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
