1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
|
#!/bin/bash -e
pkg=gffread
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
fi
cd "$AUTOPKGTEST_TMP"
# the below is copied from control
# generated via
# apt-file search --package-only --regexp '\.gff.?$' | grep -v -E "bedops|cct|ugene|gbrowse-data"
PACKAGES="augustus-doc, bedtools-test, emboss-data, emboss-test, gbrowse, genometools-common, gff2aplot, gff2ps, htslib-test, libbio-graphics-perl, python3-gffutils, r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer, seqan-apps, trinityrnaseq-examples"
if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" = "amd64" ] ; then
PACKAGES+=", cnvkit, optimir, proteinortho, python3-pybedtools, spades"
fi
if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" = "arm64" ] ; then
PACKAGES+=", cnvkit, optimir, proteinortho, python3-pybedtools"
fi
if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" = "ppc64el" ] ; then
PACKAGES+=", cnvkit, optimir, proteinortho, python3-pybedtools"
fi
if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" = "s390x" ] ; then
PACKAGES+=", proteinortho"
fi
IFS=", " read -r -a pkgs <<< ${PACKAGES}
# ugene is non-free
# bedops:
# gffread /usr/lib/R/site-library/Gviz/extdata/test.gff2
# Error parsing strand (?) from GFF line:
# chr1 Canada exon 3000 3902 . ? 2 ID=exon00003;score=4;Name=foo
# r-bioc-rtracklayer
# /usr/lib/R/site-library/rtracklayer/tests/genes.gff3
# Error parsing strand (?) from GFF line:
# chr12 rtracklayer CDS 90796 91263 . ? . Parent=4644;
# cct (and similar for cct-examples)
# /usr/share/cct/lib/assign_cogs/sample_output/sample_1.gff
# Warning: invalid start coordinate at line:
# seqname source feature start end score strand frame
# emboss-test
# /usr/share/EMBOSS/test/data/featexample2.gff3
# Warning: unrecognized parented feature without ID found before its parent:
# ctg123 . TF_binding_site 1000 1012 . + . Parent=gene00001
# gffread /usr/share/EMBOSS/test/data/gmod-quantitative.gff3
# Warning: invalid start coordinate at line:
# ctg123 affy microarray_oligo 1 100 281 . . Name=Expt1
# gbrowse
# gffread /usr/share/gbrowse/htdocs/tutorial/data_files/volvox.gff3
# Warning: unrecognized parented feature without ID found before its parent:
# ctgA example clone_start 1000 1500 . + . Parent=b101.2
# Warning: unrecognized parented feature without ID found before its parent:
# ctgA example clone_end 19500 20000 . - . Parent=b101.2
# gffread /usr/share/gbrowse/htdocs/tutorial/data_files/volvox_all.gff3
# Warning: unrecognized parented feature without ID found before its parent:
# ctgA example clone_start 1000 1500 . + . Parent=b101.2
# Warning: unrecognized parented feature without ID found before its parent:
# ctgA example clone_end 19500 20000 . - . Parent=b101.2
# gffread /usr/share/gbrowse/htdocs/tutorial/data_files/volvox_bacs.gff3
# Warning: unrecognized parented feature without ID found before its parent:
# ctgA example clone_start 1000 1500 . + . Parent=b101.2
# Warning: unrecognized parented feature without ID found before its parent:
# ctgA example clone_end 19500 20000 . - . Parent=b101.2
# gbrowse-data
# gffread /var/lib/gbrowse/databases/gbrowse_syn/rice/rice.gff3
# Error: cannot open input file /var/lib/gbrowse/databases/gbrowse_syn/rice/rice.gff3!
# ls -l /var/lib/gbrowse/databases/gbrowse_syn/rice/rice.gff3
# -rwxrwx--- 1 root www-data 235531 Jan 15 2017 /var/lib/gbrowse/databases/gbrowse_syn/rice/rice.gff3
# (it is not world readable)
# python-gffutils
# gffread /usr/lib/python3/dist-packages/gffutils/test/data/F3-unique-3.v2.gff
# Warning: invalid start coordinate at line:
# ##hdr seqname source feature start end score strand frame [attributes] [comments]
# gffread /usr/lib/python3/dist-packages/gffutils/test/data/mouse_extra_comma.gff3
# Warning: cannot parse value of GFF attribute "ID=" at line:
# chr17 RefSeq protein 6806527 6812289 . + . ID=;Parent=XM_001475631.1
# gffread /usr/lib/python3/dist-packages/gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff
# Error: discarding overlapping duplicate orthologous_region feature (11218-15711) with ID=ortho:5391
# gffread /usr/lib/python3/dist-packages/gffutils/test/data/glimmer_nokeyval.gff3
# Error: discarding overlapping duplicate mRNA feature (3-62) with ID=GL0000006
# gffread /usr/lib/python3/dist-packages/gffutils/test/data/unsanitized.gff
# Error: invalid feature coordinates (end<start!) at line:
# 3R FlyBase gene 1000 500 . + . ID=FBgnFAKE1;
# r-bioc-genomicfeatures
# gffread /usr/lib/R/site-library/GenomicFeatures/extdata/GFF3_files/TheCanonicalGene_v2.gff3
# Warning: unrecognized parented feature without ID found before its parent:
# ctg123 . TF_binding_site 1000 1012 . + . Parent=gene00001
# seqan-apps
# gffread /usr/share/doc/seqan-apps/insegt/example/annoOutput.gff
# Warning: invalid start coordinate at line:
# test_chromosome Annotation_Count region . . 3 + . ID=ENSG00000146556;459136.822773;
# optimir
# gffread /usr/lib/python3/dist-packages/optimir/resources/coordinates/hsa_miRCarta_v1.1.gff3
# Error: discarding overlapping duplicate miRNA feature (177339349-177339370) with ID=m-3914
# python-pybedtools
# gffread /usr/lib/python3/dist-packages/pybedtools/test/data/c.gff
# Error: discarding overlapping duplicate mRNA feature (496-576) with ID=AT1G01010.mRNA
SKIPS="/usr/share/doc/augustus/tutorial-cgp|/usr/share/doc/augustus/tutorial/results/augustus.abinitio.gff|/usr/share/doc/augustus/tutorial/results/augustus.hints.gff|/usr/lib/R/site-library/Gviz/extdata/test.gff2|/usr/lib/R/site-library/rtracklayer/tests/genes.gff3|/usr/share/EMBOSS/test/data/featexample2.gff3|/usr/share/EMBOSS/test/data/gmod-quantitative.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_all.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_bacs.gff3|/var/lib/gbrowse/databases/ideograms/human_cytobands.gff|/var/lib/gbrowse/databases/ideograms/mouse_cytobands.gff|/var/lib/gbrowse/databases/ideograms/rat_cytobands.gff|/var/lib/gbrowse/databases/yeast_chr1\+2/yeast_chr1\+2.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/F3-unique-3.v2.gff|/usr/lib/python3/dist-packages/gffutils/test/data/mouse_extra_comma.gff3|/usr/lib/R/site-library/GenomicFeatures/extdata/GFF3_files/TheCanonicalGene_v2.gff3|/usr/share/doc/seqan-apps/insegt/example/annoOutput.gff|/usr/lib/python3/dist-packages/optimir/resources/coordinates/hsa_miRCarta_v1.1.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff|/usr/lib/python3/dist-packages/gffutils/test/data/glimmer_nokeyval.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/unsanitized.gff|/usr/lib/python3/dist-packages/pybedtools/test/data/c.gff|/usr/lib/R/site-library/rtracklayer/tests/v2.gff|/usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.gff|/usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.sim.gff"
for package in "${pkgs[@]}"
do
gffs=$(dpkg -L ${package} | grep -E '\.gff.?$' | grep -v -E ${SKIPS})
for gff in ${gffs}
do
echo -n "${gff}: "
gffread ${gff} > /dev/null && echo is okay.
done
done
|
