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
I understand you want to automate a task to run over 200 files. Programming / scripting is for exactly this, and I'm pretty sure your request can be fulfilled elegantly and fast. Unfortunately I (at least) don't really understand what your after. Please rephrase your request, and supply representative sample data.
Thank you for your quick response and help I am a biginner on linux. I will try to run this for loop script with my data to see if it is working.
I am sorry for my english
Cordially
---------- Post updated at 09:09 PM ---------- Previous update was at 06:20 PM ----------
Dear moderator
This bash script generates a file for each command line. However all the files are empty. Is there any way that I can improve it. I am sorry if my question looks trivial.I am just starting with linux programming.
Dear folks
I have two data set which there names are "final.map" and "1.geno" and look like this structures:
final.map:
gi|358485511|ref|NC_006088.3| 2044
gi|358485511|ref|NC_006088.3| 2048
gi|358485511|ref|NC_006088.3| 2187
gi|358485511|ref|NC_006088.3| 17654
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FOR EXAMPLE
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No duplicate posting! Continue here. (0 Replies)
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