6.2 Command-Line Options
Table 6-2
through Table 6-6 summarize Readseq's command-line
options.
Table 6-2. Primary pptions
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-a[ll]
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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.
|
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-c[aselower]
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Change to lower case. "caselower"
and "CASEUPPER" will convert
sequence case.
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-C[ASEUPPER]
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Change to UPPERCASE.
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-degap[=-]
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Remove gap symbols. "degap=symbol"
will remove this symbol from output sequence (- normally).
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-f[ormat=]#
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Format number for output.
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-f[ormat=]Name
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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.
|
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-inform[at]=#
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Input format number.
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-inform[at]=Name
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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.
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-i[tem=2,3,4]
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Select Item number(s) from several.
"items=2,3,4" will select these
sequence records from a multisequence input file.
|
|
-l[ist]
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List sequences only. "list" will
list titles of sequence records.
|
|
-o[utput=]out.seq
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Redirect Output. "output=file",
sends output to named file.
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-p[ipe]
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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.
|
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-r[everse]
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Reverse-complement of input sequence.
"reverse" will write the sequence
from end to start, and DNA bases are complemented. Amino residues are
not complemented.
|
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-t[ranslate=]io
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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".
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-v[erbose]
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Verbose progress. "verbose" will
print some progress reports.
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-ch[ecksum]
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Calculate & print checksum of sequences.
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Table 6-3. Documentation and feature table extraction options
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-feat[ures]=exon,CDS...
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Extract sequence of selected features.
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-nofeat[ures]=repeat_region,intron...
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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.
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-field=AC,ID...
|
Include selected document fields in output.
|
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-nofield=COMMENT,...
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Remove selected document fields from output.
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Table 6-4. Subrange options
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-subrange=-1000..10
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Extract subrange of sequence for feature locations:
- -subrange=1..end
- -subrange=end-10..end+99
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-extract=10000..99999
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Extract all features and sequence from given base range.
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Table 6-5. Pair, unpair options
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-pair=1
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Combine features (fff,gff) and sequence files to one output.
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-unpair=1
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Split features, sequence from one input to two files.
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Table 6-6. Pretty format options
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-wid[th]=#
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Sequence line width.
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-tab=#
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Left indent.
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-col[space]=#
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Column space within sequence line on output.
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-gap[count]
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Count gap chars in sequence numbers.
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-nameleft, -nameright[=#]
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Name on left/right side [=max width].
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-nametop
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Name at top/bottom.
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-numleft, -numright
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Seq index on left/right side.
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-numtop, -numbot
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Index on top/bottom.
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-match[=.]
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Use match base for 2..n species.
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-inter[line=#]
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Blank line(s) between sequence blocks .
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