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How to fetch sequences from Proteinortho5 output containing all test species and no duplication in each genome

Hi, I want to construct a phylogenic tree on 100 Pseudomonas aeruginosa genomes. Before constructing the tree, I want to first cluster those genomes on the basis of homology and for this purpose, I am using ProteinOrtho5 software. After running the software with synteny option I want to extract protein sequences from the output those only containing all test species and no duplication in each genome. I understand I need to run grab_protein.pl on myproject.poff to do this but how can customize/filter the output before running grab_protein.pl? I followed as following proteinOrtho out put help required But grep '^4\t4' output.proteinortho didn't print anything for me. As I tested the software on 3 species, I modified it from 3 to 4. Anyone help about the filtering? Cheers

proteinortho5
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updated by AlishaQ • AlishaQ • written by saadleeshehreen saadleeshehreen

2 answers

If you run on three species, your command should be:

grep '^3\t3' output.proteinortho
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written by h.mon h.mon 
grep $'^3\t3' output.proteinortho
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updated by Ram Ram • written by AlishaQ • AlishaQ

My flavor of Linux required the $ character in front - yours might too.

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written by AlishaQ • AlishaQ

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