I was running around of 200 djob for a Blastp search in a cluster. All my input files were protein fasta file (prot.fna.1, prot.fna.2 ...prot.fna.200). The output of each individual slurm job is located in a corresponding file ending with *test (prot.fna.1.test, prot.fna.2.test ...prot.fna.200.test) in the same directory. Unfortunately, these Jobs were canceled due to time limit on the node. Now I want to extract all the remaining sequences from my protein fasta files a way to run them again and all the results could be concatenated. Here his what I doing :
1. I look for the first string of one *test file with this command:
, this scrip print me the “pattern”
2. All the sequences after this matching pattern in the corresponding fasta input (prot.fasta.1) is printed using this command :
Repeating this for 200 files one by one is time consuming. I want to run this script in all the files , but I can't. I am writing you to see if you can help me implement this please. Here is what I am doing using these scripts :
This is time consuming, I would be very grateful if you can help me to do that with one script.
Thanks in advance
Cordially
Moderator's Comments:
Please add code tags!
Last edited by MadeInGermany; 06-04-2018 at 05:22 AM..
Reason: Added code tags, removed font tags
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