6.2 Command-Line Options

Table 6-2 through Table 6-6 summarize Readseq's command-line options.

Table 6-2. Primary pptions

Option	Definition
-a[ll]	Select all sequences. "all" causes processing of all sequences (default now for Version 2, for compatibility with version 1). Use" items=1,2,3" to select a subset.
-c[aselower]	Change to lower case. "caselower" and "CASEUPPER" will convert sequence case.
-C[ASEUPPER]	Change to UPPERCASE.
-degap[=-]	Remove gap symbols. "degap=symbol" will remove this symbol from output sequence (- normally).
-f[ormat=]#	Format number for output.
-f[ormat=]Name	Format name for output. See formats list (Table 6-1) for names and numbers. "format=genbank", "format=gb", "format=xml", etc., selects an output format. You can also use format number, but these numbers may change with revisions. Alternate names of formats are listed in Table 6-1. "Pearson|FastA|fa" allows "pearson", "fasta", or "fa" as a name). This is case-insensitive.
-inform[at]=#	Input format number.
-inform[at]=Name	Input format name. Assume input data is this format. "inform=genbank" lets you specify data input format. Normally Readseq guesses the input format (usually correctly). Use this option if you wish to bypass this input format guessing.
-i[tem=2,3,4]	Select Item number(s) from several. "items=2,3,4" will select these sequence records from a multisequence input file.
-l[ist]	List sequences only. "list" will list titles of sequence records.
-o[utput=]out.seq	Redirect Output. "output=file", sends output to named file.
-p[ipe]	Pipe (command line, < stdin, > stdout). "pipe" will cause input data to come from STDIN and output go to STDOUT Unix standard files (unless -out is given and input file given), and no prompting or progress reports will occurr.
-r[everse]	Reverse-complement of input sequence. "reverse" will write the sequence from end to start, and DNA bases are complemented. Amino residues are not complemented.
-t[ranslate=]io	Translate input symbol [i] to output symbol [o]. Use several -tio to translate several symbols translates given sequence bases, e.g., -tAN to change "A" to "N".
-v[erbose]	Verbose progress. "verbose" will print some progress reports.
-ch[ecksum]	Calculate & print checksum of sequences.

Table 6-3. Documentation and feature table extraction options

Option	Definition
-feat[ures]=exon,CDS...	Extract sequence of selected features.
-nofeat[ures]=repeat_region,intron...	Remove sequence of selected features. "feature=CDS,intron" lets you specify those features to extract, or remove, in the output. Currently this causes each feature to produce a new sequence record.
-field=AC,ID...	Include selected document fields in output.
-nofield=COMMENT,...	Remove selected document fields from output.

Table 6-4. Subrange options

Option	Definition
-subrange=-1000..10	Extract subrange of sequence for feature locations: -subrange=1..end -subrange=end-10..end+99
-extract=10000..99999	Extract all features and sequence from given base range.

Table 6-5. Pair, unpair options

Option	Definition
-pair=1	Combine features (fff,gff) and sequence files to one output.
-unpair=1	Split features, sequence from one input to two files.

Table 6-6. Pretty format options

Option	Definition
-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 .