Bug #130815 for Bio-Gonzales: coords2gff.pl created empty gff file

Thu Oct 24 16:43:34 2019 ytm4 [...] cdc.gov - Ticket created

Subject:	coords2gff.pl created empty gff file
Date:	Thu, 24 Oct 2019 20:43:16 +0000
To:	"bug-Bio-Gonzales [...] rt.cpan.org" <bug-Bio-Gonzales [...] rt.cpan.org>
From:	"Wang, Haibin (CDC/DDID/NCIRD/DVD) (CTR)" <ytm4 [...] cdc.gov>

Hi, I ran the script on Centos 7 with the command "coords2gff.pl out.coords out.gff3" and the out.gff3 is empty (0 size). Attached is my coordinates file from nucmer. Thanks, Haibin Wang Research Microbiologist IHRC, Inc. NCIRD/DVD/RVB Centers for Disease Control and Prevention (CDC) Phone: 404-639-1205 Email: ytm4@cdc.gov

Download out.coords
application/octet-stream 1k

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Sun Oct 27 11:53:37 2019 cpan [...] bargsten.org - Correspondence added

On Thu Oct 24 16:43:34 2019, ytm4@cdc.gov wrote: Show quoted text

> Hi, > > I ran the script on Centos 7 with the command "coords2gff.pl > out.coords out.gff3" and the out.gff3 is empty (0 size). Attached is > my coordinates file from nucmer. > > Thanks, > > Haibin Wang

Hi Haibin, the script expects a tab-separated (-T option of show-coords) nucmer coords output. You can generate it like this (I used the default mummer example for this): $ nucmer -maxmatch -c 100 -p nucmer B_anthracis_Mslice.fasta B_anthracis_contigs.fasta 1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS # reading input file "nucmer.ntref" of length 312601 # construct suffix tree for sequence of length 312601 # (maximum reference length is 536870908) # (maximum query length is 4294967295) # process 3126 characters per dot #.................................................................................................... # CONSTRUCTIONTIME /usr/bin/mummer nucmer.ntref 0.09 # reading input file "/home/jwb/projekte/biogonzales_pl/t/coords2gff/B_anthracis_contigs.fasta" of length 308869 # matching query-file "/home/jwb/projekte/biogonzales_pl/t/coords2gff/B_anthracis_contigs.fasta" # against subject-file "nucmer.ntref" # COMPLETETIME /usr/bin/mummer nucmer.ntref 0.19 # SPACE /usr/bin/mummer nucmer.ntref 0.60 4: FINISHING DATA $ show-coords -T nucmer.delta >nucmer.coords $ coords2gff.pl nucmer.coords I'll add documentation for this.

Sun Oct 27 11:53:37 2019 The RT System itself - Status changed from 'new' to 'open'

Sun Oct 27 11:55:36 2019 cpan [...] bargsten.org - Correspondence added

made a typo, the coords2gff.pl command needs to be: $ coords2gff.pl nucmer.coords nucmer.gff3 On Sun Oct 27 11:53:37 2019, jwb wrote: Show quoted text

> On Thu Oct 24 16:43:34 2019, ytm4@cdc.gov wrote:

> > Hi, > > > > I ran the script on Centos 7 with the command "coords2gff.pl > > out.coords out.gff3" and the out.gff3 is empty (0 size). Attached is > > my coordinates file from nucmer. > > > > Thanks, > > > > Haibin Wang

> > Hi Haibin, > the script expects a tab-separated (-T option of show-coords) nucmer > coords output. You can generate it like this (I used the default > mummer example for this): > > $ nucmer -maxmatch -c 100 -p nucmer B_anthracis_Mslice.fasta > B_anthracis_contigs.fasta > 1: PREPARING DATA > 2,3: RUNNING mummer AND CREATING CLUSTERS > # reading input file "nucmer.ntref" of length 312601 > # construct suffix tree for sequence of length 312601 > # (maximum reference length is 536870908) > # (maximum query length is 4294967295) > # process 3126 characters per dot > #.................................................................................................... > # CONSTRUCTIONTIME /usr/bin/mummer nucmer.ntref 0.09 > # reading input file > "/home/jwb/projekte/biogonzales_pl/t/coords2gff/B_anthracis_contigs.fasta" > of length 308869 > # matching query-file > "/home/jwb/projekte/biogonzales_pl/t/coords2gff/B_anthracis_contigs.fasta" > # against subject-file "nucmer.ntref" > # COMPLETETIME /usr/bin/mummer nucmer.ntref 0.19 > # SPACE /usr/bin/mummer nucmer.ntref 0.60 > 4: FINISHING DATA > > $ show-coords -T nucmer.delta >nucmer.coords > $ coords2gff.pl nucmer.coords > > > I'll add documentation for this.