[med-svn] [Git][med-team/gffread][master] 7 commits: Another test exemption from rtracklayer
Michael R. Crusoe
gitlab at salsa.debian.org
Wed Nov 6 16:42:05 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / gffread
Commits:
7324d7ec by Michael R. Crusoe at 2019-11-06T16:31:01Z
Another test exemption from rtracklayer
- - - - -
6d79d533 by Michael R. Crusoe at 2019-11-06T16:31:20Z
New upstream version 0.11.6
- - - - -
33bd966c by Michael R. Crusoe at 2019-11-06T16:31:20Z
New upstream version
- - - - -
947a78f9 by Michael R. Crusoe at 2019-11-06T16:31:21Z
Update upstream source from tag 'upstream/0.11.6'
Update to upstream version '0.11.6'
with Debian dir b0ab139b2a67da29f55557bfa519b90f0113b7a0
- - - - -
7c10960e by Michael R. Crusoe at 2019-11-06T16:31:24Z
Set upstream metadata fields: Repository.
- - - - -
cb5c360a by Michael R. Crusoe at 2019-11-06T16:31:25Z
Remove obsolete fields Name from debian/upstream/metadata.
- - - - -
72098d09 by Michael R. Crusoe at 2019-11-06T16:41:30Z
needs new release of libgclib-dev
See https://github.com/gpertea/gclib/issues/5
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/tests/run-tests
- debian/upstream/metadata
- gff_utils.cpp
- gffread.cpp
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+gffread (0.11.6-1) UNRELEASED; urgency=medium
+
+ * Another test exemption from rtracklayer
+ * New upstream version
+ * Set upstream metadata fields: Repository.
+ * Remove obsolete fields Name from debian/upstream/metadata.
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Wed, 06 Nov 2019 17:31:20 +0100
+
gffread (0.11.5-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -1,10 +1,11 @@
Source: gffread
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Michael R. Crusoe <michael.crusoe at gmail.com>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
- libgclib-dev
+ libgclib-dev (>= 0.11.3)
Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/gffread
Vcs-Git: https://salsa.debian.org/med-team/gffread.git
=====================================
debian/tests/run-tests
=====================================
@@ -97,7 +97,7 @@ IFS=", " read -r -a pkgs <<< ${PACKAGES}
# 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/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"
+SKIPS="/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"
for package in "${pkgs[@]}"
do
=====================================
debian/upstream/metadata
=====================================
@@ -1,6 +1,6 @@
Registry:
- - Name: OMICtools
- Entry: OMICS_28050
- - Name: conda:bioconda
- Entry: gffread
-Name: gffread
+- Name: OMICtools
+ Entry: OMICS_28050
+- Name: conda:bioconda
+ Entry: gffread
+Repository: https://github.com/gpertea/gffread
=====================================
gff_utils.cpp
=====================================
@@ -734,7 +734,7 @@ void GffLoader::load(GList<GenomicSeqData>& seqdata, GFValidateFunc* gf_validate
GffNameList& attrnames = GffObj::names->attrs;//gffr->names->attrs;
for (int i=0;i<attrnames.Count();i++) {
char* n=attrnames[i]->name;
- if (endsiWith(n, "_type")) {
+ if (endsiWith(n, "type")) {
pseudoTypeAttrIds.Add(attrnames[i]->idx);
}// else {
char* p=strifind(n, "pseudo");
@@ -783,7 +783,7 @@ void GffLoader::load(GList<GenomicSeqData>& seqdata, GFValidateFunc* gf_validate
if (verbose) warnPseudo(*m);
continue;
}
- // *_type=*_pseudogene
+ // *type=*_pseudogene
//find all attributes ending with _type and have value like: *_pseudogene
for (int i=0;i<pseudoTypeAttrIds.Count();++i) {
char* attrv=NULL;
=====================================
gffread.cpp
=====================================
@@ -4,7 +4,7 @@
#define __STDC_FORMAT_MACROS
#include <inttypes.h>
-#define VERSION "0.11.5"
+#define VERSION "0.11.6"
#define USAGE "gffread v" VERSION ". Usage:\n\
gffread <input_gff> [-g <genomic_seqs_fasta> | <dir>][-s <seq_info.fsize>] \n\
@@ -100,7 +100,9 @@ Output options:\n\
-g full path to a multi-fasta file with the genomic sequences\n\
for all input mappings, OR a directory with single-fasta files\n\
(one per genomic sequence, with file names matching sequence names)\n\
- -w write a fasta file with spliced exons for each GFF transcript\n\
+ -w write a fasta file with spliced exons for each transcript\n\
+ --w-add <N> for the -w option, extract additional <N> bases\n\
+ both upstream and downstream of the transcript boundaries\n\
-x write a fasta file with spliced CDS for each GFF transcript\n\
-y write a protein fasta file with the translation of CDS for each record\n\
-W for -w and -x options, write in the FASTA defline the exon\n\
@@ -111,8 +113,6 @@ Output options:\n\
-m <chr_replace> is a name mapping table for converting reference \n\
sequence names, having this 2-column format:\n\
<original_ref_ID> <new_ref_ID>\n\
- WARNING: all GFF records on reference sequences whose original IDs\n\
- are not found in the 1st column of this table will be discarded!\n\
-t use <trackname> in the 2nd column of each GFF/GTF output line\n\
-o write the records into <outfile> instead of stdout\n\
-T main output will be GTF instead of GFF3\n\
@@ -184,9 +184,10 @@ class CTableField {
FILE* ffasta=NULL;
FILE* f_in=NULL;
FILE* f_out=NULL;
-FILE* f_w=NULL; //fasta with spliced exons (transcripts)
-FILE* f_x=NULL; //fasta with spliced CDS
-FILE* f_y=NULL; //fasta with translated CDS
+FILE* f_w=NULL; //writing fasta with spliced exons (transcripts)
+int wPadding = 0; //padding for -w option
+FILE* f_x=NULL; //writing fasta with spliced CDS
+FILE* f_y=NULL; //wrting fasta with translated CDS
bool wCDSonly=false;
bool wNConly=false;
@@ -697,7 +698,21 @@ bool process_transcript(GFastaDb& gfasta, GffObj& gffrec) {
uint cds_start=0;
uint cds_end=0;
seglst.Clear();
+ //TODO: ? if wPadding is set, *temporarily* change first and last exon coordinates ?!?
+ // or perhaps getSpliced() should take an additional padding parameter ?!?
+ int padLeft=0;
+ int padRight=0;
+ if (wPadding>0) {
+ padLeft= (gffrec.start>(uint)wPadding) ? wPadding : gffrec.start - 1;
+ int ediff=faseq->getseqlen()-gffrec.end;
+ padRight=(wPadding>ediff) ? ediff : wPadding;
+ gffrec.addPadding(padLeft, padRight);
+ }
char* exont=gffrec.getSpliced(faseq, false, &seqlen, &cds_start, &cds_end, &seglst);
+ //restore exons to normal (remove padding)
+ if (wPadding>0)
+ gffrec.removePadding(padLeft, padRight);
+
GStr defline(gffrec.getID());
if (exont!=NULL) {
if (gffrec.CDstart>0) {
@@ -719,6 +734,13 @@ bool process_transcript(GFastaDb& gfasta, GffObj& gffrec) {
defline.append("-");
defline+=(int)gffrec.exons[i]->end;
}
+ if (wPadding>0) {
+ defline.append(" padding:");
+ defline.append(padLeft);
+ defline+=(char)'|';
+ defline.append(padRight);
+ }
+
defline.append(" segs:");
for (int i=0;i<seglst.Count();i++) {
if (i>0) defline.append(",");
@@ -727,6 +749,7 @@ bool process_transcript(GFastaDb& gfasta, GffObj& gffrec) {
defline+=(int)seglst[i].end;
}
}
+
if (gffrec.attrs!=NULL) {
//append all attributes found for each transcripts
for (int i=0;i<gffrec.attrs->Count();i++) {
@@ -821,12 +844,13 @@ bool validateGffRec(GffObj* gffrec, GList<GffObj>* gfnew) {
if (rt) {
gffrec->setRefName(rt->new_name);
}
+ /* //no, do not discard non-matching entries, let them pass through!
else {
if (verbose)
GMessage("Info: %s discarded due to reference %s not being mapped\n",
gffrec->getID(), refname.chars());
return false; //discard, ref seq not in the given translation table
- }
+ }*/
}
if (gffloader.transcriptsOnly && gffrec->isDiscarded()) {
//discard generic "locus" features with no other detailed subfeatures
@@ -1006,7 +1030,7 @@ void printAsTable(FILE* f, GffObj* gfo, int* out_counter=NULL) {
int main(int argc, char* argv[]) {
GArgs args(argc, argv,
"version;debug;merge;adj-stop;bed;in-bed;tlf;in-tlf;cluster-only;nc;cov-info;help;"
- "sort-alpha;keep-genes;keep-comments;keep-exon-attrs;force-exons;t-adopt;gene2exon;"
+ "sort-alpha;keep-genes;w-add=;keep-comments;keep-exon-attrs;force-exons;t-adopt;gene2exon;"
"ignore-locus;no-pseudo;table=sort-by=hvOUNHPWCVJMKQYTDARSZFGLEBm:g:i:r:s:l:t:o:w:x:y:d:");
args.printError(USAGE, true);
if (args.getOpt('h') || args.getOpt("help")) {
@@ -1207,13 +1231,18 @@ int main(int argc, char* argv[]) {
//if (f_out==NULL) f_out=stdout;
if (gfasta.fastaPath==NULL && (validCDSonly || spliceCheck || args.getOpt('w')!=NULL || args.getOpt('x')!=NULL || args.getOpt('y')!=NULL))
GError("Error: -g option is required for options -w, -x, -y, -V, -N, -M !\n");
-
openfw(f_w, args, 'w');
openfw(f_x, args, 'x');
openfw(f_y, args, 'y');
+ s=args.getOpt("w-add");
+ if (!s.is_empty()) {
+ if (f_w==NULL) GError("Error: --w-add option requires -w option!\n");
+ wPadding=s.asInt();
+ }
if (f_out==NULL && f_w==NULL && f_x==NULL && f_y==NULL && !covInfo)
f_out=stdout;
+
//if (f_y!=NULL || f_x!=NULL) wCDSonly=true;
//useBadCDS=useBadCDS || (fgtfok==NULL && fgtfbad==NULL && f_y==NULL && f_x==NULL);
View it on GitLab: https://salsa.debian.org/med-team/gffread/compare/810cee750b894bc2b0d57978ea1a3c64494adcb9...72098d09bba35e0e0f71b7fb1e573cb8b8a3ad2c
--
View it on GitLab: https://salsa.debian.org/med-team/gffread/compare/810cee750b894bc2b0d57978ea1a3c64494adcb9...72098d09bba35e0e0f71b7fb1e573cb8b8a3ad2c
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