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方法一:(多个fasta汇总在一个文件中)
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使用Rosetta将<-11的pose名字放入一个文件中,并对这个文件生成fasta
首先创建一个文本文件metric_thresholds.txt
req total_score value < -1010
req interface_delta_B value < -11
output sortmin interface_delta_B
接着筛选出interface_delta_B<-11的pose,生成filtered_designs1.sc文件
unbuntu@unbuntu-virtual-machine:~/chapter4$ perl /home/unbuntu/rosetta2019/main/source/src/apps/public/enzdes/DesignSelect.pl -d <(grep SCORE design_results3.sc) -c metric_thresholds.txt -tag_column last > filtered_designs1.sc
接着提取filtered_designs1.sc中含有的pdb,全部存放在filtered_pdbs.txt文件中
unbuntu@unbuntu-virtual-machine:~/chapter4$ awk '{print $NF ".pdb"}' filtered_designs1.sc > filtered_pdbs.txt
生成filtered_pdbs.txt文件中所有pdb的fasta,存放在selected_sequences.fasta文件中
unbuntu@unbuntu-virtual-machine:~/chapter4$ /home/unbuntu/rosetta2019/main/source/scripts/python/public/pdb2fasta.py $(cat filtered_pdbs.txt) > selected_sequences.fasta
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方法二:(fasta分别生成后,再汇入一个文件中)
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首先筛选出最好的5个pdb,pdb名字存放在best.list文件中(筛选从大到小)
unbuntu@unbuntu-virtual-machine:~/chapter4$ grep pose 01_*.pdb | sort -nk 23 | head -5 | awk '{print(substr($1,1,length($1)-5))}' > best.list
将best.list中的pdb分别生成fasta
unbuntu@unbuntu-virtual-machine:~/chapter4$ cat best.list | awk '{system("python2.7 /home/unbuntu/rosetta2019/tools/protein_tools/scripts/get_fasta_from_pdb.py "$1" A "substr($1,1,length($1)-3)"fasta")}'
然后将所有后缀名为.fasta的文本全部汇总在all_fasts.txt文本中
unbuntu@unbuntu-virtual-machine:~/chapter4$ cat *.fasta > all_fasts.txt