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A command-line utility to manipulate biological sequences from a FASTA or FASTQ file. It can, given a list of identifiers, get only a subset of the sequences (or their complement, i.e., sequences NOT in the list). Can also get sequence number N only. Compressed sequences files are supported if readable by zcat.
Features
- collect only some sequences out of a large FASTA or FASTQ file
- get sequence number N only, regardless of ID
- complement mode: return all sequences that are NOT in the list of IDs
- "matching" mode: choose which part (between | characters) of the ID should match
- sequence names provided one per line in a text file (first word in line used, or whatever is given to the -k option)
- the > and @ symbols are ignored if present in the beginning of IDs in the list (useful if using FASTA or FASTQ identifiers)
- if only one sequence is needed, its ID can be given directly to the -l option (no need of a file)
- add a suffix to IDs before searching (useful when IDs come from proteins that have _1 in the ID, but genes do not)
- compressed sequence database files (-s) are supported
- quite mode, output only important warnings and errors
Categories
Bio-InformaticsLicense
GNU General Public License version 3.0 (GPLv3)Follow selectseq
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