6.2 Command-Line Options

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

Table 6-2. Primary pptions




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.


Change to lower case. "caselower" and "CASEUPPER" will convert sequence case.


Change to UPPERCASE.


Remove gap symbols. "degap=symbol" will remove this symbol from output sequence (- normally).


Format number for output.


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.


Input format number.


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.


Select Item number(s) from several. "items=2,3,4" will select these sequence records from a multisequence input file.


List sequences only. "list" will list titles of sequence records.


Redirect Output. "output=file", sends output to named file.


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.


Reverse-complement of input sequence. "reverse" will write the sequence from end to start, and DNA bases are complemented. Amino residues are not complemented.


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".


Verbose progress. "verbose" will print some progress reports.


Calculate & print checksum of sequences.

Table 6-3. Documentation and feature table extraction options




Extract sequence of selected features.


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.


Include selected document fields in output.


Remove selected document fields from output.

Table 6-4. Subrange options




Extract subrange of sequence for feature locations:



Extract all features and sequence from given base range.

Table 6-5. Pair, unpair options




Combine features (fff,gff) and sequence files to one output.


Split features, sequence from one input to two files.

Table 6-6. Pretty format options




Sequence line width.


Left indent.


Column space within sequence line on output.


Count gap chars in sequence numbers.

-nameleft, -nameright[=#]

Name on left/right side [=max width].


Name at top/bottom.

-numleft, -numright

Seq index on left/right side.

-numtop, -numbot

Index on top/bottom.


Use match base for 2..n species.


Blank line(s) between sequence blocks .

Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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