Skip to content

Fix some linter errors #338

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
niyarin merged 2 commits into from
Mar 25, 2025
Merged

Fix some linter errors #338

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
909e6d2
style: Remove unnecessary type hints
alumi Mar 24, 2025
f13581a
style: Unwind single-level threading macros
alumi Mar 25, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
200 changes: 106 additions & 94 deletions test/cljam/io/gff_test.clj
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,13 +16,14 @@

(def ^:private ^String
simple-gff
(->> ["##gff-version 3"
"ctg123 . exon 1300 1500 . + . ID=exon00001"
"ctg123 . exon 1050 1500 . + . ID=exon00002"
"ctg123 . exon 3000 3902 . + . ID=exon00003"
"ctg123 . exon 5000 5500 . + . ID=exon00004"
"ctg123 . exon 7000 9000 . + . ID=exon00005"]
(cstr/join \newline)))
(cstr/join
\newline
["##gff-version 3"
"ctg123 . exon 1300 1500 . + . ID=exon00001"
"ctg123 . exon 1050 1500 . + . ID=exon00002"
"ctg123 . exon 3000 3902 . + . ID=exon00003"
"ctg123 . exon 5000 5500 . + . ID=exon00004"
"ctg123 . exon 7000 9000 . + . ID=exon00005"]))

(def ^:private
simple-edn
Expand All @@ -34,14 +35,15 @@

(def ^:private ^String
nested-gff-1
(->> ["##gff-version 3"
"ctg123 . mRNA 1300 9000 . + . ID=mrna0001;Name=foobar"
"ctg123 . exon 1300 1500 . + . ID=exon00001;Parent=mrna0001"
"ctg123 . exon 1050 1500 . + . ID=exon00002;Parent=mrna0001"
"ctg123 . exon 3000 3902 . + . ID=exon00003;Parent=mrna0001"
"ctg123 . exon 5000 5500 . + . ID=exon00004;Parent=mrna0001"
"ctg123 . exon 7000 9000 . + . ID=exon00005;Parent=mrna0001"]
(cstr/join \newline)))
(cstr/join
\newline
["##gff-version 3"
"ctg123 . mRNA 1300 9000 . + . ID=mrna0001;Name=foobar"
"ctg123 . exon 1300 1500 . + . ID=exon00001;Parent=mrna0001"
"ctg123 . exon 1050 1500 . + . ID=exon00002;Parent=mrna0001"
"ctg123 . exon 3000 3902 . + . ID=exon00003;Parent=mrna0001"
"ctg123 . exon 5000 5500 . + . ID=exon00004;Parent=mrna0001"
"ctg123 . exon 7000 9000 . + . ID=exon00005;Parent=mrna0001"]))

(def ^:private
nested-edn-1
Expand All @@ -54,18 +56,19 @@

(def ^:private ^String
nested-gff-2
(->> ["##gff-version 3"
"ctg123 . operon 1300 15000 . + . ID=operon001;Name=Operon"
"ctg123 . mRNA 1300 9000 . + . ID=mrna0001;Parent=operon001;Name=foobar"
"ctg123 . exon 1300 1500 . + . Parent=mrna0001"
"ctg123 . exon 1050 1500 . + . Parent=mrna0001"
"ctg123 . exon 3000 3902 . + . Parent=mrna0001"
"ctg123 . exon 5000 5500 . + . Parent=mrna0001"
"ctg123 . exon 7000 9000 . + . Parent=mrna0001"
"ctg123 . mRNA 10000 15000 . + . ID=mrna0002;Parent=operon001;Name=baz"
"ctg123 . exon 10000 12000 . + . Parent=mrna0002"
"ctg123 . exon 14000 15000 . + . Parent=mrna0002"]
(cstr/join \newline)))
(cstr/join
\newline
["##gff-version 3"
"ctg123 . operon 1300 15000 . + . ID=operon001;Name=Operon"
"ctg123 . mRNA 1300 9000 . + . ID=mrna0001;Parent=operon001;Name=foobar"
"ctg123 . exon 1300 1500 . + . Parent=mrna0001"
"ctg123 . exon 1050 1500 . + . Parent=mrna0001"
"ctg123 . exon 3000 3902 . + . Parent=mrna0001"
"ctg123 . exon 5000 5500 . + . Parent=mrna0001"
"ctg123 . exon 7000 9000 . + . Parent=mrna0001"
"ctg123 . mRNA 10000 15000 . + . ID=mrna0002;Parent=operon001;Name=baz"
"ctg123 . exon 10000 12000 . + . Parent=mrna0002"
"ctg123 . exon 14000 15000 . + . Parent=mrna0002"]))

(def ^:private
nested-edn-2
Expand All @@ -82,13 +85,14 @@

(def ^:private ^String
discontinuous-gff
(->> ["##gff-version 3"
"ctg123 example match 26122 26126 . + . ID=match001"
"ctg123 example match 26497 26869 . + . ID=match001"
"ctg123 example match 27201 27325 . + . ID=match001"
"ctg123 example match 27372 27433 . + . ID=match001"
"ctg123 example match 27565 27565 . + . ID=match001"]
(cstr/join \newline)))
(cstr/join
\newline
["##gff-version 3"
"ctg123 example match 26122 26126 . + . ID=match001"
"ctg123 example match 26497 26869 . + . ID=match001"
"ctg123 example match 27201 27325 . + . ID=match001"
"ctg123 example match 27372 27433 . + . ID=match001"
"ctg123 example match 27565 27565 . + . ID=match001"]))

(def ^:private
discontinuous-edn
Expand All @@ -100,32 +104,33 @@

(def ^:private ^String
example-gene-gff
(->> ["##gff-version 3.2.1"
"##sequence-region ctg123 1 1497228"
"ctg123 . gene 1000 9000 . + . ID=gene00001;Name=EDEN"
"ctg123 . TF_binding_site 1000 1012 . + . ID=tfbs00001;Parent=gene00001"
"ctg123 . mRNA 1050 9000 . + . ID=mRNA00001;Parent=gene00001;Name=EDEN.1"
"ctg123 . mRNA 1050 9000 . + . ID=mRNA00002;Parent=gene00001;Name=EDEN.2"
"ctg123 . mRNA 1300 9000 . + . ID=mRNA00003;Parent=gene00001;Name=EDEN.3"
"ctg123 . exon 1300 1500 . + . ID=exon00001;Parent=mRNA00003"
"ctg123 . exon 1050 1500 . + . ID=exon00002;Parent=mRNA00001,mRNA00002"
"ctg123 . exon 3000 3902 . + . ID=exon00003;Parent=mRNA00001,mRNA00003"
"ctg123 . exon 5000 5500 . + . ID=exon00004;Parent=mRNA00001,mRNA00002,mRNA00003"
"ctg123 . exon 7000 9000 . + . ID=exon00005;Parent=mRNA00001,mRNA00002,mRNA00003"
"ctg123 . CDS 1201 1500 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1"
"ctg123 . CDS 3000 3902 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1"
"ctg123 . CDS 5000 5500 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1"
"ctg123 . CDS 7000 7600 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1"
"ctg123 . CDS 1201 1500 . + 0 ID=cds00002;Parent=mRNA00002;Name=edenprotein.2"
"ctg123 . CDS 5000 5500 . + 0 ID=cds00002;Parent=mRNA00002;Name=edenprotein.2"
"ctg123 . CDS 7000 7600 . + 0 ID=cds00002;Parent=mRNA00002;Name=edenprotein.2"
"ctg123 . CDS 3301 3902 . + 0 ID=cds00003;Parent=mRNA00003;Name=edenprotein.3"
"ctg123 . CDS 5000 5500 . + 1 ID=cds00003;Parent=mRNA00003;Name=edenprotein.3"
"ctg123 . CDS 7000 7600 . + 1 ID=cds00003;Parent=mRNA00003;Name=edenprotein.3"
"ctg123 . CDS 3391 3902 . + 0 ID=cds00004;Parent=mRNA00003;Name=edenprotein.4"
"ctg123 . CDS 5000 5500 . + 1 ID=cds00004;Parent=mRNA00003;Name=edenprotein.4"
"ctg123 . CDS 7000 7600 . + 1 ID=cds00004;Parent=mRNA00003;Name=edenprotein.4"]
(cstr/join \newline)))
(cstr/join
\newline
["##gff-version 3.2.1"
"##sequence-region ctg123 1 1497228"
"ctg123 . gene 1000 9000 . + . ID=gene00001;Name=EDEN"
"ctg123 . TF_binding_site 1000 1012 . + . ID=tfbs00001;Parent=gene00001"
"ctg123 . mRNA 1050 9000 . + . ID=mRNA00001;Parent=gene00001;Name=EDEN.1"
"ctg123 . mRNA 1050 9000 . + . ID=mRNA00002;Parent=gene00001;Name=EDEN.2"
"ctg123 . mRNA 1300 9000 . + . ID=mRNA00003;Parent=gene00001;Name=EDEN.3"
"ctg123 . exon 1300 1500 . + . ID=exon00001;Parent=mRNA00003"
"ctg123 . exon 1050 1500 . + . ID=exon00002;Parent=mRNA00001,mRNA00002"
"ctg123 . exon 3000 3902 . + . ID=exon00003;Parent=mRNA00001,mRNA00003"
"ctg123 . exon 5000 5500 . + . ID=exon00004;Parent=mRNA00001,mRNA00002,mRNA00003"
"ctg123 . exon 7000 9000 . + . ID=exon00005;Parent=mRNA00001,mRNA00002,mRNA00003"
"ctg123 . CDS 1201 1500 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1"
"ctg123 . CDS 3000 3902 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1"
"ctg123 . CDS 5000 5500 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1"
"ctg123 . CDS 7000 7600 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1"
"ctg123 . CDS 1201 1500 . + 0 ID=cds00002;Parent=mRNA00002;Name=edenprotein.2"
"ctg123 . CDS 5000 5500 . + 0 ID=cds00002;Parent=mRNA00002;Name=edenprotein.2"
"ctg123 . CDS 7000 7600 . + 0 ID=cds00002;Parent=mRNA00002;Name=edenprotein.2"
"ctg123 . CDS 3301 3902 . + 0 ID=cds00003;Parent=mRNA00003;Name=edenprotein.3"
"ctg123 . CDS 5000 5500 . + 1 ID=cds00003;Parent=mRNA00003;Name=edenprotein.3"
"ctg123 . CDS 7000 7600 . + 1 ID=cds00003;Parent=mRNA00003;Name=edenprotein.3"
"ctg123 . CDS 3391 3902 . + 0 ID=cds00004;Parent=mRNA00003;Name=edenprotein.4"
"ctg123 . CDS 5000 5500 . + 1 ID=cds00004;Parent=mRNA00003;Name=edenprotein.4"
"ctg123 . CDS 7000 7600 . + 1 ID=cds00004;Parent=mRNA00003;Name=edenprotein.4"]))

(def ^:private
example-gene-edn
Expand Down Expand Up @@ -155,12 +160,13 @@

(def ^:private ^String
circular-gff
(->> ["##gff-version 3.2.1"
"# organism Enterobacteria phage f1"
"# Note Bacteriophage f1, complete genome."
"J02448 GenBank region 1 6407 . + . ID=J02448;Name=J02448;Is_circular=true"
"J02448 GenBank CDS 6006 7238 . + 0 ID=geneII;Name=II;Note=protein II"]
(cstr/join \newline)))
(cstr/join
\newline
["##gff-version 3.2.1"
"# organism Enterobacteria phage f1"
"# Note Bacteriophage f1, complete genome."
"J02448 GenBank region 1 6407 . + . ID=J02448;Name=J02448;Is_circular=true"
"J02448 GenBank CDS 6006 7238 . + 0 ID=geneII;Name=II;Note=protein II"]))

(def ^:private
circular-edn
Expand All @@ -169,10 +175,11 @@

(def ^:private ^String
gap-gff
(->> ["##gff-version 3.2.1"
"chr3 . Match 1 23 . . . ID=Match1;Target=EST23 1 21;Gap=M8 D3 M6 I1 M6"
"ctg123 . nucleotide_to_protein 100 129 . + . ID=match008;Target=p101 1 10;Gap=M3 I1 M2 D1 M4"]
(cstr/join \newline)))
(cstr/join
\newline
["##gff-version 3.2.1"
"chr3 . Match 1 23 . . . ID=Match1;Target=EST23 1 21;Gap=M8 D3 M6 I1 M6"
"ctg123 . nucleotide_to_protein 100 129 . + . ID=match008;Target=p101 1 10;Gap=M3 I1 M2 D1 M4"]))

(def ^:private
gap-edn
Expand All @@ -183,9 +190,10 @@

(def ^:private ^String
alignment-gff
(->> ["##gff-version 3.2.1"
"ctg123 . cDNA_match 1050 9000 6.2e-45 + . ID=match00001;Target=cdna0123 12 2964;Gap=M451 D3499 M501 D1499 M2001"]
(cstr/join \newline)))
(cstr/join
\newline
["##gff-version 3.2.1"
"ctg123 . cDNA_match 1050 9000 6.2e-45 + . ID=match00001;Target=cdna0123 12 2964;Gap=M451 D3499 M501 D1499 M2001"]))

(def ^:private
alignment-edn
Expand All @@ -194,11 +202,12 @@

(def ^:private ^String
alignment-multiple-gff
(->> ["##gff-version 3.2.1"
"ctg123 . cDNA_match 1050 1500 5.8e-42 + . ID=match00001;Target=cdna0123 12 462"
"ctg123 . cDNA_match 5000 5500 8.1e-43 + . ID=match00001;Target=cdna0123 463 963"
"ctg123 . cDNA_match 7000 9000 1.4e-40 + . ID=match00001;Target=cdna0123 964 2964"]
(cstr/join \newline)))
(cstr/join
\newline
["##gff-version 3.2.1"
"ctg123 . cDNA_match 1050 1500 5.8e-42 + . ID=match00001;Target=cdna0123 12 462"
"ctg123 . cDNA_match 5000 5500 8.1e-43 + . ID=match00001;Target=cdna0123 463 963"
"ctg123 . cDNA_match 7000 9000 1.4e-40 + . ID=match00001;Target=cdna0123 964 2964"]))

(def ^:private
alignment-multiple-edn
Expand All @@ -208,10 +217,11 @@

(def ^:private ^String
alignment-reverse-gff
(->> ["##gff-version 3.2.1"
"ctg123 . EST_match 1200 3200 2.2e-30 + . ID=match00002;Target=mjm1123.5 5 506;Gap=M301 D1499 M201"
"ctg123 . EST_match 7000 9000 7.4e-32 - . ID=match00003;Target=mjm1123.3 1 502;Gap=M101 D1499 M401"]
(cstr/join \newline)))
(cstr/join
\newline
["##gff-version 3.2.1"
"ctg123 . EST_match 1200 3200 2.2e-30 + . ID=match00002;Target=mjm1123.5 5 506;Gap=M301 D1499 M201"
"ctg123 . EST_match 7000 9000 7.4e-32 - . ID=match00003;Target=mjm1123.3 1 502;Gap=M101 D1499 M401"]))

(def ^:private
alignment-reverse-edn
Expand All @@ -222,11 +232,12 @@

(def ^:private ^String
alignment-group-gff
(->> ["##gff-version 3.2.1"
"ctg123 . cDNA_match 1200 9000 . . . ID=cDNA00001"
"ctg123 . match_part 1200 3200 2.2e-30 + . ID=match00002;Parent=cDNA00001;Target=mjm1123.5 5 506;Gap=M301 D1499 M201"
"ctg123 . match_part 7000 9000 7.4e-32 - . ID=match00003;Parent=cDNA00001;Target=mjm1123.3 1 502;Gap=M101 D1499 M401"]
(cstr/join \newline)))
(cstr/join
\newline
["##gff-version 3.2.1"
"ctg123 . cDNA_match 1200 9000 . . . ID=cDNA00001"
"ctg123 . match_part 1200 3200 2.2e-30 + . ID=match00002;Parent=cDNA00001;Target=mjm1123.5 5 506;Gap=M301 D1499 M201"
"ctg123 . match_part 7000 9000 7.4e-32 - . ID=match00003;Parent=cDNA00001;Target=mjm1123.3 1 502;Gap=M101 D1499 M401"]))

(def ^:private
alignment-group-edn
Expand All @@ -239,11 +250,12 @@

(def ^:private ^String
encoding-gff
(->> ["##gff-version 3.2"
"ch r;1 sour =ce ty &p,e 1 10 9.0 ? . ."
"chr%253B1 sour%253Dce ty%2526p%252Ce 1 10 . + . Target=Foo%20Bar 1 10 +;Dbxref=EMBL:AA816246,NCBI_gi:10727410;Foo=Bar%2C,Baz "
" !\"#$%25&'%09()*+,-./%0A0123456789:;<=>?@[\\]^_`{|}~ . type 1 10 . . . ID= !\"#$%25%26'%09()*+%2C-./%0A0123456789:%3B<%3D>?@[\\]^_`{|}~;Target=%20!\"#$%25%26'%09()*+%2C-./%0A0123456789:%3B<%3D>?@[\\]^_`{|}~ 1 10 -"]
(cstr/join \newline)))
(cstr/join
\newline
["##gff-version 3.2"
"ch r;1 sour =ce ty &p,e 1 10 9.0 ? . ."
"chr%253B1 sour%253Dce ty%2526p%252Ce 1 10 . + . Target=Foo%20Bar 1 10 +;Dbxref=EMBL:AA816246,NCBI_gi:10727410;Foo=Bar%2C,Baz "
" !\"#$%25&'%09()*+,-./%0A0123456789:;<=>?@[\\]^_`{|}~ . type 1 10 . . . ID= !\"#$%25%26'%09()*+%2C-./%0A0123456789:%3B<%3D>?@[\\]^_`{|}~;Target=%20!\"#$%25%26'%09()*+%2C-./%0A0123456789:%3B<%3D>?@[\\]^_`{|}~ 1 10 -"]))

(def ^:private
encoding-edn
Expand Down Expand Up @@ -316,7 +328,7 @@
(deftest read-features
(are [?str ?edn]
(= ?edn
(with-open [bais (ByteArrayInputStream. (.getBytes ^String ?str))
(with-open [bais (ByteArrayInputStream. (.getBytes ?str))
r (gff/reader bais)]
(doall (gff/read-features r))))
simple-gff simple-edn
Expand Down Expand Up @@ -364,7 +376,7 @@
(are [?edn ?str]
;; ignore directives and comment lines
(= (cstr/replace ?str #"(?<=\n)#.*?\n" "")
(with-open [bais (ByteArrayInputStream. (.getBytes ^String ?str))
(with-open [bais (ByteArrayInputStream. (.getBytes ?str))
baos (ByteArrayOutputStream.)]
(let [v (with-open [r (gff/reader bais)]
(gff/version r))]
Expand Down