Provided by: genometools_1.5.10+ds-3_amd64
gt-fingerprint - Compute MD5 fingerprints for each sequence given in a set of sequence files.
gt fingerprint [option ...] sequence_file [...]
-check [filename] compare all fingerprints contained in the given checklist file with checksums in given sequence_files(s). The comparison is successful, if all fingerprints given in checkfile can be found in the sequence_file(s) in the exact same quantity and vice versa. (default: undefined) -duplicates [yes|no] show duplicate fingerprints from given sequence_file(s). (default: no) -extract [string] extract the sequence(s) with the given fingerprint from sequence file(s) and show them on stdout. (default: undefined) -width [value] set output width for FASTA sequence printing (0 disables formatting) (default: 0) -o [filename] redirect output to specified file (default: undefined) -gzip [yes|no] write gzip compressed output file (default: no) -bzip2 [yes|no] write bzip2 compressed output file (default: no) -force [yes|no] force writing to output file (default: no) -help display help and exit -version display version information and exit If neither option -check nor option -duplicates is used, the fingerprints for all sequences are shown on stdout. Fingerprint of a sequence is case insensitive. Thus MD5 fingerprint of two identical sequences will be the same even if one is soft-masked.
Compute (unified) list of fingerprints: $ gt fingerprint U89959_ests.fas | sort | uniq > U89959_ests.checklist_uniq Compare fingerprints: $ gt fingerprint -check U89959_ests.checklist_uniq U89959_ests.fas 950b7715ab6cc030a8c810a0dba2dd33 only in sequence_file(s) Make sure a sequence file contains no duplicates (not the case here): $ gt fingerprint -duplicates U89959_ests.fas 950b7715ab6cc030a8c810a0dba2dd33 2 gt fingerprint: error: duplicates found: 1 out of 200 (0.500%) Extract sequence with given fingerprint: $ gt fingerprint -extract 6d3b4b9db4531cda588528f2c69c0a57 U89959_ests.fas >SQ;8720010 TTTTTTTTTTTTTTTTTCCTGACAAAACCCCAAGACTCAATTTAATCAATCCTCAAATTTACATGATAC CAACGTAATGGGAGCTTAAAAATA
· 0 everything went fine (-check: the comparison was successful; -duplicates: no duplicates found) · 1 an error occurred (-check: the comparison was not successful; -duplicates: duplicates found)
Report bugs to https://github.com/genometools/genometools/issues.