Next: wcd inside stackPACK, Previous: Installing wcd, Up: Top
wcd can be invoked in different ways. The first just shows the usage;
the others are functional. They take an input file in FASTA format
and process it in some way. wcd numbers the sequences in the file
from 0 upwards, and these indices are used to refer to the sequences.
Options or switches to wcd can be given in short form
(e.g. -D) or long form (e.g. --cluster_compare). On some
systems, only the short form options are supported.
Usage: wcd -v | -u |-h
-v: version
-u: usage
-h: usage
Usage: wcd [opts] <filename>
-c, --show_clusters: show clusters compactly
-d fname: use the file as a dump file
-F fun, --function fun: say which distance function to use -f fname, --init_cluster: use file as initial cluster
-g, --histogram: show histogram
-H val, --common_word val: set common word heuristic threshold (default 5)
-j fname, --constraint1 fname: set constraint file 1.
-J fname, --constraint2 fname: set constraint file 2.
-K val, --sample_thresh val: give sample heuristic threshold
-l val, --window_len: set window len (default 100)
-n, --no_rc: don't do RC check
-o fname , --output fname: send output to file [stdout] -P fname, --parameter fname : parameter file for distance function
-R <filename> <ind1> <ind2>: perform cluster on a range
-s, --performance: show performance stats
-S val, --skip val: set skip value
-t, --show_ext: show extended cluster table
-T val, --threshold val: set threshold to value
-w val, --word_len: set d2 word length (default 6)
-X: clone linking
Usage: wcd [-i|--show_seq] <index> <filename>
show the sequence with the given index
Usage: wcd [-I|--show_rc_seq] <index> <filename>
show the RC of the sequence with the given index
Usage: wcd [-E|-e|-p] <filename> <ind1> <ind2>
-E, --compare: show seqs, number common words, and d2scores
-e, --abbrev_compare: show min of d2scores (pos + rc)
-p, --pairwise: show pairwise d2 scores of all windows
Usage: wcd [--cluster_compare,-D] <seqfile> <indicesfile>
compare two clusters
Usage: wcd [--merge,-m] <seqf1> <clf1> <seqf2> <clf2>
merge two clusterings
Usage: wcd [--add,-a] <seqf1> <clf1> <seqf2>
add a set of sequences to a known clustering
Usage: wcd [--recluster,-r] <clf1> <seqf1>
recluster from a less stringent clustering