SHORE Subprograms
From SHORE wiki
shore compress
Compress files to indexed gzip format
Usage: shore compress [OPTIONS] FILES
| Allowed options | ||
| --outfile=<arg> | Write to the file <arg> instead of <infile>.gz | |
| --replace | Remove original files after compression. If the input file is already compressed it will be recompressed and replaced | |
| --tail=<arg> | Instead of compressing files, dump the last <arg> bytes of a seekable file | |
| --dumpgzx | Print out the index for each file | |
shore 2dex
Range-indexing and query for tab-delimited text files
Usage: shore 2dex [OPTIONS] [TEXT_FILES]
| Mandatory | ||
| -i, --infiles=<arg[,...]> | A comma-separated list of tab-delimited plain-text input files (can also be any SHORE directory when -f MAPLIST is set) | |
| Format Options | ||
| -f, --format=<arg> | Provide file type for automatic settings, valid file types: MAPLIST, GFF, SAM | |
| -c, --chr-column=<arg> | Column w. chromosome or sequence name, provide the column name or @<column_number> | |
| -p, --pos-column=<arg> | Column w. start position, provide the column name or @<column_number> | |
| -s, --size-column=<arg> | Column w. feature size, provide the column name or @<column_number> | |
| -e, --end-column=<arg> | Column w. end position (inclusive), provide the column name or @<column_number> | |
| -x, --xend-column=<arg> | Column w. end position (exclusive), provide the column name or @<column_number> | |
| -C, --commentchar=<arg> | Comment line symbol | |
| Index Options | ||
| -B, --blocksize=<arg> | (Default: 131072) | Block size determining the index resolution in bytes |
| -G, --maxgap=<arg> | (Default: 131072) | Maximum sequence gap in a block |
| Query Options | ||
| -q, --query=<arg> | A range to query; prints all overlapping records. Valid ranges: 'SEQ:POS~SIZE', 'SEQ:POS..END', 'SEQ1:POS..SEQ2:END', 'SEQ:POS...XEND', 'SEQ1:POS...SEQ2:XEND' (END: inclusive, XEND: exclusive) | |
| Other | ||
| -v, --verbose | Be more verbose | |
| -Q, --quiet | Be less verbose | |
shore idtrans
SHORE uses numerical identifiers for all sequences of the reference. shore idtrans simplifies translating these numbers in some of the result files back into chromosome names as specified in the reference fasta file (and vice versa).
Required is either a *.trans file which is stored in the IndexFolder by shore preprocess, or a ref.txt file generated by shore mapflowcell.
Usage: shore idtrans [OPTIONS] FILES
| Allowed options | ||
| -t, --transfile=<arg> | *.trans file from IndexFolder | |
| -r, --reffile=<arg> | ref.txt file generated by mapflowcell | |
| -o, --outfile=<arg> | Output file (default: <infile>.idtrans) | |
| -c, --columns=<arg[,...]> | (Default: chr) | Columns to be translated (column names or @<column_number>) |
| --name2id | Translate names to IDs (default: translate IDs to names) | |
| --nocompress | Do not compress output files | |
