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Aflitos, Saulo Alves
webmummer
Commits
734f5d20
There was a problem fetching the pipeline summary.
Commit
734f5d20
authored
9 years ago
by
Saulo Aflitos
Browse files
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run.sh
parent
8491a61d
Branches
develop
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Pipeline
#
Changes
5
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1
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5 changed files
.gitignore
+1
-0
1 addition, 0 deletions
.gitignore
config.py
+13
-20
13 additions, 20 deletions
config.py
delta2js.py
+11
-7
11 additions, 7 deletions
delta2js.py
mummer_iterate.py
+38
-28
38 additions, 28 deletions
mummer_iterate.py
run.sh
+19
-0
19 additions, 0 deletions
run.sh
with
82 additions
and
55 deletions
.gitignore
+
1
−
0
View file @
734f5d20
...
...
@@ -2,3 +2,4 @@ data/*
*.tar.xz
*.pyc
Thumbs.db
*~
This diff is collapsed.
Click to expand it.
config.py
+
13
−
20
View file @
734f5d20
genomes
=
{
'
ath
'
:
{
'
name
'
:
'
Arabidopsis thaliana
'
,
'
folder
'
:
'
arabidopsis_thaliana
'
,
'
prefix
'
:
'
Arabidopsis_thaliana.TAIR10.18.dna.chromosome.
'
,
'
begin
'
:
1
,
'
end
'
:
5
,
'
fmt
'
:
'
%d
'
},
'
bol
'
:
{
'
name
'
:
'
Brassica oleracea
'
,
'
folder
'
:
'
brassica_oleracea
'
,
'
prefix
'
:
''
,
'
begin
'
:
1
,
'
end
'
:
9
,
'
fmt
'
:
'
%d
'
'
sly
'
:
{
'
name
'
:
'
Solanum lycopersicum
'
,
'
folder
'
:
'
Solanum_lycopersicum
'
,
'
prefix
'
:
'
SL2.40ch
'
,
'
begin
'
:
0
,
'
end
'
:
12
,
'
fmt
'
:
'
%02d
'
},
'
bra
'
:
{
'
name
'
:
'
Brassica rapa
'
,
'
folder
'
:
'
brassica_rapa
'
,
'
prefix
'
:
'
ch
rA
'
,
'
stu
'
:
{
'
name
'
:
'
Solanum tuberosum
'
,
'
folder
'
:
'
Solanum_tuberosum
'
,
'
prefix
'
:
'
ST4.03
ch
'
,
'
begin
'
:
1
,
'
end
'
:
1
0
,
'
end
'
:
1
2
,
'
fmt
'
:
'
%02d
'
}
}
...
...
@@ -31,6 +23,7 @@ notindestiny = ['slyref']
dosymetrical
=
False
doreciprocal
=
True
create_make_file
=
True
create_html
=
False
#maxX = 1
#maxY = 2
This diff is collapsed.
Click to expand it.
delta2js.py
+
11
−
7
View file @
734f5d20
...
...
@@ -192,8 +192,11 @@ class exp(object):
self
.
linec
+=
1
minx
=
x1
if
x1
<
x2
else
x2
maxx
=
x1
if
x1
>
x2
else
x2
minx
=
x1
if
(
x1
<
x2
)
else
x2
maxx
=
x1
if
(
x1
>
x2
)
else
x2
print
"
minx %d maxx %d x1 %d x2 %d
"
%
(
minx
,
maxx
,
x1
,
x2
)
assert
minx
<
maxx
,
"
minx (%d) > maxx(%d) for %s
"
%
(
minx
,
maxx
,
name
)
if
name
not
in
self
.
tgts
:
self
.
tgts
[
name
]
=
len
(
self
.
tgts
)
...
...
@@ -207,7 +210,8 @@ class exp(object):
gffId
=
"
%s_frag_%05d
"
%
(
refName
+
'
_
'
+
name
,
len
(
self
.
gffReg
[
name
]
)
)
gffName
=
"
%s_frag_%05d
"
%
(
name
,
len
(
self
.
gffReg
[
name
]
)
)
self
.
gffReg
[
name
].
append
(
[
refName
,
'
.
'
,
'
CDS
'
,
minx
,
maxx
,
'
.
'
,
'
+
'
if
sense
==
'
fwd
'
else
'
-
'
,
len
(
self
.
gffReg
[
name
]
)
-
1
,
'
ID=%s;Name=%s;Parent=%s
'
%
(
gffId
,
gffName
,
refName
+
'
_
'
+
name
)
]
)
#self.gffReg[name].append( [refName, '.', 'CDS', minx, maxx, '.', '+' if sense == 'fwd' else '-', len( self.gffReg[ name ] )-1, 'ID=%s;Name=%s;Parent=%s' % (gffId, gffName, refName+'_'+name) ] )
self
.
gffReg
[
name
].
append
(
[
refName
,
'
.
'
,
'
CDS
'
,
minx
,
maxx
,
'
.
'
,
'
+
'
if
sense
==
'
fwd
'
else
'
-
'
,
0
,
'
ID=%s;Name=%s;Parent=%s
'
%
(
gffId
,
gffName
,
refName
+
'
_
'
+
name
)
]
)
self
.
gffReg
[
name
][
0
][
4
]
=
maxx
name
=
self
.
tgts
[
name
]
...
...
@@ -321,10 +325,10 @@ def parseDelta(delta):
#print "identity %.2f" % ( idd )
#print
refMin
=
min
(
refStart
,
refEnd
)
refMax
=
max
(
refStart
,
refEnd
)
tgtMin
=
min
(
tgtStart
,
tgtEnd
)
tgtMax
=
max
(
tgtStart
,
tgtEnd
)
refMin
=
min
(
[
refStart
,
refEnd
]
)
refMax
=
max
(
[
refStart
,
refEnd
]
)
tgtMin
=
min
(
[
tgtStart
,
tgtEnd
]
)
tgtMax
=
max
(
[
tgtStart
,
tgtEnd
]
)
d
=
[
refStart
,
refEnd
,
tgtStart
,
tgtEnd
,
refLen
,
tgtLen
,
refSub
,
tgtSub
,
idd
,
refName
,
tgtName
]
#print d
...
...
This diff is collapsed.
Click to expand it.
mummer_iterate.py
+
38
−
28
View file @
734f5d20
...
...
@@ -12,6 +12,7 @@ notindestiny = []
dosymetrical
=
True
doreciprocal
=
True
create_make_file
=
True
create_html
=
False
html2pdf
=
None
pdf2img
=
None
maxX
=
-
1
...
...
@@ -162,18 +163,18 @@ def mapgenomes( org1, org2 ):
alt
=
"
%s chr %s vs %s chr %s
"
%
(
org1name
,
org1str
,
org2name
,
org2str
)
reportouter
.
append
(
'
\t\t\t\t
<td><img src=
"
%s
"
title=
"
%s
"
/></td>
'
%
(
outpngl
,
alt
))
cmd1
=
"
../
nucmer -o -p %s %s %s
"
%
(
outname
,
org2fasta
,
org1fasta
)
cmd1
=
"
nucmer -o -p %s %s %s
"
%
(
outname
,
org2fasta
,
org1fasta
)
makefile
.
append
(
outdelta
+
'
:
'
+
org1fasta
+
'
'
+
org2fasta
)
makefile
.
append
(
'
\t
%s
\n
'
%
cmd1
)
cmd2
=
'
../
mummerplot -f -p %s --large --png %s
'
%
(
outdelta
,
outdelta
)
cmd2
=
'
mummerplot -f -p %s --large --png %s
'
%
(
outdelta
,
outdelta
)
makefile
.
append
(
outpng
+
'
'
+
outfilter
+
'
:
'
+
outdelta
)
#makefile.append('\tif [ $( shell cat %s | wc -l ) -gt 2 ]; then %s; else touch %s; touch %s; fi\n' % (outdelta, cmd2, outpng, outfilter))
makefile
.
append
(
'
\t
%s
\n
'
%
(
cmd2
))
outfiles
.
append
(
outpng
)
cmd3
=
'
../
show-aligns -r %s.filter
"
%s
"
"
%s
"
> %s
'
%
(
outdelta
,
org2seqname
,
org1seqname
,
outaln
)
cmd3
=
'
show-aligns -r %s.filter
"
%s
"
"
%s
"
> %s
'
%
(
outdelta
,
org2seqname
,
org1seqname
,
outaln
)
makefile
.
append
(
outaln
+
'
:
'
+
outfilter
)
makefile
.
append
(
'
\t
%s
\n
'
%
cmd3
)
outfiles
.
append
(
outaln
)
...
...
@@ -494,36 +495,45 @@ def main():
print
"
creating html
"
genHtml
(
divnames
)
print
"
creating html ok
"
if
create_html
:
print
"
creating html
"
genHtml
(
divnames
)
print
"
creating html ok
"
if
create_make_file
:
print
"
creating makefile
"
html
=
'
report.html.tar.xz
'
makefile
.
append
(
html
+
'
:
'
+
"
"
.
join
(
allfiles
))
makefile
.
append
(
'
\t
tar --exclude=report.html.png -acvf %s *.html */*.html */*.png
\n
'
%
html
)
png
=
'
report.png.tar.xz
'
makefile
.
append
(
png
+
'
:
'
+
"
"
.
join
(
allfiles
))
makefile
.
append
(
'
\t
tar -acvf %s */report.html.png
\n
'
%
png
)
pdf
=
'
report.pdf.tar.xz
'
makefile
.
append
(
pdf
+
'
:
'
+
"
"
.
join
(
allfiles
))
makefile
.
append
(
'
\t
tar -acvf %s */report.html.pdf
\n
'
%
pdf
)
allf
=
'
report.all.tar.xz
'
makefile
.
append
(
allf
+
'
:
'
+
"
"
.
join
(
allfiles
))
makefile
.
append
(
'
\t
tar -acvf %s *.html */*.html */*.png */*.pdf
\n
'
%
allf
)
allr
=
'
report.raw.tar.xz
'
makefile
.
append
(
allr
+
'
:
'
+
"
"
.
join
(
allfiles
))
makefile
.
append
(
'
\t
tar -acvf %s */*.coords */*.delta */*.filter */*.aln */*.fplot */*.rplot */*.gp
\n
'
%
allr
)
allstr
=
'
all:
'
+
"
"
.
join
(
[
html
,
png
,
pdf
,
allf
,
allr
]
)
+
"
\n
"
makefile
.
insert
(
0
,
allstr
)
if
create_html
:
html
=
'
report.html.tar.xz
'
makefile
.
append
(
html
+
'
:
'
+
"
"
.
join
(
allfiles
))
makefile
.
append
(
'
\t
tar --exclude=report.html.png -acvf %s *.html */*.html */*.png
\n
'
%
html
)
png
=
'
report.png.tar.xz
'
makefile
.
append
(
png
+
'
:
'
+
"
"
.
join
(
allfiles
))
makefile
.
append
(
'
\t
tar -acvf %s */report.html.png
\n
'
%
png
)
pdf
=
'
report.pdf.tar.xz
'
makefile
.
append
(
pdf
+
'
:
'
+
"
"
.
join
(
allfiles
))
makefile
.
append
(
'
\t
tar -acvf %s */report.html.pdf
\n
'
%
pdf
)
allf
=
'
report.all.tar.xz
'
makefile
.
append
(
allf
+
'
:
'
+
"
"
.
join
(
allfiles
))
makefile
.
append
(
'
\t
tar -acvf %s *.html */*.html */*.png */*.pdf
\n
'
%
allf
)
allr
=
'
report.raw.tar.xz
'
makefile
.
append
(
allr
+
'
:
'
+
"
"
.
join
(
allfiles
))
makefile
.
append
(
'
\t
tar -acvf %s */*.coords */*.delta */*.filter */*.aln */*.fplot */*.rplot */*.gp
\n
'
%
allr
)
allstr
=
'
all:
'
+
"
"
.
join
(
[
html
,
png
,
pdf
,
allf
,
allr
]
)
+
"
\n
"
makefile
.
insert
(
0
,
allstr
)
else
:
allr
=
'
report.raw.tar.xz
'
makefile
.
append
(
allr
+
'
:
'
+
"
"
.
join
(
allfiles
))
makefile
.
append
(
'
\t
tar -acvf %s */*.coords */*.delta */*.filter */*.aln */*.fplot */*.rplot */*.gp
\n
'
%
allr
)
allstr
=
'
all:
'
+
"
"
.
join
(
[
allr
]
)
+
"
\n
"
makefile
.
insert
(
0
,
allstr
)
...
...
This diff is collapsed.
Click to expand it.
run.sh
0 → 100644
+
19
−
0
View file @
734f5d20
1861
ln
-s
/media/lidija/bigDisk/W05-SolEtu/00-genomes/ input
1863
mkdir
Solanum_tuberosum
1864
cd
Solanum_tuberosum/
1865 fastaexplode ../input/SolTub-PGSC_DM_v4.03_pseudomolecules.fasta
1868
cd
..
1869
mkdir
Solanum_lycopersicum
1870
cd
Solanum_lycopersicum/
1871 fastaexplode ../input/SolLyc-genome-chromosomes.2.40.fa
python mummer_iterate.py config.py
make
-f
makefile
cd
data
../delta2js.py ../config_ath.py ../sly_sly/
*
.delta ../sly_stu/
*
.delta ../stu_stu/
*
.delta
cp
../sly_sly/
*
.js sly_stu/
*
.js stu_stu/
*
.js
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