Rename fasta files

This command will create final. If your dataset uses a name file, you will want to include it to avoid downstream name mismatch issues. The file option allows you to provide a 2 or 3 column file. The first column contains the file type: fasta or qfile. This command supports codons containing any ambiguous base.

Please switch on flag -L INT for details. When searching by sequences, it's partly matching, and both positive and negative strands are searched. When providing search patterns motifs via flag '-p', please use double quotation marks for patterns containing comma, e.

Because the command line argument parser accepts comma-separated-values CSV for multiple values motifs. Patterns in file do not follow this rule. The order of sequences in result is consistent with that in original file, not the order of the query patterns.

For multiple patterns, you can either set "-p" multiple times, i. You can specify the sequence region for searching with the flag -R --region. Attention: use double quotation marks for patterns containing comma, e. Searching with list of sequence names they may contain whitespace. Extract human hairpins i. Base S stands for C or G. When using flag --circular, end position of matched subsequence that crossing genome sequence end would be greater than sequence length.

Usage: seqkit locate [flags] Flags: --bed output in BED6 format -c, --circular circular genome. Only one the longest matching location is returned for every primer pair. Mismatch is allowed, but the mismatch location 5' or 3' is not controled.

Examples: 0. When comparing by sequences, both positive and negative strands are compared. Usage: seqkit rmdup [flags] Flags: -n, --by-name by full name instead of just id -s, --by-seq by seq -D, --dup-num-file string file to save number and list of duplicated seqs -d, --dup-seqs-file string file to save duplicated seqs -h, --help help for rmdup -i, --ignore-case ignore case -P, --only-positive-strand only considering positive strand when comparing by sequence Examples Similar to common.

So the records number may be larger than that of the smallest file. If you just want to split by parts or sizes, please use "seqkit split2", which also apply for paired- and single-end FASTQ.

The file extensions of output are automatically detected and created according to the input files. Orders of headers in the two files better be the same not shuffled , otherwise it consumes huge number of memory for buffering reads in memory. Otherwise names are kept untouched in the given output directory. This command is used to restrieve sequences of the first strain, i.

I tried putting a dollar at the end of the key names, but I get the same error. Add a comment. Active Oldest Votes. Improve this answer. I just don't know sed.

I need to learn it. It works a bit like grep which you know how to use , but then with replacement function. Anchoring the pattern to the beginning of the line should speed things up for large files. Otherwise, sed will have to scan the entire length of each line in case there's a match. But does it work with fasta? Show 1 more comment. Already have an account? Sign in to comment. You signed in with another tab or window.

Reload to refresh your session. You signed out in another tab or window. ARGV holds command line arguments. In this case it will be the name of our input fasta. Open two files for output.