TeXshade package - ruler missing position when “-” in consensus
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2
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I am using the texshade package, and have run into a problem I was hoping someone may be able to help with.
I am using the diverse shading mode to compare mutated antibody sequences to their unmutated germline precursor. There is an insertion in the antibody sequences relative to germline. If I represent the insertion as "-", it causes the ruler to miss a numbering position at that point. Does anyone know of a way this can be corrected?
Thanks in advance for your help.
Tex code:
documentclass[10pt]{article}
usepackage{texshade}
headheight=0pt
headsep=0pt
hoffset=0pt
voffset=0pt
paperwidth=8.27in
paperheight=11.69in
ifxpdfoutputundefined
relax
else
pdfpagewidth=paperwidth
pdfpageheight=paperheight
fi
oddsidemargin=-0.25in
topmargin=0.3in
textwidth=7in
textheight=11.62in
pagestyle{empty}
begin{document}
newline
begin{texshade}{aligned.heavy.fasta}
setsize{features}{footnotesize}
shadingmode{diverse}
hidenumbering
showruler{1}{top}
setsize{ruler}{scriptsize}
rulersteps{1}
shownames{left}
end{texshade}
end{document}
And the aligned.heavy.fasta file:
>germline_comparator
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE-EEEEEEEEEEEEEEE
>seq1
EEEEQEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEETEEEEEEEEEEEEEEE
>seq2
EEEEQEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEETEEEEEEEEEEEEEEE
>seq3
EEEEQEEEEEEEEEEEEFEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEETEEEEEEEEEEEEEEE
packages align environments
asked Jan 20 '17 at 10:58
shakey
111
bumped to the homepage by Community♦ 14 mins ago
This question has answers that may be good or bad; the system has marked it active so that they can be reviewed.
add a comment |
up vote
2
down vote
favorite
I am using the texshade package, and have run into a problem I was hoping someone may be able to help with.
I am using the diverse shading mode to compare mutated antibody sequences to their unmutated germline precursor. There is an insertion in the antibody sequences relative to germline. If I represent the insertion as "-", it causes the ruler to miss a numbering position at that point. Does anyone know of a way this can be corrected?
Thanks in advance for your help.
Tex code:
documentclass[10pt]{article}
usepackage{texshade}
headheight=0pt
headsep=0pt
hoffset=0pt
voffset=0pt
paperwidth=8.27in
paperheight=11.69in
ifxpdfoutputundefined
relax
else
pdfpagewidth=paperwidth
pdfpageheight=paperheight
fi
oddsidemargin=-0.25in
topmargin=0.3in
textwidth=7in
textheight=11.62in
pagestyle{empty}
begin{document}
newline
begin{texshade}{aligned.heavy.fasta}
setsize{features}{footnotesize}
shadingmode{diverse}
hidenumbering
showruler{1}{top}
setsize{ruler}{scriptsize}
rulersteps{1}
shownames{left}
end{texshade}
end{document}
And the aligned.heavy.fasta file:
>germline_comparator
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE-EEEEEEEEEEEEEEE
>seq1
EEEEQEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEETEEEEEEEEEEEEEEE
>seq2
EEEEQEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEETEEEEEEEEEEEEEEE
>seq3
EEEEQEEEEEEEEEEEEFEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEETEEEEEEEEEEEEEEE
packages align environments
asked Jan 20 '17 at 10:58
shakey
111
bumped to the homepage by Community♦ 14 mins ago
This question has answers that may be good or bad; the system has marked it active so that they can be reviewed.
1
This seems to be a feature, the germline line is the reference sequence, and the numbering follows the reference, which seems to be a valid consideration. I don't thinktexshadeprovides an option to change this. It could be done by changing the package source, but that is a rather difficult task.
– Marijn
Jan 20 '17 at 20:56
1
What is it that you want to do? The numbering is by default relative to the first sequence, and "-" is a gap, so not counted. If you want your numbering to include this gap as a position, then you should take the sequence that has no gaps for the numbering reference. From the texshade manual (page 58): showruler[〈color〉]{〈position〉}{〈seqref〉}
– Joe H.
Sep 6 '17 at 7:58
add a comment |
up vote
2
down vote
favorite
up vote
2
down vote
favorite
I am using the texshade package, and have run into a problem I was hoping someone may be able to help with.
I am using the diverse shading mode to compare mutated antibody sequences to their unmutated germline precursor. There is an insertion in the antibody sequences relative to germline. If I represent the insertion as "-", it causes the ruler to miss a numbering position at that point. Does anyone know of a way this can be corrected?
Thanks in advance for your help.
Tex code:
documentclass[10pt]{article}
usepackage{texshade}
headheight=0pt
headsep=0pt
hoffset=0pt
voffset=0pt
paperwidth=8.27in
paperheight=11.69in
ifxpdfoutputundefined
relax
else
pdfpagewidth=paperwidth
pdfpageheight=paperheight
fi
oddsidemargin=-0.25in
topmargin=0.3in
textwidth=7in
textheight=11.62in
pagestyle{empty}
begin{document}
newline
begin{texshade}{aligned.heavy.fasta}
setsize{features}{footnotesize}
shadingmode{diverse}
hidenumbering
showruler{1}{top}
setsize{ruler}{scriptsize}
rulersteps{1}
shownames{left}
end{texshade}
end{document}
And the aligned.heavy.fasta file:
>germline_comparator
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE-EEEEEEEEEEEEEEE
>seq1
EEEEQEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEETEEEEEEEEEEEEEEE
>seq2
EEEEQEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEETEEEEEEEEEEEEEEE
>seq3
EEEEQEEEEEEEEEEEEFEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEETEEEEEEEEEEEEEEE
packages align environments
asked Jan 20 '17 at 10:58
shakey
111
I am using the texshade package, and have run into a problem I was hoping someone may be able to help with.
I am using the diverse shading mode to compare mutated antibody sequences to their unmutated germline precursor. There is an insertion in the antibody sequences relative to germline. If I represent the insertion as "-", it causes the ruler to miss a numbering position at that point. Does anyone know of a way this can be corrected?
Thanks in advance for your help.
Tex code:
documentclass[10pt]{article}
usepackage{texshade}
headheight=0pt
headsep=0pt
hoffset=0pt
voffset=0pt
paperwidth=8.27in
paperheight=11.69in
ifxpdfoutputundefined
relax
else
pdfpagewidth=paperwidth
pdfpageheight=paperheight
fi
oddsidemargin=-0.25in
topmargin=0.3in
textwidth=7in
textheight=11.62in
pagestyle{empty}
begin{document}
newline
begin{texshade}{aligned.heavy.fasta}
setsize{features}{footnotesize}
shadingmode{diverse}
hidenumbering
showruler{1}{top}
setsize{ruler}{scriptsize}
rulersteps{1}
shownames{left}
end{texshade}
end{document}
And the aligned.heavy.fasta file:
>germline_comparator
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE-EEEEEEEEEEEEEEE
>seq1
EEEEQEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEETEEEEEEEEEEEEEEE
>seq2
EEEEQEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEETEEEEEEEEEEEEEEE
>seq3
EEEEQEEEEEEEEEEEEFEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEETEEEEEEEEEEEEEEE
packages align environments
packages align environments
asked Jan 20 '17 at 10:58
shakey
111
asked Jan 20 '17 at 10:58
shakey
111
asked Jan 20 '17 at 10:58
shakey
111
asked Jan 20 '17 at 10:58
shakey
111
asked Jan 20 '17 at 10:58
shakey
111
111
bumped to the homepage by Community♦ 14 mins ago
This question has answers that may be good or bad; the system has marked it active so that they can be reviewed.
bumped to the homepage by Community♦ 14 mins ago
This question has answers that may be good or bad; the system has marked it active so that they can be reviewed.
1
This seems to be a feature, the germline line is the reference sequence, and the numbering follows the reference, which seems to be a valid consideration. I don't thinktexshadeprovides an option to change this. It could be done by changing the package source, but that is a rather difficult task.
– Marijn
Jan 20 '17 at 20:56
1
What is it that you want to do? The numbering is by default relative to the first sequence, and "-" is a gap, so not counted. If you want your numbering to include this gap as a position, then you should take the sequence that has no gaps for the numbering reference. From the texshade manual (page 58): showruler[〈color〉]{〈position〉}{〈seqref〉}
– Joe H.
Sep 6 '17 at 7:58
add a comment |
1
This seems to be a feature, the germline line is the reference sequence, and the numbering follows the reference, which seems to be a valid consideration. I don't thinktexshadeprovides an option to change this. It could be done by changing the package source, but that is a rather difficult task.
– Marijn
Jan 20 '17 at 20:56
1
What is it that you want to do? The numbering is by default relative to the first sequence, and "-" is a gap, so not counted. If you want your numbering to include this gap as a position, then you should take the sequence that has no gaps for the numbering reference. From the texshade manual (page 58): showruler[〈color〉]{〈position〉}{〈seqref〉}
– Joe H.
Sep 6 '17 at 7:58
1
1
This seems to be a feature, the germline line is the reference sequence, and the numbering follows the reference, which seems to be a valid consideration. I don't think
texshade provides an option to change this. It could be done by changing the package source, but that is a rather difficult task.– Marijn
Jan 20 '17 at 20:56
This seems to be a feature, the germline line is the reference sequence, and the numbering follows the reference, which seems to be a valid consideration. I don't think
texshade provides an option to change this. It could be done by changing the package source, but that is a rather difficult task.– Marijn
Jan 20 '17 at 20:56
1
1
What is it that you want to do? The numbering is by default relative to the first sequence, and "-" is a gap, so not counted. If you want your numbering to include this gap as a position, then you should take the sequence that has no gaps for the numbering reference. From the texshade manual (page 58): showruler[〈color〉]{〈position〉}{〈seqref〉}
– Joe H.
Sep 6 '17 at 7:58
What is it that you want to do? The numbering is by default relative to the first sequence, and "-" is a gap, so not counted. If you want your numbering to include this gap as a position, then you should take the sequence that has no gaps for the numbering reference. From the texshade manual (page 58): showruler[〈color〉]{〈position〉}{〈seqref〉}
– Joe H.
Sep 6 '17 at 7:58
add a comment |
1 Answer
1
active
oldest
votes
up vote
0
down vote
You can add in a Dummy sequence on the second line with no gaps:
>Dummy
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
And then use the commands:
showruler{2}{top}
hideseq{2}
to use it for numbering and prevent it from being displayed. This will fix the numbering.
answered Dec 13 '17 at 17:22
Nick
1011
add a comment |
1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
0
down vote
You can add in a Dummy sequence on the second line with no gaps:
>Dummy
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
And then use the commands:
showruler{2}{top}
hideseq{2}
to use it for numbering and prevent it from being displayed. This will fix the numbering.
answered Dec 13 '17 at 17:22
Nick
1011
add a comment |
up vote
0
down vote
You can add in a Dummy sequence on the second line with no gaps:
>Dummy
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
And then use the commands:
showruler{2}{top}
hideseq{2}
to use it for numbering and prevent it from being displayed. This will fix the numbering.
answered Dec 13 '17 at 17:22
Nick
1011
add a comment |
up vote
0
down vote
up vote
0
down vote
You can add in a Dummy sequence on the second line with no gaps:
>Dummy
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
And then use the commands:
showruler{2}{top}
hideseq{2}
to use it for numbering and prevent it from being displayed. This will fix the numbering.
answered Dec 13 '17 at 17:22
Nick
1011
You can add in a Dummy sequence on the second line with no gaps:
>Dummy
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
And then use the commands:
showruler{2}{top}
hideseq{2}
to use it for numbering and prevent it from being displayed. This will fix the numbering.
answered Dec 13 '17 at 17:22
Nick
1011
answered Dec 13 '17 at 17:22
Nick
1011
answered Dec 13 '17 at 17:22
Nick
1011
answered Dec 13 '17 at 17:22
Nick
1011
1011
add a comment |
add a comment |
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1
This seems to be a feature, the germline line is the reference sequence, and the numbering follows the reference, which seems to be a valid consideration. I don't think
texshadeprovides an option to change this. It could be done by changing the package source, but that is a rather difficult task.– Marijn
Jan 20 '17 at 20:56
1
What is it that you want to do? The numbering is by default relative to the first sequence, and "-" is a gap, so not counted. If you want your numbering to include this gap as a position, then you should take the sequence that has no gaps for the numbering reference. From the texshade manual (page 58): showruler[〈color〉]{〈position〉}{〈seqref〉}
– Joe H.
Sep 6 '17 at 7:58