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scorerrunner |
Standard (Mandatory) qualifiers: [-commandpath] directory Directory where alignment executables live [-goldseqsdir] dirlist First directory containing paired traces [-testseqsdir] dirlist Second directory containing paired traces [-scoresoutdir] outdir Name of directory containing output scores [-scoresoutfilename] string Name of comma-separated variable file containing identity scores for pairs of gold and test sequences directory Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: (none) General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report deaths |
Standard (Mandatory) qualifiers | Allowed values | Default | |
---|---|---|---|
[-commandpath] (Parameter 1) |
Directory where alignment executables live | Directory | |
[-goldseqsdir] (Parameter 2) |
First directory containing paired traces | Directory with files | . |
[-testseqsdir] (Parameter 3) |
Second directory containing paired traces | Directory with files | . |
[-scoresoutdir] (Parameter 4) |
Name of directory containing output scores | Output directory | |
[-scoresoutfilename] (Parameter 5) |
Name of comma-separated variable file containing identity scores for pairs of gold and test sequences directory | Any string is accepted | scores.csv |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
(none) |
Under development, no example input file(s) yet
Under development, no example output file(s) yet
Program name | Description |
---|---|
alignrunner | Align sequence pairs in a directory |
comparator | Compare contact scores of two sequence alignments |
contactalign | Damian Counsell's experimental 2.5-D alignment algorithm |
esim4 | Align an mRNA to a genomic DNA sequence |
est2genome | Align EST and genomic DNA sequences |
nawalign | Damian Counsell's NW implementation |
nawalignrunner | Nawalign all sequence pairs in a directory |
needle | Needleman-Wunsch global alignment |
needlerunner | Needle all sequence pairs in a directory |
scorer | Score alignments using structural alignments |
stretcher | Finds the best global alignment between two sequences |
substitute | Substitute matches into a template |
substituterunner | Run SUBSTITUTE on a directory of traces |