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tomachinztomachinz
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html pages much improved
1 parent 941056b commit 3491256

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+453
-520
lines changed

‎build-credits.sh‎

Lines changed: 25 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -2,33 +2,37 @@
22
CREDITS="src/public/credits.txt"
33
TIMESTAMP=$(date +%s)
44
DATE=$(date)
5-
TOMSSOURCE="toms_source_temp.txt"
6-
echo GENERATE CREDITS.TXT FILE
5+
TOMSSOURCE="build/temp_file_for_credits.txt"
6+
echo GENERATE CREDITS.TXT FILE at $CREDITS
7+
echo
78
mkdir -p build
8-
rm -rf build/TOBEDELETED
9-
mv build/* build/TOBEDELETED
9+
10+
rm -f $TOMSSOURCE
1011
rm -v $CREDITS
12+
touch $TOMSSOURCE
13+
touch $CREDITS
14+
cp src/ascii-logo.txt $CREDITS
15+
tail -f $CREDITS &
1116

17+
cat src/public/aminosee-gui-web.js >> $TOMSSOURCE
18+
cat src/public/aminosee-web-socket.js >> $TOMSSOURCE
19+
cat src/aminosee-html-template.js >> $TOMSSOURCE
20+
cat src/aminosee-server.js >> $TOMSSOURCE
21+
cat src/aminosee-data.js >> $TOMSSOURCE
22+
cat src/aminosee-cli.js >> $TOMSSOURCE
23+
# cat src/aminosee-carlo.js >> $TOMSSOURCE
24+
cat src/aminosee-settings.js >> $TOMSSOURCE
25+
cat src/aminosee-version.js >> $TOMSSOURCE
26+
cat src/aminosee-stdinpipe.js >> $TOMSSOURCE
27+
# cat src/main.js >> $TOMSSOURCE
28+
# cat src/renderer.js >> $TOMSSOURCE
29+
# cat src/console.js >> $TOMSSOURCE
30+
cat src/ascii-logo.txt >> $TOMSSOURCE
31+
cat src/index.html >> $TOMSSOURCE
1232

13-
cat src/public/aminosee-gui-web.js >> build/toms_source.txt
14-
cat src/public/aminosee-web-socket.js >> build/toms_source.txt
15-
cat src/aminosee-server.js >> build/toms_source.txt
16-
cat src/aminosee-data.js >> build/toms_source.txt
17-
cat src/aminosee-cli.js >> build/toms_source.txt
18-
cat src/aminosee-carlo.js >> build/toms_source.txt
19-
cat src/aminosee-settings.js >> build/toms_source.txt
20-
cat src/aminosee-version.js >> build/toms_source.txt
21-
cat src/aminosee-stdinpipe.js >> build/toms_source.txt
22-
# cat src/main.js >> build/toms_source.txt
23-
# cat src/renderer.js >> build/toms_source.txt
24-
# cat src/console.js >> build/toms_source.txt
25-
cat src/ascii-logo.txt >> build/toms_source.txt
26-
cat src/index.html >> build/toms_source.txt
33+
LINES=$(cat $TOMSSOURCE | wc -l)
2734

28-
LINES=$(cat build/toms_source.txt | wc -l)
2935

30-
cp src/ascii-logo.txt $CREDITS
31-
tail -f $CREDITS &
3236
echo >> $CREDITS
3337
echo "Thanks to Christos Georghiou who designed the 'See No Evil Hear No Evil Monkeys' http://christosgeorghiou.com/" >> $CREDITS
3438
echo >> $CREDITS

‎dna/batch-peptides.sh‎

Lines changed: 50 additions & 49 deletions
Original file line numberDiff line numberDiff line change
@@ -72,58 +72,58 @@ series_peptides () {
7272
find_way_peptides () {
7373

7474
echo
75-
nice -n 1 aminosee *
76-
nice -n 2 aminosee * --peptide=Glutamic_acid
77-
nice -n 2 aminosee * --peptide=Aspartic_acid
78-
nice -n 2 aminosee * --peptide=Ochre
79-
nice -n 2 aminosee * --peptide=Amber
80-
nice -n 2 aminosee * --peptide=Opal
81-
nice -n 2 aminosee * --peptide=Methionine
82-
nice -n 2 aminosee * --peptide=Cysteine
83-
nice -n 2 aminosee * --peptide=Glycine
84-
nice -n 2 aminosee * --peptide=Alanine
85-
nice -n 2 aminosee * --peptide=Valine
86-
nice -n 2 aminosee * --peptide=Leucine
87-
nice -n 2 aminosee * --peptide=Isoleucine
88-
nice -n 2 aminosee * --peptide=Phenylalanine
89-
nice -n 2 aminosee * --peptide=Proline
90-
nice -n 2 aminosee * --peptide=Tryptophan
91-
nice -n 2 aminosee * --peptide=Serine
92-
nice -n 2 aminosee * --peptide=Threonine
93-
nice -n 2 aminosee * --peptide=Glutamine
94-
nice -n 2 aminosee * --peptide=Asparagine
95-
nice -n 2 aminosee * --peptide=Tyrosine
96-
nice -n 2 aminosee * --peptide=Arginine
97-
nice -n 2 aminosee * --peptide=Lysine
98-
nice -n 2 aminosee * --peptide=Histidine
75+
nice -n 1 aminosee $*
76+
nice -n 2 aminosee $* --peptide=Glutamic_acid
77+
nice -n 2 aminosee $* --peptide=Aspartic_acid
78+
nice -n 2 aminosee $* --peptide=Ochre
79+
nice -n 2 aminosee $* --peptide=Amber
80+
nice -n 2 aminosee $* --peptide=Opal
81+
nice -n 2 aminosee $* --peptide=Methionine
82+
nice -n 2 aminosee $* --peptide=Cysteine
83+
nice -n 2 aminosee $* --peptide=Glycine
84+
nice -n 2 aminosee $* --peptide=Alanine
85+
nice -n 2 aminosee $* --peptide=Valine
86+
nice -n 2 aminosee $* --peptide=Leucine
87+
nice -n 2 aminosee $* --peptide=Isoleucine
88+
nice -n 2 aminosee $* --peptide=Phenylalanine
89+
nice -n 2 aminosee $* --peptide=Proline
90+
nice -n 2 aminosee $* --peptide=Tryptophan
91+
nice -n 2 aminosee $* --peptide=Serine
92+
nice -n 2 aminosee $* --peptide=Threonine
93+
nice -n 2 aminosee $* --peptide=Glutamine
94+
nice -n 2 aminosee $* --peptide=Asparagine
95+
nice -n 2 aminosee $* --peptide=Tyrosine
96+
nice -n 2 aminosee $* --peptide=Arginine
97+
nice -n 2 aminosee $* --peptide=Lysine
98+
nice -n 2 aminosee $* --peptide=Histidine
9999
echo
100100
echo end of batch peptides
101101

102102
# echo
103-
# nice -n 1 aminosee --index -m5 *
104-
# nice -n 2 aminosee -m5 --quiet * --peptide=Glutamic_acid
105-
# nice -n 2 aminosee -m5 --quiet * --peptide=Aspartic_acid
106-
# nice -n 2 aminosee -m5 --quiet * --peptide=Ochre
107-
# nice -n 2 aminosee -m5 --quiet * --peptide=Amber
108-
# nice -n 2 aminosee -m5 --quiet * --peptide=Opal
109-
# nice -n 2 aminosee -m5 --quiet * --peptide=Methionine
110-
# nice -n 2 aminosee -m5 --quiet * --peptide=Cysteine
111-
# nice -n 2 aminosee -m5 --quiet * --peptide=Glycine
112-
# nice -n 2 aminosee -m5 --quiet * --peptide=Alanine
113-
# nice -n 2 aminosee -m5 --quiet * --peptide=Valine
114-
# nice -n 2 aminosee --index -m5 * --peptide=Leucine
115-
# nice -n 2 aminosee -m5 --quiet * --peptide=Isoleucine
116-
# nice -n 2 aminosee -m5 --quiet * --peptide=Phenylalanine
117-
# nice -n 2 aminosee -m5 --quiet * --peptide=Proline
118-
# nice -n 2 aminosee -m5 --quiet * --peptide=Tryptophan
119-
# nice -n 2 aminosee -m5 --quiet * --peptide=Serine
120-
# nice -n 2 aminosee -m5 --quiet * --peptide=Threonine
121-
# nice -n 2 aminosee -m5 --quiet * --peptide=Glutamine
122-
# nice -n 2 aminosee -m5 --quiet * --peptide=Asparagine
123-
# nice -n 2 aminosee -m5 --quiet * --peptide=Tyrosine
124-
# nice -n 2 aminosee -m5 --quiet * --peptide=Arginine
125-
# nice -n 2 aminosee -m5 --quiet * --peptide=Lysine
126-
# nice -n 2 aminosee -m5 * --peptide=Histidine
103+
# nice -n 1 aminosee --index -m5 $*
104+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Glutamic_acid
105+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Aspartic_acid
106+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Ochre
107+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Amber
108+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Opal
109+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Methionine
110+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Cysteine
111+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Glycine
112+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Alanine
113+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Valine
114+
# nice -n 2 aminosee --index -m5 $* --peptide=Leucine
115+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Isoleucine
116+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Phenylalanine
117+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Proline
118+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Tryptophan
119+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Serine
120+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Threonine
121+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Glutamine
122+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Asparagine
123+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Tyrosine
124+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Arginine
125+
# nice -n 2 aminosee -m5 --quiet $* --peptide=Lysine
126+
# nice -n 2 aminosee -m5 $* --peptide=Histidine
127127
# echo
128128
# echo end of batch peptides
129129

@@ -134,7 +134,7 @@ find_way_peptides () {
134134
# if [ $(uname)="Darwin" ]; then
135135
# echo macos
136136
# # DASHF=" -f "
137-
# DASHF=" -L * | grep -E \"(txt|mfa|gbk|txt|fa)\""
137+
# DASHF=" -L $* | grep -E \"(txt|mfa|gbk|txt|fa)\""
138138
# fi
139139
#
140140
# if [ $(uname)="Linux" ]; then
@@ -230,6 +230,7 @@ if [ -z "$1" ]; then
230230
echo ow doing "find way" brute forcing it
231231
# exit
232232
find_way_peptides
233+
find_way_peptides --reg --index
233234
else
234235
series_peptides $*
235236
fi

‎dna/batch-sizes.sh‎

Lines changed: 10 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,7 @@ FAST=megabase.fa
33
QUICK=Caenorhabditis_elegans-WBcel235-dna-chromosome-V.fa
44

55
aminosee_do () {
6-
nice -n 8 aminosee --quiet --ratio=sqr --reg $* &
7-
sleep 2
6+
nice -n 8 aminosee --force --quiet --ratio=sqr --reg $*
87
}
98

109

@@ -16,11 +15,15 @@ many_size_hilbert() {
1615
echo "-------------------------------------------"
1716
echo " =///"
1817

19-
aminosee -m10 --quiet --ratio=sqr --reg $* &
20-
aminosee_do -m9 $*
21-
aminosee_do -m8 $*
22-
aminosee_do -m7 $*
23-
aminosee_do -m6 $*
18+
# aminosee -m10 --quiet --ratio=sqr --reg $* &
19+
aminosee_do -m9 $* &
20+
sleep 3
21+
aminosee_do -m8 $* &
22+
sleep 3
23+
aminosee_do -m7 $* &
24+
sleep 3
25+
aminosee_do -m6 $* &
26+
sleep 3
2427
aminosee_do -m5 $*
2528

2629
# aminosee_do $*

‎dna/find-rm-reference.sh‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
#!/bin/bash
22
# example: AminoSee_BUSY_LOCK_Pongoabelii._c11__Lysine_fix_sci.txt
33
# COMMAND=" find . | grep AminoSee_BUSY_LOCK "
4-
MACCOMMAND="find ~/AminoSee_webroot/output/ | grep Reference "
4+
MACCOMMAND="find ~/AminoSee_webroot/output/* | grep Reference "
55
LINUXCOMMAND="find ~/AminoSee_webroot/output/ | grep Reference "
66
PREVIEW="$1 | xargs $XARGPARAM $ ls -laH $ "
77
DELETE="$1 | xargs $XARGPARAM $ rm -v $ "

‎dna/find-rm-touch-files.sh‎

Lines changed: 5 additions & 35 deletions
Original file line numberDiff line numberDiff line change
@@ -1,55 +1,25 @@
11
#!/bin/bash
22
# example: AminoSee_BUSY_LOCK_Pongoabelii._c11__Lysine_fix_sci.txt
33
# COMMAND=" find . | grep AminoSee_BUSY_LOCK "
4-
COMMAND=" find ~/AminoSee_webroot/ | grep AminoSee_BUSY_LOCK "
4+
COMMAND=" find ~/AminoSee_webroot/ | grep LOCK "
55
PREVIEW="$1 | xargs $XARGPARAM $ ls -laH $ "
66
DELETE="$1 | xargs $XARGPARAM $ rm -v $ "
77

88

99

1010
if [ $(uname)=Darwin ]; then
1111
echo macos
12-
find -f ~/AminoSee_webroot/ | grep AminoSee_BUSY_LOCK | xargs -J $ ls -laH $
12+
find -f ~/AminoSee_webroot/ | grep LOCK | xargs -J $ ls -laH $
1313
echo "DELETING THE FILES ABOVE IN 7 SECONDS"
1414
sleep 7
15-
find -f ~/AminoSee_webroot/ | grep AminoSee_BUSY_LOCK | xargs -J $ rm -v $
15+
find -f ~/AminoSee_webroot/ | grep LOCK | xargs -J $ rm -v $
1616
fi
1717

1818
if [ $(uname)=Linux ]; then
1919
echo linux
20-
find ~/AminoSee_webroot/ | grep AminoSee_BUSY_LOCK | xargs -I $ ls -laH $
20+
find ~/AminoSee_webroot/ | grep LOCK | xargs -I $ ls -laH $
2121
echo "DELETING THE FILES ABOVE IN 7 SECONDS"
2222
sleep 7
23-
find ~/AminoSee_webroot/ | grep AminoSee_BUSY_LOCK | xargs -I $ rm -v $
23+
find ~/AminoSee_webroot/ | grep LOCK | xargs -I $ rm -v $
2424

2525
fi
26-
27-
28-
29-
#
30-
#
31-
#
32-
#
33-
#
34-
#
35-
# pwd
36-
# echo find $DASHF . -name $LOCKFILES
37-
# find $DASHF . -name $LOCKFILES
38-
#
39-
# echo "About to delete these touch files matching: $LOCKFILES"
40-
# sleep 5
41-
# echo "Deleting these touch files: $LOCKFILES"
42-
# find $DASHF . -name $LOCKFILES -exec rm -v {} \;
43-
# find ./output/ -name AminoSee_BUSY_LOCK*.txt -exec rm -v {} \;
44-
# find ./output/ -name AminoSee_BUSY_LOCK*.txt -exec rm -v {} \;
45-
# find . -name 'AminoSee_BUSY_LOCK*.txt' -exec rm -v {} \;
46-
# sleep 2
47-
48-
# find -f ./output/ 'AminoSee_BUSY_LOCK*.txt'
49-
# find -f ./output/ | grep linear | grep -E "linear_[ABCDEFGHIJKLMNOPQRSTUVWXYZ]"
50-
# macos
51-
# find ./output/ -name AminoSee_BUSY_LOCK*.txt -exec rm -v {} \;
52-
# find . -name 'AminoSee_BUSY_LOCK*.txt' -exec rm -v {} \;
53-
54-
# linux
55-
# find . | grep AminoSee_BUSY_LOCK

‎installer.sh‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -30,10 +30,11 @@ echo "npm run start --test -m8"
3030
echo
3131
whereis aminosee
3232
which aminosee
33+
aminosee --test -m8
3334
# locate aminosee | grep aminosee$ &
3435
sleep 1
35-
echo about to run
36+
echo about to create symlinks in /usr/local/bin
3637
COMMMAND="sudo ln -s /usr/local/lib/node_modules/aminosee/bin/aminosee /usr/local/bin/aminosee"
3738
echo $COMMAND
38-
sleep 5
39-
eval $($COMMAND)
39+
sleep 1
40+
eval $COMMAND

‎package.json‎

Lines changed: 9 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
{
22
"name": "aminosee",
3-
"version": "1.31.8",
3+
"version": "1.31.9",
44
"owner": "Thomas Bieder Atkinson",
55
"author": "Tom Atkinson <tom@funk.co.nz>",
66
"website": "http://aminosee.funk.nz",
@@ -10,7 +10,7 @@
1010
"url": "git://github.com/tomachinz/AminoSee.git"
1111
},
1212
"description": "A unique visualisation of any large chunk of DNA or RNA residing in ASCII text files (such as FASTA, GBK etc and also just .txt like my hand-made test files), AminoSee is a way to render huge genomics files into a left-to-right top-bottom PNG linear image, a 2D infinite space filling square curve from 18th century, and a 3D hilbert curve from this century! Computation is done locally, without the files leaving your machine. A back-end terminal daemon cli command that can be scripted is combined with a front-end GUI using the Carlo, AminoSee features asynchronous streaming processing enabling arbitrary size files to be processed. It has been tested with files in excess of 4 GB and does not need the whole file in memory at any time. Try running 'aminosee *' in a directory with DNA files, or better run the batch script 'batch-peptides.sh'. The folder 'dna' is provided for bulk rendering it already has those scripts present. The GUI is not finished at this time. it is using THREEjs and a 3D Hilbert Curve, Carlo. Command line options allow one to filter by peptide, for example 'aminosee * --peptide=Ochre'. Allows genomics researchers to convert any file containing blocks of text format DNA (Fasta, GBK, .txt) into an interactive experience.",
13-
"main": "./bin/aminosee.js",
13+
"main": "./bin/aminosee",
1414
"bin": {
1515
"aminosee": "./bin/aminosee"
1616
},
@@ -76,8 +76,9 @@
7676
"hammerjs": "^2.0.8",
7777
"hilbert-2d": "0.0.1",
7878
"http-server": "^0.12.3",
79+
"internal-ip": "^4.3.0",
7980
"json-beautify": "^1.1.1",
80-
"node-fetch": "^2.6.0",
81+
"node-fetch": "^2.6.1",
8182
"open": "^6.4.0",
8283
"parallax-js": "^3.1.0",
8384
"phoenix": "^1.5.4",
@@ -107,7 +108,6 @@
107108
"get-cursor-position": "^1.0.5",
108109
"humanize-duration": "^3.23.1",
109110
"husky": "^3.1.0",
110-
"internal-ip": "^4.3.0",
111111
"keypress": "^0.2.1",
112112
"lazyness": "^1.2.0",
113113
"local-web-server": "^4.2.1",
@@ -153,14 +153,15 @@
153153
"macos",
154154
"win"
155155
],
156-
"scripts": [],
156+
"scripts": [
157+
],
157158
"assets": [
158-
"node_modules/terminal-kit/lib/termconfig",
159-
"node_modules/terminal-kit/lib/colorScheme",
160159
"node_modules/terminal-kit/lib/Palette.js",
161160
"node_modules/terminal-kit/lib/image.js",
162-
"node_modules/open/xdg-open",
163161
"node_modules/hilbert-2d/hilbert.js",
162+
"node_modules/terminal-kit/lib/termconfig",
163+
"node_modules/terminal-kit/lib/colorScheme",
164+
"node_modules/open/xdg-open",
164165
"src/*",
165166
"src/public/*",
166167
"package.json"

‎run-test.sh‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -34,7 +34,7 @@ test_do "Test use of --maxpix=5000000" --maxpix=5000000 -v $SLOW $MEDIUM $FAST $
3434
test_do "Forced re-render verbose no image" -fv $MEDIUM $FAST $* --no-image
3535
test_do "Demo -m4 no image" --demo -m4 --no-image $*
3636
test_do "Test -m5" --demo -m4 -q $*
37-
test_do "Test -m5" --test -p=Red -m4 $*
37+
test_do "Test -m5" --test -m5
3838
test_do "Test -m5" --test -p=Green -m4 $*
3939
test_do 'Curious back walk bug debug' -d --debug $FAST Influenza-A-virus-H9N2-NC_004905.gbk Streptococcus_virus_2972.gbk $*
4040
test_do "QUIET MODE WITH PARAMS" -q $* --no-image

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