strand in Bio::SearchIO when parsing fasta35 output
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strand in Bio::SearchIO when parsing fasta35 output
by michael watson (IAH-C)
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Dear all
Where does this go? Perhaps I am doing something wrong. Fasta35 output puts the strand in the hit list at the top: cluster_99033:3 ( 23) [r] 115 37.9 0.0011 cluster_79238:1 ( 27) [f] 126 38.0 0.00097 0.963 0.963 27 The [r] stands for reverse and the [f] stands for forward. There is also the text "rev-comp" after the hit line further down. However, when I parse fasta35 output using SearchIO and output the strand of the HSP: print $hsp->strand('hit'), ","; print $hsp->strand('query'), "\n"; This simply prints out 0, 0 (I assume 0 is the default in BioPerl for "I don't know which strand it's on"). So the information is there, but it's not getting parsed. Alternatively, I've missed something and will feel a bit foolish. Currently using BioPerl 1.6.0 Thanks Mick _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: strand in Bio::SearchIO when parsing fasta35 output
by Jason Stajich-3
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Is this -m9 -d 0 output or standard default? I think the strand is parsed in the HSP parsing. Can you double check what $hsp->query->strand and $hsp->hit->strand prints? A full example report as a bug request will be next step if that doesn't resolve. -jason On Oct 26, 2009, at 10:04 AM, michael watson (IAH-C) wrote: > Dear all > > Where does this go? Perhaps I am doing something wrong. > > Fasta35 output puts the strand in the hit list at the top: > > cluster_99033:3 ( 23) [r] 115 37.9 > 0.0011 > cluster_79238:1 ( 27) [f] 126 38.0 0.00097 0.963 > 0.963 27 > > The [r] stands for reverse and the [f] stands for forward. > > There is also the text "rev-comp" after the hit line further down. > > However, when I parse fasta35 output using SearchIO and output the > strand of the HSP: > > print $hsp->strand('hit'), ","; > print $hsp->strand('query'), "\n"; > > This simply prints out 0, 0 (I assume 0 is the default in BioPerl > for "I don't know which strand it's on"). > > So the information is there, but it's not getting parsed. > Alternatively, I've missed something and will feel a bit foolish. > > Currently using BioPerl 1.6.0 > > Thanks > Mick > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich jason.stajich@... jason@... _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: strand in Bio::SearchIO when parsing fasta35 output
by michael watson (IAH-C)
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Hi Jason
They both print 0 also. A bug report it is Mick -----Original Message----- From: Jason Stajich [mailto:jason.stajich@...] On Behalf Of Jason Stajich Sent: 26 October 2009 18:46 To: michael watson (IAH-C) Cc: bioperl-l Subject: Re: [Bioperl-l] strand in Bio::SearchIO when parsing fasta35 output Is this -m9 -d 0 output or standard default? I think the strand is parsed in the HSP parsing. Can you double check what $hsp->query->strand and $hsp->hit->strand prints? A full example report as a bug request will be next step if that doesn't resolve. -jason On Oct 26, 2009, at 10:04 AM, michael watson (IAH-C) wrote: > Dear all > > Where does this go? Perhaps I am doing something wrong. > > Fasta35 output puts the strand in the hit list at the top: > > cluster_99033:3 ( 23) [r] 115 37.9 > 0.0011 > cluster_79238:1 ( 27) [f] 126 38.0 0.00097 0.963 > 0.963 27 > > The [r] stands for reverse and the [f] stands for forward. > > There is also the text "rev-comp" after the hit line further down. > > However, when I parse fasta35 output using SearchIO and output the > strand of the HSP: > > print $hsp->strand('hit'), ","; > print $hsp->strand('query'), "\n"; > > This simply prints out 0, 0 (I assume 0 is the default in BioPerl > for "I don't know which strand it's on"). > > So the information is there, but it's not getting parsed. > Alternatively, I've missed something and will feel a bit foolish. > > Currently using BioPerl 1.6.0 > > Thanks > Mick > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich jason.stajich@... jason@... _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: strand in Bio::SearchIO when parsing fasta35 output
by michael watson (IAH-C)
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Hello
I was just wondering if anyone had had time to look into this? I posted a bug: http://bugzilla.open-bio.org/show_bug.cgi?id=2937 Thanks Mick -----Original Message----- From: bioperl-l-bounces@... [mailto:bioperl-l-bounces@...] On Behalf Of michael watson (IAH-C) Sent: 27 October 2009 09:01 To: 'Jason Stajich' Cc: bioperl-l Subject: Re: [Bioperl-l] strand in Bio::SearchIO when parsing fasta35 output Hi Jason They both print 0 also. A bug report it is Mick -----Original Message----- From: Jason Stajich [mailto:jason.stajich@...] On Behalf Of Jason Stajich Sent: 26 October 2009 18:46 To: michael watson (IAH-C) Cc: bioperl-l Subject: Re: [Bioperl-l] strand in Bio::SearchIO when parsing fasta35 output Is this -m9 -d 0 output or standard default? I think the strand is parsed in the HSP parsing. Can you double check what $hsp->query->strand and $hsp->hit->strand prints? A full example report as a bug request will be next step if that doesn't resolve. -jason On Oct 26, 2009, at 10:04 AM, michael watson (IAH-C) wrote: > Dear all > > Where does this go? Perhaps I am doing something wrong. > > Fasta35 output puts the strand in the hit list at the top: > > cluster_99033:3 ( 23) [r] 115 37.9 > 0.0011 > cluster_79238:1 ( 27) [f] 126 38.0 0.00097 0.963 > 0.963 27 > > The [r] stands for reverse and the [f] stands for forward. > > There is also the text "rev-comp" after the hit line further down. > > However, when I parse fasta35 output using SearchIO and output the > strand of the HSP: > > print $hsp->strand('hit'), ","; > print $hsp->strand('query'), "\n"; > > This simply prints out 0, 0 (I assume 0 is the default in BioPerl > for "I don't know which strand it's on"). > > So the information is there, but it's not getting parsed. > Alternatively, I've missed something and will feel a bit foolish. > > Currently using BioPerl 1.6.0 > > Thanks > Mick > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich jason.stajich@... jason@... _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: strand in Bio::SearchIO when parsing fasta35 output
by Chris Fields-5
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Mick,
Short answer, no. It was in the queue to be fixed at some point in 1.6.x, but that queue is quite long. I'm pushing it into the queue specifically for 1.6.2, so it should be addressed soon. chris On Nov 20, 2009, at 4:07 AM, michael watson (IAH-C) wrote: > Hello > > I was just wondering if anyone had had time to look into this? > > I posted a bug: http://bugzilla.open-bio.org/show_bug.cgi?id=2937 > > Thanks > Mick > > -----Original Message----- > From: bioperl-l-bounces@... [mailto:bioperl-l-bounces@...] On Behalf Of michael watson (IAH-C) > Sent: 27 October 2009 09:01 > To: 'Jason Stajich' > Cc: bioperl-l > Subject: Re: [Bioperl-l] strand in Bio::SearchIO when parsing fasta35 output > > Hi Jason > > They both print 0 also. > > A bug report it is > > Mick > > -----Original Message----- > From: Jason Stajich [mailto:jason.stajich@...] On Behalf Of Jason Stajich > Sent: 26 October 2009 18:46 > To: michael watson (IAH-C) > Cc: bioperl-l > Subject: Re: [Bioperl-l] strand in Bio::SearchIO when parsing fasta35 output > > > Is this -m9 -d 0 output or standard default? I think the strand is > parsed in the HSP parsing. > > Can you double check what $hsp->query->strand and $hsp->hit->strand > prints? > > A full example report as a bug request will be next step if that > doesn't resolve. > > -jason > On Oct 26, 2009, at 10:04 AM, michael watson (IAH-C) wrote: > >> Dear all >> >> Where does this go? Perhaps I am doing something wrong. >> >> Fasta35 output puts the strand in the hit list at the top: >> >> cluster_99033:3 ( 23) [r] 115 37.9 >> 0.0011 >> cluster_79238:1 ( 27) [f] 126 38.0 0.00097 0.963 >> 0.963 27 >> >> The [r] stands for reverse and the [f] stands for forward. >> >> There is also the text "rev-comp" after the hit line further down. >> >> However, when I parse fasta35 output using SearchIO and output the >> strand of the HSP: >> >> print $hsp->strand('hit'), ","; >> print $hsp->strand('query'), "\n"; >> >> This simply prints out 0, 0 (I assume 0 is the default in BioPerl >> for "I don't know which strand it's on"). >> >> So the information is there, but it's not getting parsed. >> Alternatively, I've missed something and will feel a bit foolish. >> >> Currently using BioPerl 1.6.0 >> >> Thanks >> Mick >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@... >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > Jason Stajich > jason.stajich@... > jason@... > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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