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  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

    -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
    -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

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