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Aflitos, Saulo Alves
mapper
Commits
9b2ca054
Commit
9b2ca054
authored
12 years ago
by
Aflitos, Saulo Alves
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bug fix
parent
c4347ffc
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.gitignore
+1
-0
1 addition, 0 deletions
.gitignore
SConstruct.run
+1
-0
1 addition, 0 deletions
SConstruct.run
SConstruct.tree.sh
+1
-1
1 addition, 1 deletion
SConstruct.tree.sh
all.csv
+13
-0
13 additions, 0 deletions
all.csv
run2.py
+183
-121
183 additions, 121 deletions
run2.py
sp1/sp.csv
+11
-11
11 additions, 11 deletions
sp1/sp.csv
with
210 additions
and
133 deletions
.gitignore
+
1
−
0
View file @
9b2ca054
...
@@ -6,3 +6,4 @@
...
@@ -6,3 +6,4 @@
*.dot
*.dot
*.png
*.png
*.html
*.html
*.out
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SConstruct.run
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9b2ca054
#!/bin/bash
#!/bin/bash
set
-xeu
LOGFILE
=
"SConstruct.run.log."
`
date
+%Y%m%d_%H%M%S
`
".out"
LOGFILE
=
"SConstruct.run.log."
`
date
+%Y%m%d_%H%M%S
`
".out"
#echo "LOGFILE $LOGFILE"
#echo "LOGFILE $LOGFILE"
python scons/scons.py
-n
--stack-size
=
1024
--diskcheck
=
none
$@
2>&1 |
tee
$LOGFILE
python scons/scons.py
-n
--stack-size
=
1024
--diskcheck
=
none
$@
2>&1 |
tee
$LOGFILE
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SConstruct.tree.sh
+
1
−
1
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9b2ca054
...
@@ -4,7 +4,7 @@ rm SConstruct.tree.png 2>/dev/null
...
@@ -4,7 +4,7 @@ rm SConstruct.tree.png 2>/dev/null
rm
SConstruct.tree.gif 2>/dev/null
rm
SConstruct.tree.gif 2>/dev/null
rm
SConstruct.tree.html 2>/dev/null
rm
SConstruct.tree.html 2>/dev/null
bash SConstruct.run
-n
--tree
=
prune,status
$@
>
SConstruct.tree.dat
bash SConstruct.run
-n
--tree
=
prune,status
$@
|
grep
-v
'+-/'
>
SConstruct.tree.dat
#,derived
#,derived
cat
SConstruct.tree.dat | python SConstruct.graph.py
$@
cat
SConstruct.tree.dat | python SConstruct.graph.py
$@
...
...
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all.csv
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9b2ca054
#in fasta in csv
sa1/sa.fa sa1/sa.csv
#sa2/sa.fa sa2/sa.csv
sh1/sh.fa sh1/sh.csv
#sh2/sh.fa sh2/sh.csv
#sl1/sl.fa sl1/sl.csv
#sl2/sl.fa sl2/sl.csv
sp1/sp.fa sp1/sp.csv
#sp2/sp.fa sp2/sp.csv
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run2.py
+
183
−
121
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9b2ca054
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sp1/sp.csv
+
11
−
11
View file @
9b2ca054
#group name platform library name library size library size min library size max file names
#group name platform library name library size library size min library size max file names
1205
1
2_I238_FC
C0U42
ACXX_L
1
_SZAXPI00
8753-79
illumina pe
500 450 550
/home/assembly/tomato150/
reseq/raw/074
/illumina/pairedend_
50
0/1205
1
2_I238_FC
C0U42
ACXX_L
1
_SZAXPI00
8753-79_1
.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/
reseq/raw/074
/illumina/pairedend_
50
0/1205
1
2_I238_FC
C0U42
ACXX_L
1
_SZAXPI00
8753-79_2
.fq.gz.clean.dup.clean.gz
12052
4
_I238_FC
D1174
ACXX_L
4
_SZAXPI00
9266-140
illumina pe
170 153 187
/home/assembly/tomato150/
denovo/pennellii/filtered
/illumina/pairedend_
17
0/12052
4
_I238_FC
D1174
ACXX_L
4
_SZAXPI00
9266-140_2
.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/
denovo/pennellii/filtered
/illumina/pairedend_
17
0/12052
4
_I238_FC
D1174
ACXX_L
4
_SZAXPI00
9266-140_1
.fq.gz.clean.dup.clean.gz
1205
24
_I23
8
_FC
D1174
ACXX_L4_SZAXPI009266-140 illumina pe 170 153 187 /home/assembly/tomato150/denovo/pennellii/
raw
/illumina/pairedend_170/1205
24
_I23
8
_FC
D1174
ACXX_L4_SZAXPI009266-140_
2
.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
raw
/illumina/pairedend_170/1205
24
_I23
8
_FC
D1174
ACXX_L4_SZAXPI009266-140_
1
.fq.gz.clean.dup.clean.gz
1205
30
_I23
5
_FC
C0U06
ACXX_L4_SZAXPI009266-140 illumina pe 170 153 187 /home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/pairedend_170/1205
30
_I23
5
_FC
C0U06
ACXX_L4_SZAXPI009266-140_
1
.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/pairedend_170/1205
30
_I23
5
_FC
C0U06
ACXX_L4_SZAXPI009266-140_
2
.fq.gz.clean.dup.clean.gz
120530_I235_FC
C0U06
ACXX_L
4
_SZAXPI009266-140 illumina pe 170 153 187 /home/assembly/tomato150/denovo/pennellii/
raw
/illumina/pairedend_170/120530_I235_FC
C0U06
ACXX_L
4
_SZAXPI009266-140_
1
.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
raw
/illumina/pairedend_170/120530_I235_FC
C0U06
ACXX_L
4
_SZAXPI009266-140_
2
.fq.gz.clean.dup.clean.gz
120530_I235_FC
D117Y
ACXX_L
1
_SZAXPI009266-140 illumina pe 170 153 187 /home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/pairedend_170/120530_I235_FC
D117Y
ACXX_L
1
_SZAXPI009266-140_
2
.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/pairedend_170/120530_I235_FC
D117Y
ACXX_L
1
_SZAXPI009266-140_
1
.fq.gz.clean.dup.clean.gz
1205
30
_I23
5
_FC
D117Y
ACXX_L1_SZAXPI00
9266-140
illumina pe
170 153 187
/home/assembly/tomato150/
denovo/pennellii/raw
/illumina/pairedend_
17
0/1205
30
_I23
5
_FC
D117Y
ACXX_L1_SZAXPI00
9266-140_2
.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/
denovo/pennellii/raw
/illumina/pairedend_
17
0/1205
30
_I23
5
_FC
D117Y
ACXX_L1_SZAXPI00
9266-140_1
.fq.gz.clean.dup.clean.gz
1205
12
_I23
8
_FC
C0U42
ACXX_L1_SZAXPI00
8753-79
illumina pe
500 450 550
/home/assembly/tomato150/
reseq/filtered/074
/illumina/pairedend_
50
0/1205
12
_I23
8
_FC
C0U42
ACXX_L1_SZAXPI00
8753-79_1
.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/
reseq/filtered/074
/illumina/pairedend_
50
0/1205
12
_I23
8
_FC
C0U42
ACXX_L1_SZAXPI00
8753-79_2
.fq.gz.clean.dup.clean.gz
120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120530_I235_FCD117YACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz
120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120615_I248_FCD14ADACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz
120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz
120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120624_I232_FCC0U3HACXX_L6_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz
120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120524_I238_FCD1174ACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
raw
/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89 illumina mp 2000 1800 2200 /home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89_2.fq.gz.clean.dup.clean.gz;/home/assembly/tomato150/denovo/pennellii/
filtered
/illumina/matepair_2000/120527_I247_FCC0U0NACXX_L8_TOMxitDGLDWAAPEI-89_1.fq.gz.clean.dup.clean.gz
20000.dedup
454 mp
20000
18000
22000
/home/assembly/tomato150/denovo/pennellii/filtered/454/20000/20000.dedup.sff
20000.dedup
454 mp
20000
18000
22000
/home/assembly/tomato150/denovo/pennellii/filtered/454/20000/20000.dedup.sff
8000.dedup
454 mp 8000 7200 8800
/home/assembly/tomato150/denovo/pennellii/filtered/454/8000/8000.dedup.sff
8000.dedup
454 mp 8000 7200 8800
/home/assembly/tomato150/denovo/pennellii/filtered/454/8000/8000.dedup.sff
3000.dedup 454 mp 3000 2700 3300 /home/assembly/tomato150/denovo/pennellii/filtered/454/3000/3000.dedup.sff
3000.dedup 454 mp 3000 2700 3300 /home/assembly/tomato150/denovo/pennellii/filtered/454/3000/3000.dedup.sff
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