Download fasta file prefix

That is why we can use such simple pattern. Of course, for more complicated file formats a more elaborate pattern can be used. By default, csplit reads the input file, and every time the specified pattern is encountered, csplit will start a new file. See below for examples of changing these defaults. The csplit commands splits the FASTA file into individual chromosome files, and names them xx00 , xx01 , xx02 , etc. Instead of using head , we can instruct sed to stop processing after the first line.

The next command is equivalent to using head -n1 :. Lastly, many FASTA files contains additional information following the initial identifiers, separated by a space character:. We extend our sed command to remove all characters following the space and print only the actual identifier in case there is any additional information :. Using the above sed command we can store the chromosome name in a shell variable, and later use it in our rename command:. The example above extracted the chromosome name from a single file xx00 and renamed it.

Instead of decompressing gunzip ing the input file, we can send it directly to csplit :. The default output suffix is two digits, and will automatically increase to more digits if there are more than 99 files. The best answers are voted up and rise to the top. Stack Overflow for Teams — Collaborate and share knowledge with a private group. Create a free Team What is Teams? Learn more. Download Fasta protein sequences as a file from the selected categories Ask Question.

Asked 1 year, 10 months ago. Active 1 year, 10 months ago. Viewed 59 times. Improve this question. Could you add that as well? Also, I believe the indentation in your post is broken.

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