt
		
grep -Fwf Z_Ortho_Names.txt singleLineGenes.txt | gsed 's/[[:blank:]]*\([^[:blank:]]*\)$/\n\1/' > Z_Orthologs.txt

gsed '/^>/ s/^.*gene=\([Aa-Zz]\+\).*/\1/' Z_Orthologs.txt | gsed '1~2s/^/>/' > /Users/you/Documents/PhyloTree-main/Tree_Genes/geneList.txt

Remember to swap your path with the path used in the above example.

I'd appreciate any input from Mac user's as to why the comparison in the IF statement in PhyloGenes.sh isn't working, and workarounds for the SED, given that SED differs between Linux and Mac.

There's the possibility that running PhyloGenes on a Windows 11 (or perhaps 10) terminal using Ubuntu it may return a SED error - if this occurs, the fix is to go into the script for PhyloGenes.sh and change line 163 from:

sed '/^>/ s/^.*gene=\([Aa-Zz]\+\).*/\1/' Z_Orthologs.txt | sed '1~2s/^/>/' > $genesForTree/geneList.txt

to:

sed '/^>/ s/^.*gene=\([A-z]\+\)].*/\1/' Z_Orthologs.txt | sed '1~2s/^/>/' > $genesForTree/geneList.txt

And it should work fine. Remember to alter the line back to the original if switching to anything other than Windows Terminal.