From gbottu at ben.vub.ac.be Thu Mar 3 13:51:03 2005 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Thu, 3 Mar 2005 19:51:03 +0100 Subject: question about type gapany Message-ID: <20050303185103.GB16138@bigben.ulb.ac.be> Dear colleagues, I just noticed a strange thing. The ACD file for emma contains : seqall: sequence [ parameter: "Y" type: "gapany" ] I tried to replace "gapany" by "gap", so that the input sequences should be degapped before the alignment procedure starts. I was surprised to get an output file with unaligned sequences. As if the degapping was also performed on the output instead of just on the input. Is this normal ? I ask the question because I have developed programs that work like emma an I was busy adding the "type" attributes, in order to improve them. Has anybody already seen such behaviour ? Or am I misunderstanding something ? Regards, Guy Bottu From pmr at ebi.ac.uk Thu Mar 3 17:52:24 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Thu, 3 Mar 2005 22:52:24 -0000 (GMT) Subject: question about type gapany In-Reply-To: <20050303185103.GB16138@bigben.ulb.ac.be> References: <20050303185103.GB16138@bigben.ulb.ac.be> Message-ID: <1490.62.135.132.22.1109890344.squirrel@webmail.ebi.ac.uk> Dear Guy, > I just noticed a strange thing. The ACD file for emma contains : > > seqall: sequence [ > parameter: "Y" > type: "gapany" > ] > > I tried to replace "gapany" by "gap", so that the input sequences should > be degapped before the alignment procedure starts. I was surprised to get > an output file with unaligned sequences. As if the degapping was also > performed on the output instead of just on the input. Is this normal ? > I ask the question because I have developed programs that work like emma > an I was busy adding the "type" attributes, in order to improve them. Has > anybody already seen such behaviour ? Or am I misunderstanding something ? There is a general principle that the output sequence type matches the input unless explicitly stated (transeq for example). This is so that wrappers, GUIs, etc. know what output sequence type to expect. You can try to specify gapany as the output sequence type. I think this will fix your modified ACD file (I'm away from EBI until next week and will look more closely then). regards, Peter From gbottu at ben.vub.ac.be Fri Mar 4 05:22:25 2005 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Fri, 4 Mar 2005 11:22:25 +0100 Subject: question about type gapany In-Reply-To: <1490.62.135.132.22.1109890344.squirrel@webmail.ebi.ac.uk> References: <20050303185103.GB16138@bigben.ulb.ac.be> <1490.62.135.132.22.1109890344.squirrel@webmail.ebi.ac.uk> Message-ID: <20050304102225.GB21895@bigben.ulb.ac.be> On Thu, Mar 03, 2005 at 10:52:24PM -0000, pmr at ebi.ac.uk wrote: > There is a general principle that the output sequence type matches the > input unless explicitly stated (transeq for example). > > This is so that wrappers, GUIs, etc. know what output sequence type to > expect. > > You can try to specify gapany as the output sequence type. I think this > will fix your modified ACD file (I'm away from EBI until next week and > will look more closely then). Yes, that's it, it works. With this I have leraned something new about EMBOSS and ACD :-) Guy Bottu From pmr at ebi.ac.uk Mon Mar 7 04:04:38 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 07 Mar 2005 09:04:38 +0000 Subject: question about type gapany In-Reply-To: <20050304102225.GB21895@bigben.ulb.ac.be> References: <20050303185103.GB16138@bigben.ulb.ac.be> <1490.62.135.132.22.1109890344.squirrel@webmail.ebi.ac.uk> <20050304102225.GB21895@bigben.ulb.ac.be> Message-ID: <422C1926.3030107@ebi.ac.uk> Guy Bottu wrote: >>You can try to specify gapany as the output sequence type. I think this >>will fix your modified ACD file (I'm away from EBI until next week and >>will look more closely then). > > > Yes, that's it, it works. With this I have leraned something new about > EMBOSS and ACD :-) ... and it will be a very good example for ACD courses :-) Peter From gbottu at ben.vub.ac.be Thu Mar 3 18:51:03 2005 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Thu, 3 Mar 2005 19:51:03 +0100 Subject: question about type gapany Message-ID: <20050303185103.GB16138@bigben.ulb.ac.be> Dear colleagues, I just noticed a strange thing. The ACD file for emma contains : seqall: sequence [ parameter: "Y" type: "gapany" ] I tried to replace "gapany" by "gap", so that the input sequences should be degapped before the alignment procedure starts. I was surprised to get an output file with unaligned sequences. As if the degapping was also performed on the output instead of just on the input. Is this normal ? I ask the question because I have developed programs that work like emma an I was busy adding the "type" attributes, in order to improve them. Has anybody already seen such behaviour ? Or am I misunderstanding something ? Regards, Guy Bottu From pmr at ebi.ac.uk Thu Mar 3 22:52:24 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Thu, 3 Mar 2005 22:52:24 -0000 (GMT) Subject: question about type gapany In-Reply-To: <20050303185103.GB16138@bigben.ulb.ac.be> References: <20050303185103.GB16138@bigben.ulb.ac.be> Message-ID: <1490.62.135.132.22.1109890344.squirrel@webmail.ebi.ac.uk> Dear Guy, > I just noticed a strange thing. The ACD file for emma contains : > > seqall: sequence [ > parameter: "Y" > type: "gapany" > ] > > I tried to replace "gapany" by "gap", so that the input sequences should > be degapped before the alignment procedure starts. I was surprised to get > an output file with unaligned sequences. As if the degapping was also > performed on the output instead of just on the input. Is this normal ? > I ask the question because I have developed programs that work like emma > an I was busy adding the "type" attributes, in order to improve them. Has > anybody already seen such behaviour ? Or am I misunderstanding something ? There is a general principle that the output sequence type matches the input unless explicitly stated (transeq for example). This is so that wrappers, GUIs, etc. know what output sequence type to expect. You can try to specify gapany as the output sequence type. I think this will fix your modified ACD file (I'm away from EBI until next week and will look more closely then). regards, Peter From gbottu at ben.vub.ac.be Fri Mar 4 10:22:25 2005 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Fri, 4 Mar 2005 11:22:25 +0100 Subject: question about type gapany In-Reply-To: <1490.62.135.132.22.1109890344.squirrel@webmail.ebi.ac.uk> References: <20050303185103.GB16138@bigben.ulb.ac.be> <1490.62.135.132.22.1109890344.squirrel@webmail.ebi.ac.uk> Message-ID: <20050304102225.GB21895@bigben.ulb.ac.be> On Thu, Mar 03, 2005 at 10:52:24PM -0000, pmr at ebi.ac.uk wrote: > There is a general principle that the output sequence type matches the > input unless explicitly stated (transeq for example). > > This is so that wrappers, GUIs, etc. know what output sequence type to > expect. > > You can try to specify gapany as the output sequence type. I think this > will fix your modified ACD file (I'm away from EBI until next week and > will look more closely then). Yes, that's it, it works. With this I have leraned something new about EMBOSS and ACD :-) Guy Bottu From pmr at ebi.ac.uk Mon Mar 7 09:04:38 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 07 Mar 2005 09:04:38 +0000 Subject: question about type gapany In-Reply-To: <20050304102225.GB21895@bigben.ulb.ac.be> References: <20050303185103.GB16138@bigben.ulb.ac.be> <1490.62.135.132.22.1109890344.squirrel@webmail.ebi.ac.uk> <20050304102225.GB21895@bigben.ulb.ac.be> Message-ID: <422C1926.3030107@ebi.ac.uk> Guy Bottu wrote: >>You can try to specify gapany as the output sequence type. I think this >>will fix your modified ACD file (I'm away from EBI until next week and >>will look more closely then). > > > Yes, that's it, it works. With this I have leraned something new about > EMBOSS and ACD :-) ... and it will be a very good example for ACD courses :-) Peter