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readseq help
Guest on 12th February 2023 01:32:09 PM


  1.   Read & reformat biosequences, Java command-line version
  2.   Usage: java -cp readseq.jar run [options] input-file(s)
  3.   For more details: java -cp readseq.jar help more
  4.  
  5.   Options
  6.     -a[ll]              select All sequences
  7.     -c[aselower]        change to lower case
  8.     -C[ASEUPPER]        change to UPPER CASE
  9.     -ch[ecksum]         calculate & print checksum of sequences
  10.     -degap[=-]          remove gap symbols
  11.     -f[ormat=]#         Format number for output,  or
  12.     -f[ormat=]Name      Format name for output
  13.           see Formats   list below for names and numbers
  14.     -inform[at]=#       input format number,  or
  15.     -inform[at]=Name    input format name.  Assume input data is this format
  16.     -i[tem=2,3,4]       select Item number(s) from several
  17.     -l[ist]             List sequences only
  18.     -o[utput=]out.seq   redirect Output
  19.     -p[ipe]             Pipe (command line, < stdin, > stdout)
  20.     -r[everse]          reverse-complement of input sequence
  21.     -t[ranslate=]io     translate input symbol [i] to output symbol [o]
  22.                         use several -tio to translate several symbols
  23.     -v[erbose]          Verbose progress
  24.                 -compare=1          Compare to sequence files, reporting differences
  25.                
  26.    Documentation and Feature Table extraction:
  27.     -feat[ures]=exon,CDS...   extract sequence of selected features
  28.     -nofeat[ures]=repeat_region,intron... remove sequence of selected features
  29.     -field=AC,ID...      include selected document fields in output
  30.     -nofield=COMMENT,... remove selected document fields from output
  31.    
  32.     -extract=1000..9999  * extract all features, sequence from given base range
  33.     -subrange=-1000..10  * extract subrange of sequence for feature locations
  34.     -subrange=1..end      
  35.     -subrange=end-10..end+99  
  36.     -pair=1              * combine features (fff,gff) and sequence files to one output
  37.     -unpair=1            * split features,sequence from one input to two files
  38.                              
  39.    Pretty format options:
  40.     -wid[th]=#            sequence line width
  41.     -tab=#                left indent
  42.     -col[space]=#         column space within sequence line on output
  43.     -gap[count]           count gap chars in sequence numbers
  44.     -nameleft, -nameright[=#]   name on left/right side [=max width]
  45.     -nametop              name at top/bottom
  46.     -numleft, -numright   seq index on left/right side
  47.     -numtop, -numbot      index on top/bottom
  48.     -match[=.]            use match base for 2..n species
  49.     -inter[line=#]        blank line(s) between sequence blocks
  50.  
  51. This program requires a Java runtime (java or jre) program, version 1.1.x, 1.2 or later
  52. The leading '-' on option is optional if '=' is present.  All non-options
  53. (no leading '-' or embedded '=') are used as input file names.
  54. These options and call format are compatible with the classic readseq (v.1992)
  55. * New experimental feature handling options, may not yet work as desired.
  56. To test readeq, use: java -cp readseq.jar test
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