Read & reformat biosequences, Java command-line version Usage: java -cp readseq.jar run [options] input-file(s) For more details: java -cp readseq.jar help more Options -a[ll] select All sequences -c[aselower] change to lower case -C[ASEUPPER] change to UPPER CASE -ch[ecksum] calculate & print checksum of sequences -degap[=-] remove gap symbols -f[ormat=]# Format number for output, or -f[ormat=]Name Format name for output see Formats list below for names and numbers -inform[at]=# input format number, or -inform[at]=Name input format name. Assume input data is this format -i[tem=2,3,4] select Item number(s) from several -l[ist] List sequences only -o[utput=]out.seq redirect Output -p[ipe] Pipe (command line, < stdin, > stdout) -r[everse] reverse-complement of input sequence -t[ranslate=]io translate input symbol [i] to output symbol [o] use several -tio to translate several symbols -v[erbose] Verbose progress -compare=1 Compare to sequence files, reporting differences Documentation and Feature Table extraction: -feat[ures]=exon,CDS... extract sequence of selected features -nofeat[ures]=repeat_region,intron... remove sequence of selected features -field=AC,ID... include selected document fields in output -nofield=COMMENT,... remove selected document fields from output -extract=1000..9999 * extract all features, sequence from given base range -subrange=-1000..10 * extract subrange of sequence for feature locations -subrange=1..end -subrange=end-10..end+99 -pair=1 * combine features (fff,gff) and sequence files to one output -unpair=1 * split features,sequence from one input to two files Pretty format options: -wid[th]=# sequence line width -tab=# left indent -col[space]=# column space within sequence line on output -gap[count] count gap chars in sequence numbers -nameleft, -nameright[=#] name on left/right side [=max width] -nametop name at top/bottom -numleft, -numright seq index on left/right side -numtop, -numbot index on top/bottom -match[=.] use match base for 2..n species -inter[line=#] blank line(s) between sequence blocks This program requires a Java runtime (java or jre) program, version 1.1.x, 1.2 or later The leading '-' on option is optional if '=' is present. All non-options (no leading '-' or embedded '=') are used as input file names. These options and call format are compatible with the classic readseq (v.1992) * New experimental feature handling options, may not yet work as desired. To test readeq, use: java -cp readseq.jar test