READSEQ
D. Gilbert
format
readseq
readseq
perl
readseq
0
seq
Sequence File
perl
" $value"
2
readseq_ok_alig
perl
1
outfile
perl
""
"readseq.out"
seqfile
perl
1
outformat
Output Sequence Format
perl
" -f$value"
8
3
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
select
Selection parameters
items
select Item number(s) from several
perl
($value)? " \\-i" . join(",",split(/[,\\s]/,$value)) : ""
3
allseq
perl
(! $items)? " -a":""
3
output
Output parameters
lowcase
Change to lower case (-c)
perl
($value)? " -c":""
0
3
uppcase
Change to UPPER case (-C)
perl
($value)? " -C":""
0
3
degap
Remove gap symbols (-degap)
perl
($value)? " -degap":""
0
3
reverse
Change to Reverse-complement (-r)
perl
($value)? " -r":""
0
3
listonly
List sequences only (-l)
perl
($value)? " -l":""
0
3
pretty
Pretty format (18) parameters
width
Sequence line width (-width)
perl
(defined $value)?" -width=$value":""
3
tab
Left indent (-tab)
perl
(defined $value)?" -tab=$value":""
3
col
Column space within sequence line on output (-col)
perl
(defined $value)?" -col=$value":""
3
gap
Count gap chars in sequence numbers (-gap)
perl
(defined $value)? " -gap" : ""
3
nameleft
Name on left/right side
perl
($value)? " -name$value" : ""
3
left
right
nametop
Name at top (-nametop)
perl
($value)? " -nametop" : ""
0
3
numleft
Sequence index on left/right side
perl
($value)? " -num$value" : ""
3
left
right
numtop
Index on top/bottom
perl
($value)? " -num$value" : ""
3
top
bot
match
Use match base (.) for 2..n species (-match)
perl
($value)? " -match=." : ""
0
3
interline
How many blank line(s) between sequence blocks
perl
(defined $value)?" -inter=$value":""
3