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LCrossmanLCrossman
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fixing some warnings
1 parent 554617a commit 6cbbecb

8 files changed

Lines changed: 188 additions & 16 deletions

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‎heatmap/Cargo.toml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -20,6 +20,6 @@ opt-level = "z"
2020
serde-wasm-bindgen = "0.6.5"
2121
serde = { version = "1.0.213", features = ["derive"] }
2222
serde_derive = "1.0"
23-
wasm-bindgen = "0.2.91"
24-
web-sys = { version = "0.3.72", features = ["console","CanvasRenderingContext2d", "HtmlCanvasElement", "Document", "Window"] }
23+
wasm-bindgen = "0.2.100"
24+
web-sys = { version = "0.3.77", features = ["console","CanvasRenderingContext2d", "HtmlCanvasElement", "Document", "Window"] }
2525
csv = "1.1"

‎heatmap/src/canvas/drawing.rs‎

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -44,14 +44,16 @@ pub fn draw_responsive_heatmap(
4444
2 => "#de2d26",
4545
_ => "#FFFFFF",
4646
};
47-
context.set_fill_style(&JsValue::from_str(color));
47+
//context.set_fill_style_str(&JsValue::from(color));
48+
context.set_fill_style_str(color);
4849

4950
let x = padding_left + (col as f64 * box_width);
5051
let y = padding_top + (row as f64 * box_height);
5152
context.fill_rect(x, y, box_width, box_height);
5253

5354
// Draw box borders
54-
context.set_stroke_style(&JsValue::from_str("#FFFFFF"));
55+
//context.set_stroke_style(&JsValue::from("#FFFFFF"));
56+
context.set_stroke_style_str("#FFFFFF");
5557
context.set_line_width(2.0 / device_pixel_ratio);
5658

5759
if row < rows - 1 {
@@ -77,7 +79,8 @@ pub fn draw_responsive_heatmap(
7779

7880
// Draw X-axis
7981
context.begin_path();
80-
context.set_stroke_style(&JsValue::from_str("#000000"));
82+
//context.set_stroke_style_str(&JsValue::from("#000000"));
83+
context.set_stroke_style_str("#000000");
8184
context.move_to(padding_left, (box_height * rows as f64) + padding_bottom);
8285
context.line_to((box_height * rows as f64) + padding_bottom, (box_height * rows as f64) + padding_left);
8386
context.stroke();

‎microBioRust/new_output.gbk‎

Lines changed: 104 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -257,3 +257,107 @@ ORIGIN
257257
841 GATTTTTACG TCAACGCCGG CAGGAACAAC GACCGGTGCT TTAGCAACAC GAGACA
258258

259259
//
260+
LOCUS source_1 LOCUS 910source_1 910 bp DNA linear CON bp DNA linear CON 02-JUN-202502-JUN-2025
261+
262+
DEFINITION Escherichia coli K-12 substr. MG1655.
263+
ACCESSION source_1
264+
KEYWORDS .
265+
SOURCE Escherichia coli K-12 substr. MG1655
266+
ORGANISM Escherichia coliDEFINITION Escherichia coli K-12 substr. MG1655K-12 substr. MG1655
267+
.
268+
FEATURES Location/Qualifiers
269+
ACCESSION source 1..source_1910
270+
271+
KEYWORDS .
272+
/organism="SOURCE K-12 substr. MG1655Escherichia coli"
273+
/mol_type="K-12 substr. MG1655DNA
274+
"
275+
ORGANISM Escherichia coli K-12 substr. MG1655 /strain="
276+
K-12 substr. MG1655FEATURES Location/Qualifiers
277+
"
278+
source 1.. /type_material="910type strain of Escherichia coli K12
279+
"
280+
/organism=" /db_xref="K-12 substr. MG1655PRJNA57779"
281+
"
282+
/mol_type="DNA"
283+
gene complement( /strain="1K-12 substr. MG1655..354)
284+
/locus_tag="b3304"
285+
"
286+
CDS complement(1 /type_material="..type strain of Escherichia coli K12354"
287+
/db_xref=")
288+
PRJNA57779"
289+
/locus_tag="b3304 gene complement("
290+
1 /codon_start="..1354"
291+
)
292+
/gene=" /locus_tag="rplRb3304"
293+
"
294+
CDS complement(1 /translation="MDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGS
295+
LVAASTVEKAIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGRVQAL
296+
DAAREAGLQ"..
297+
354 /product=")
298+
50S ribosomal subunit protein L18 /locus_tag=""
299+
b3304"
300+
gene complement( /codon_start="3641.."
301+
897 /gene=")
302+
/locus_tag="b3305"
303+
CDS complement(364..rplR897"
304+
)
305+
/locus_tag="b3305"
306+
/translation="MDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGS
307+
LVAASTVEKAIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGRVQAL
308+
DAAREAGLQ" /codon_start="
309+
1 /product=""
310+
50S ribosomal subunit protein L18 /gene=""
311+
rplF gene complement("
312+
364..897)
313+
/locus_tag="b3305"
314+
CDS complement(364 /translation="MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKH
315+
NTLTFGPRDGYADGWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLS
316+
GFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYAD
317+
VVRTKEAKK"..
318+
897 /product=")
319+
50S ribosomal subunit protein L6 /locus_tag=""
320+
b3305ORIGIN
321+
"
322+
/codon_start="1"
323+
/gene="rplF"
324+
/translation="MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKH
325+
NTLTFGPRDGYADGWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLS
326+
GFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYAD
327+
VVRTKEAKK"
328+
/product="50S ribosomal subunit protein L6"
329+
ORIGIN
330+
1 TTAGAACTGA AGGCCAGCTT CACGGGCAGC ATCTGCCAGT GCCTGGACAC GACCATGATA
331+
61 TTGGAACCCG GAACGGTCAA AGGATACATC TTTGATGCCT TTTTCCAGAG CGCGTTCAGC
332+
121 GACAGCTTTA CCCACAGCTG CAGCCGCGTC TTTGTTACCG GTGTACTTCA GTTGTTCAGC
333+
181 GATAGCTTTT TCTACAGTAG AAGCAGCTAC CAGAACTTCA GAACCGTTCG GTGCAATTAC
334+
241 CTGTGCGTAA ATGTGACGCG GGGTACGATG TACCACCAGG CGAGTTGCGC CCAGCTCCTG
335+
301 GAGCTTGCGG CGTGCGCGGG TCGCACGACG GATACGAGCA GATTTCTTAT CCATAGTGTT
336+
361 ACCTTACTTC TTCTTAGCCT CTTTGGTACG CACGACTTCG TCGGCGTAAC GAACACCCTT
337+
421 GCCTTTATAA GGCTCAGGAC GACGGTAGGC GCGCAGATCC GCTGCAACCT GGCCGATCAC
338+
481 CTGCTTATCA GCGCCTTTCA GCACGATTTC AGTCTGAGTC GGACATTCAG CAGTGATACC
339+
541 CGCAGGCAGC TGATGGTCAA CAGGATGAGA GAAACCCAGA GACAGGTTAA TCACATTGCC
340+
601 TTTAACCGCT GCACGGTAAC CTACACCAAC CAGCTGCAGC TTCTTAGTGA AGCCTTCGGT
341+
661 AACACCGATA ACCATTGAGT TCAGCAGGGC ACGCGCGGTA CCAGCCTGTG CCCAACCGTC
342+
721 TGCGTAACCA TCACGCGGAC CGAAGGTCAG GGTATTATCT GCATGTTTAA CTTCAACAGC
343+
781 ATCGTTGAGA GTACGAGTCA GCTCGCCGTT TTTACCTTTG ATCGTAATAA CCTGACCGTT
344+
841 GATTTTTACG TCAACGCCGG CAGGAACAAC GACCGGTGCT TTAGCAACAC GAGACA
345+
346+
//
347+
1 TTAGAACTGA AGGCCAGCTT CACGGGCAGC ATCTGCCAGT GCCTGGACAC GACCATGATA
348+
61 TTGGAACCCG GAACGGTCAA AGGATACATC TTTGATGCCT TTTTCCAGAG CGCGTTCAGC
349+
121 GACAGCTTTA CCCACAGCTG CAGCCGCGTC TTTGTTACCG GTGTACTTCA GTTGTTCAGC
350+
181 GATAGCTTTT TCTACAGTAG AAGCAGCTAC CAGAACTTCA GAACCGTTCG GTGCAATTAC
351+
241 CTGTGCGTAA ATGTGACGCG GGGTACGATG TACCACCAGG CGAGTTGCGC CCAGCTCCTG
352+
301 GAGCTTGCGG CGTGCGCGGG TCGCACGACG GATACGAGCA GATTTCTTAT CCATAGTGTT
353+
361 ACCTTACTTC TTCTTAGCCT CTTTGGTACG CACGACTTCG TCGGCGTAAC GAACACCCTT
354+
421 GCCTTTATAA GGCTCAGGAC GACGGTAGGC GCGCAGATCC GCTGCAACCT GGCCGATCAC
355+
481 CTGCTTATCA GCGCCTTTCA GCACGATTTC AGTCTGAGTC GGACATTCAG CAGTGATACC
356+
541 CGCAGGCAGC TGATGGTCAA CAGGATGAGA GAAACCCAGA GACAGGTTAA TCACATTGCC
357+
601 TTTAACCGCT GCACGGTAAC CTACACCAAC CAGCTGCAGC TTCTTAGTGA AGCCTTCGGT
358+
661 AACACCGATA ACCATTGAGT TCAGCAGGGC ACGCGCGGTA CCAGCCTGTG CCCAACCGTC
359+
721 TGCGTAACCA TCACGCGGAC CGAAGGTCAG GGTATTATCT GCATGTTTAA CTTCAACAGC
360+
781 ATCGTTGAGA GTACGAGTCA GCTCGCCGTT TTTACCTTTG ATCGTAATAA CCTGACCGTT
361+
841 GATTTTTACG TCAACGCCGG CAGGAACAAC GACCGGTGCT TTAGCAACAC GAGACA
362+
363+
//

‎microBioRust/src/embl.rs‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -284,7 +284,7 @@ use chrono::prelude::*;
284284

285285

286286
/// macro to create get_ functions for the values
287-
#[macro_use]
287+
#[macro_export]
288288
macro_rules! create_getters {
289289
// macro for creating get methods
290290
($struct_name:ident, $attributes:ident, $enum_name:ident, $( $field:ident { value: $type:ty } ),* ) => {
@@ -311,7 +311,8 @@ macro_rules! create_getters {
311311
};
312312
}
313313

314-
/// macro to create the set_ functions for the values in a Builder format
314+
/// macro to create the set_ functions for the values in a Builder format
315+
#[macro_export]
315316
macro_rules! create_builder {
316317
// Macro for creating attribute builders for SourceAttributes, FeatureAttributes and SequenceAttributes
317318
($builder_name:ident, $attributes:ident, $enum_name:ident, $counter_name:ident, $( $field:ident { value: $type:ty } ),* ) => {
@@ -857,7 +858,7 @@ pub enum SourceAttributes {
857858
DbXref { value:String}
858859
}
859860

860-
///macro for creating the getters
861+
//macro for creating the getters
861862
create_getters!(
862863
SourceAttributeBuilder,
863864
source_attributes,

‎microBioRust/src/main.rs‎

Lines changed: 1 addition & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,4 @@
11
use clap::Parser;
2-
use std::fs::File;
3-
use microBioRust::gbk::Reader;
4-
use std::io;
52
use microBioRust::genbank;
63

74

@@ -16,7 +13,7 @@ fn main() -> Result<(), anyhow::Error> {
1613
let args = Arguments::parse();
1714
let records = genbank!(&args.filename);
1815
for record in records.iter() {
19-
for (k, v) in &record.cds.attributes {
16+
for (k, _v) in &record.cds.attributes {
2017
if let Some(seq) = record.seq_features.get_sequence_faa(k) {
2118
println!(">{}|{}\n{}", &record.id, &k, seq);
2219
}

‎microBioRust/test_output.gff‎

Lines changed: 49 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -118,3 +118,52 @@ source_source_1_1 . CDS 364 897 0 - 0 id=b3305;name=source_source_1_1;gene=rplF;
118118
>test_output.gff
119119

120120
TTAGAACTGAAGGCCAGCTTCACGGGCAGCATCTGCCAGTGCCTGGACACGACCATGATATTGGAACCCGGAACGGTCAAAGGATACATCTTTGATGCCTTTTTCCAGAGCGCGTTCAGCGACAGCTTTACCCACAGCTGCAGCCGCGTCTTTGTTACCGGTGTACTTCAGTTGTTCAGCGATAGCTTTTTCTACAGTAGAAGCAGCTACCAGAACTTCAGAACCGTTCGGTGCAATTACCTGTGCGTAAATGTGACGCGGGGTACGATGTACCACCAGGCGAGTTGCGCCCAGCTCCTGGAGCTTGCGGCGTGCGCGGGTCGCACGACGGATACGAGCAGATTTCTTATCCATAGTGTTACCTTACTTCTTCTTAGCCTCTTTGGTACGCACGACTTCGTCGGCGTAACGAACACCCTTGCCTTTATAAGGCTCAGGACGACGGTAGGCGCGCAGATCCGCTGCAACCTGGCCGATCACCTGCTTATCAGCGCCTTTCAGCACGATTTCAGTCTGAGTCGGACATTCAGCAGTGATACCCGCAGGCAGCTGATGGTCAACAGGATGAGAGAAACCCAGAGACAGGTTAATCACATTGCCTTTAACCGCTGCACGGTAACCTACACCAACCAGCTGCAGCTTCTTAGTGAAGCCTTCGGTAACACCGATAACCATTGAGTTCAGCAGGGCACGCGCGGTACCAGCCTGTGCCCAACCGTCTGCGTAACCATCACGCGGACCGAAGGTCAGGGTATTATCTGCATGTTTAACTTCAACAGCATCGTTGAGAGTACGAGTCAGCTCGCCGTTTTTACCTTTGATCGTAATAACCTGACCGTTGATTTTTACGTCAACGCCGGCAGGAACAACGACCGGTGCTTTAGCAACACGAGACA
121+
##sequence-region ##sequence-region source_1 source_11 1910
122+
source_1 910.
123+
CDS 1 source_1354 .0 CDS- 10 354id=b3304;name=source_1;gene=rplR;locus_tag=b3304;product=50S ribosomal subunit protein L18
124+
0source_1 -. 0CDS id=b3304;name=source_1;gene=rplR;locus_tag=b3304;product=50S ribosomal subunit protein L18364
125+
897 0source_1 -. 0CDS id=b3305;name=source_1;gene=rplF;locus_tag=b3305;product=50S ribosomal subunit protein L6364
126+
##FASTA
127+
897> test_output.gff0
128+
129+
TTAGAACTGAAGGCCAGCTTCACGGGCAGCATCTGCCAGTGCCTGGACACGACCATGATA
130+
TTGGAACCCGGAACGGTCAAAGGATACATCTTTGATGCCTTTTTCCAGAGCGCGTTCAGC
131+
GACAGCTTTACCCACAGCTGCAGCCGCGTCTTTGTTACCGGTGTACTTCAGTTGTTCAGC
132+
GATAGCTTTTTCTACAGTAGAAGCAGCTACCAGAACTTCAGAACCGTTCGGTGCAATTAC
133+
CTGTGCGTAAATGTGACGCGGGGTACGATGTACCACCAGGCGAGTTGCGCCCAGCTCCTG
134+
GAGCTTGCGGCGTGCGCGGGTCGCACGACGGATACGAGCAGATTTCTTATCCATAGTGTT
135+
ACCTTACTTCTTCTTAGCCTCTTTGGTACGCACGACTTCGTCGGCGTAACGAACACCCTT
136+
GCCTTTATAAGGCTCAGGACGACGGTAGGCGCGCAGATCCGCTGCAACCTGGCCGATCAC
137+
CTGCTTATCAGCGCCTTTCAGCACGATTTCAGTCTGAGTCGGACATTCAGCAGTGATACC
138+
CGCAGGCAGCTGATGGTCAACAGGATGAGAGAAACCCAGAGACAGGTTAATCACATTGCC
139+
TTTAACCGCTGCACGGTAACCTACACCAACCAGCTGCAGCTTCTTAGTGAAGCCTTCGGT
140+
AACACCGATAACCATTGAGTTCAGCAGGGCACGCGCGGTACCAGCCTGTGCCCAACCGTC
141+
TGCGTAACCATCACGCGGACCGAAGGTCAGGGTATTATCTGCATGTTTAACTTCAACAGC
142+
ATCGTTGAGAGTACGAGTCAGCTCGCCGTTTTTACCTTTGATCGTAATAACCTGACCGTT
143+
GATTTTTACGTCAACGCCGGCAGGAACAACGACCGGTGCTTTAGCAACACGAGACA-
144+
0 id=b3305;name=source_1;gene=rplF;locus_tag=b3305;product=50S ribosomal subunit protein L6
145+
##FASTA
146+
>test_output.gff
147+
148+
TTAGAACTGAAGGCCAGCTTCACGGGCAGCATCTGCCAGTGCCTGGACACGACCATGATA
149+
TTGGAACCCGGAACGGTCAAAGGATACATCTTTGATGCCTTTTTCCAGAGCGCGTTCAGC
150+
GACAGCTTTACCCACAGCTGCAGCCGCGTCTTTGTTACCGGTGTACTTCAGTTGTTCAGC
151+
GATAGCTTTTTCTACAGTAGAAGCAGCTACCAGAACTTCAGAACCGTTCGGTGCAATTAC
152+
CTGTGCGTAAATGTGACGCGGGGTACGATGTACCACCAGGCGAGTTGCGCCCAGCTCCTG
153+
GAGCTTGCGGCGTGCGCGGGTCGCACGACGGATACGAGCAGATTTCTTATCCATAGTGTT
154+
ACCTTACTTCTTCTTAGCCTCTTTGGTACGCACGACTTCGTCGGCGTAACGAACACCCTT
155+
GCCTTTATAAGGCTCAGGACGACGGTAGGCGCGCAGATCCGCTGCAACCTGGCCGATCAC
156+
CTGCTTATCAGCGCCTTTCAGCACGATTTCAGTCTGAGTCGGACATTCAGCAGTGATACC
157+
CGCAGGCAGCTGATGGTCAACAGGATGAGAGAAACCCAGAGACAGGTTAATCACATTGCC
158+
TTTAACCGCTGCACGGTAACCTACACCAACCAGCTGCAGCTTCTTAGTGAAGCCTTCGGT
159+
AACACCGATAACCATTGAGTTCAGCAGGGCACGCGCGGTACCAGCCTGTGCCCAACCGTC
160+
TGCGTAACCATCACGCGGACCGAAGGTCAGGGTATTATCTGCATGTTTAACTTCAACAGC
161+
ATCGTTGAGAGTACGAGTCAGCTCGCCGTTTTTACCTTTGATCGTAATAACCTGACCGTT
162+
GATTTTTACGTCAACGCCGGCAGGAACAACGACCGGTGCTTTAGCAACACGAGACA
163+
##sequence-region source_source_1_1 1 910
164+
source_source_1_1 . CDS 1 354 0 - 0 id=b3304;name=source_source_1_1;gene=rplR;locus_tag=b3304;product=50S ribosomal subunit protein L18
165+
source_source_1_1 . CDS 364 897 0 - 0 id=b3305;name=source_source_1_1;gene=rplF;locus_tag=b3305;product=50S ribosomal subunit protein L6
166+
##FASTA
167+
>test_output.gff
168+
169+
TTAGAACTGAAGGCCAGCTTCACGGGCAGCATCTGCCAGTGCCTGGACACGACCATGATATTGGAACCCGGAACGGTCAAAGGATACATCTTTGATGCCTTTTTCCAGAGCGCGTTCAGCGACAGCTTTACCCACAGCTGCAGCCGCGTCTTTGTTACCGGTGTACTTCAGTTGTTCAGCGATAGCTTTTTCTACAGTAGAAGCAGCTACCAGAACTTCAGAACCGTTCGGTGCAATTACCTGTGCGTAAATGTGACGCGGGGTACGATGTACCACCAGGCGAGTTGCGCCCAGCTCCTGGAGCTTGCGGCGTGCGCGGGTCGCACGACGGATACGAGCAGATTTCTTATCCATAGTGTTACCTTACTTCTTCTTAGCCTCTTTGGTACGCACGACTTCGTCGGCGTAACGAACACCCTTGCCTTTATAAGGCTCAGGACGACGGTAGGCGCGCAGATCCGCTGCAACCTGGCCGATCACCTGCTTATCAGCGCCTTTCAGCACGATTTCAGTCTGAGTCGGACATTCAGCAGTGATACCCGCAGGCAGCTGATGGTCAACAGGATGAGAGAAACCCAGAGACAGGTTAATCACATTGCCTTTAACCGCTGCACGGTAACCTACACCAACCAGCTGCAGCTTCTTAGTGAAGCCTTCGGTAACACCGATAACCATTGAGTTCAGCAGGGCACGCGCGGTACCAGCCTGTGCCCAACCGTCTGCGTAACCATCACGCGGACCGAAGGTCAGGGTATTATCTGCATGTTTAACTTCAACAGCATCGTTGAGAGTACGAGTCAGCTCGCCGTTTTTACCTTTGATCGTAATAACCTGACCGTTGATTTTTACGTCAACGCCGGCAGGAACAACGACCGGTGCTTTAGCAACACGAGACA

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