From prateek.vit at gmail.com Thu May 10 03:49:10 2012 From: prateek.vit at gmail.com (prateek.vit at gmail.com) Date: Thu, 10 May 2012 03:49:10 -0400 Subject: [EMBOSS] (no subject) Message-ID: <4fabc75b.5051cd0a.66d1.ffff95d6@mx.google.com> get ready for something big to happen to the online world http://www.cnbc7.net/0412/ take advantage of this today From p.j.a.cock at googlemail.com Mon May 14 12:51:52 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 14 May 2012 17:51:52 +0100 Subject: [EMBOSS] Documentation suggestion for preg/dreg Message-ID: Dear EMBOSS, I would find it helpful if the "see also" documentation for preg and dreg referenced each other (since they are both regex based sequence searching tools). http://emboss.open-bio.org/wiki/Appdoc:Dreg#See_also http://emboss.open-bio.org/wiki/Appdoc:Preg#See_also Thanks, Peter From ricepeterm at yahoo.co.uk Mon May 14 14:54:33 2012 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Mon, 14 May 2012 19:54:33 +0100 Subject: [EMBOSS] Documentation suggestion for preg/dreg In-Reply-To: References: Message-ID: <4FB154E9.2080301@yahoo.co.uk> On 05/14/12 17:51, Peter Cock wrote: > Dear EMBOSS, > > I would find it helpful if the "see also" documentation for preg and > dreg referenced each other (since they are both regex based sequence > searching tools). > > http://emboss.open-bio.org/wiki/Appdoc:Dreg#See_also > http://emboss.open-bio.org/wiki/Appdoc:Preg#See_also An interesting challenge. The "See also" documentation is generated by finding all programs in the same group (the "groups:" application attribute in the ACD file). These are classified as Nucleic:Motifs and Protein:Motifs so they are currently kept apart. We'll have a look and see if a general "regular expression search" (or similar) group would be useful ... and similar general groups for other applications. regards, Peter Rice EMBOSS Team From hnorpois at googlemail.com Mon May 14 15:41:33 2012 From: hnorpois at googlemail.com (Hermann Norpois) Date: Mon, 14 May 2012 21:41:33 +0200 Subject: [EMBOSS] jaspextract does not work Message-ID: To whom it may conern. I have problems to install the jaspar database. My emboss database directory is /usr/share/EMBOSS/data. The jaspar files are dummies. This is okay. I downloaded Archive.zip from the jaspar site, extracted it to ~/jaspar and got 3 directories: drwxr-xr-x 5 hnorpois hnorpois 4096 2012-05-14 21:04 all_data drwxr-xr-x 10 hnorpois hnorpois 4096 2012-05-14 21:04 jaspar_collections drwxr-xr-x 4 hnorpois hnorpois 4096 2012-05-14 21:04 jaspar_CORE Now i started from the command line jaspextract and get Extract data from JASPAR JASPAR database directory [.]: I do not understand what to type after JASPAR database directory [.]: I tried all variations I can imagine (e.g.: ~/jaspar, ~/jaspar/all_data, ~/jaspar/all_data/FlatFileDir) but I always get the answer: Error: Unable to open directory '~/jaspar/' Could anybody give me an instruction? Thank you and sincerely Hermann Norpois From ricepeterm at yahoo.co.uk Mon May 14 16:02:16 2012 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Mon, 14 May 2012 21:02:16 +0100 Subject: [EMBOSS] jaspextract does not work In-Reply-To: References: Message-ID: <4FB164C8.9090103@yahoo.co.uk> On 05/14/12 20:41, Hermann Norpois wrote: > To whom it may conern. > > I have problems to install the jaspar database. My emboss database > directory is /usr/share/EMBOSS/data. The jaspar files are dummies. This is > okay. > I downloaded Archive.zip from the jaspar site, extracted it to ~/jaspar and > got 3 directories: > > drwxr-xr-x 5 hnorpois hnorpois 4096 2012-05-14 21:04 all_data > drwxr-xr-x 10 hnorpois hnorpois 4096 2012-05-14 21:04 jaspar_collections > drwxr-xr-x 4 hnorpois hnorpois 4096 2012-05-14 21:04 jaspar_CORE > > Now i started from the command line > jaspextract > and get > > Extract data from JASPAR > JASPAR database directory [.]: > > I do not understand what to type after JASPAR database directory [.]: > > I tried all variations I can imagine (e.g.: ~/jaspar, ~/jaspar/all_data, > ~/jaspar/all_data/FlatFileDir) but I always get the answer: > > Error: Unable to open directory '~/jaspar/' > > Could anybody give me an instruction? The help (jaspextract -help) has a clue. The directory is 'The FlatFileDir directory containing the .pfm files and the matrix_list.txt file' so if you are in the jaspar directory you could reply with all_data/FlatFileDir/ You are being (reasonably) confused because EMBOSS is not interpreting the '~' in your response. That is an omission by us ... it will fill in the directory when it sees '~' for an input file, but not for an input directory. This will be fixed in the next release. Meanwhile a full or relative path will be fine. Hope this helps, Peter Rice EMBOSS Team From hnorpois at googlemail.com Tue May 15 16:23:59 2012 From: hnorpois at googlemail.com (Hermann Norpois) Date: Tue, 15 May 2012 22:23:59 +0200 Subject: [EMBOSS] jaspscan from the commandline Message-ID: Hello, I tried to execute jaspscan from the command line and got the menu again. This is my syntax: (1) ~/embl/jtest$ jaspscan -sequence sequence.fasta -matrices @matrix_mouse -threshold 89.0 matrix_mouse is a file and looks like this: ma0042.1, ma0090.1 I tried it with upper case as well (MA..., MA...). matrix_mouse is in the same directory like sequence.fasta. It is the directory in which I start jaspscan. If I execute (1) I have to read: Scans DNA sequences for transcription factors Jaspar matrix set C : Core F : Fam P : Phylofacts N : CNE O : POLII S : SPLICE B : PBM L : PBM_HLH H : PBM_HOMEO So jaspscan did not recognise my file matrix_mouse. I tried it with "@matrix_mouse", '@matrix_mouse' etc .. Always the same. Could you please give me a hint concerning the correct syntax? In addition: I would prefer an outputfile with the transcription factors in a list, e.g. like this accessionnumber of input sequence: TFa, TFb etc Thank you very much. Sincerel Hermann From ricepeterm at yahoo.co.uk Wed May 16 03:59:52 2012 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Wed, 16 May 2012 08:59:52 +0100 Subject: [EMBOSS] jaspscan from the commandline In-Reply-To: References: Message-ID: <4FB35E78.2090907@yahoo.co.uk> On 15/05/2012 21:23, Hermann Norpois wrote: > Hello, > > I tried to execute jaspscan from the command line and got the menu again. > This is my syntax: > (1) ~/embl/jtest$ jaspscan -sequence sequence.fasta -matrices @matrix_mouse > -threshold 89.0 > > matrix_mouse is a file and looks like this: > ma0042.1, ma0090.1 > > I tried it with upper case as well (MA..., MA...). > > matrix_mouse is in the same directory like sequence.fasta. It is the > directory in which I start jaspscan. > > If I execute (1) I have to read: > > Scans DNA sequences for transcription factors > Jaspar matrix set > C : Core > F : Fam > P : Phylofacts > N : CNE > O : POLII > S : SPLICE > B : PBM > L : PBM_HLH > H : PBM_HOMEO > > So jaspscan did not recognise my file matrix_mouse. I tried it with > "@matrix_mouse", '@matrix_mouse' etc .. Always the same. Could you please > give me a hint concerning the correct syntax? Your matrix.list file has a list of matrix names (the default is to use all matrices) but you still need to say which matrix set they belong to so jaspscan knows which directory to search. You can simply add -menu c (or whatever section you are searching), or for the default value -auto which defaults all remaining prompted values. > In addition: I would prefer an outputfile with the transcription factors in > a list, e.g. like this > accessionnumber of input sequence: TFa, TFb etc The output is an EMBOSS "report" so you do have a choice of report formats available with the command line qualifier -rformat. For example, you could use -rformat excel and then use excel or any other spreadsheet tool to select the columns you need. We could also add more report formats to the next release, but I am not convinced this one is useful as it removes too much information. However, we may be able to reduce the extra tags included in jaspscan output. We may also be able to provide an applicationn that will post-propcess a standard report format and produce the summary you ask for, again in the next release. Hope this helps Peter Rice EMBOSS Team From prateek.vit at gmail.com Thu May 10 07:49:10 2012 From: prateek.vit at gmail.com (prateek.vit at gmail.com) Date: Thu, 10 May 2012 03:49:10 -0400 Subject: [EMBOSS] (no subject) Message-ID: <4fabc75b.5051cd0a.66d1.ffff95d6@mx.google.com> get ready for something big to happen to the online world http://www.cnbc7.net/0412/ take advantage of this today From p.j.a.cock at googlemail.com Mon May 14 16:51:52 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 14 May 2012 17:51:52 +0100 Subject: [EMBOSS] Documentation suggestion for preg/dreg Message-ID: Dear EMBOSS, I would find it helpful if the "see also" documentation for preg and dreg referenced each other (since they are both regex based sequence searching tools). http://emboss.open-bio.org/wiki/Appdoc:Dreg#See_also http://emboss.open-bio.org/wiki/Appdoc:Preg#See_also Thanks, Peter From ricepeterm at yahoo.co.uk Mon May 14 18:54:33 2012 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Mon, 14 May 2012 19:54:33 +0100 Subject: [EMBOSS] Documentation suggestion for preg/dreg In-Reply-To: References: Message-ID: <4FB154E9.2080301@yahoo.co.uk> On 05/14/12 17:51, Peter Cock wrote: > Dear EMBOSS, > > I would find it helpful if the "see also" documentation for preg and > dreg referenced each other (since they are both regex based sequence > searching tools). > > http://emboss.open-bio.org/wiki/Appdoc:Dreg#See_also > http://emboss.open-bio.org/wiki/Appdoc:Preg#See_also An interesting challenge. The "See also" documentation is generated by finding all programs in the same group (the "groups:" application attribute in the ACD file). These are classified as Nucleic:Motifs and Protein:Motifs so they are currently kept apart. We'll have a look and see if a general "regular expression search" (or similar) group would be useful ... and similar general groups for other applications. regards, Peter Rice EMBOSS Team From hnorpois at googlemail.com Mon May 14 19:41:33 2012 From: hnorpois at googlemail.com (Hermann Norpois) Date: Mon, 14 May 2012 21:41:33 +0200 Subject: [EMBOSS] jaspextract does not work Message-ID: To whom it may conern. I have problems to install the jaspar database. My emboss database directory is /usr/share/EMBOSS/data. The jaspar files are dummies. This is okay. I downloaded Archive.zip from the jaspar site, extracted it to ~/jaspar and got 3 directories: drwxr-xr-x 5 hnorpois hnorpois 4096 2012-05-14 21:04 all_data drwxr-xr-x 10 hnorpois hnorpois 4096 2012-05-14 21:04 jaspar_collections drwxr-xr-x 4 hnorpois hnorpois 4096 2012-05-14 21:04 jaspar_CORE Now i started from the command line jaspextract and get Extract data from JASPAR JASPAR database directory [.]: I do not understand what to type after JASPAR database directory [.]: I tried all variations I can imagine (e.g.: ~/jaspar, ~/jaspar/all_data, ~/jaspar/all_data/FlatFileDir) but I always get the answer: Error: Unable to open directory '~/jaspar/' Could anybody give me an instruction? Thank you and sincerely Hermann Norpois From ricepeterm at yahoo.co.uk Mon May 14 20:02:16 2012 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Mon, 14 May 2012 21:02:16 +0100 Subject: [EMBOSS] jaspextract does not work In-Reply-To: References: Message-ID: <4FB164C8.9090103@yahoo.co.uk> On 05/14/12 20:41, Hermann Norpois wrote: > To whom it may conern. > > I have problems to install the jaspar database. My emboss database > directory is /usr/share/EMBOSS/data. The jaspar files are dummies. This is > okay. > I downloaded Archive.zip from the jaspar site, extracted it to ~/jaspar and > got 3 directories: > > drwxr-xr-x 5 hnorpois hnorpois 4096 2012-05-14 21:04 all_data > drwxr-xr-x 10 hnorpois hnorpois 4096 2012-05-14 21:04 jaspar_collections > drwxr-xr-x 4 hnorpois hnorpois 4096 2012-05-14 21:04 jaspar_CORE > > Now i started from the command line > jaspextract > and get > > Extract data from JASPAR > JASPAR database directory [.]: > > I do not understand what to type after JASPAR database directory [.]: > > I tried all variations I can imagine (e.g.: ~/jaspar, ~/jaspar/all_data, > ~/jaspar/all_data/FlatFileDir) but I always get the answer: > > Error: Unable to open directory '~/jaspar/' > > Could anybody give me an instruction? The help (jaspextract -help) has a clue. The directory is 'The FlatFileDir directory containing the .pfm files and the matrix_list.txt file' so if you are in the jaspar directory you could reply with all_data/FlatFileDir/ You are being (reasonably) confused because EMBOSS is not interpreting the '~' in your response. That is an omission by us ... it will fill in the directory when it sees '~' for an input file, but not for an input directory. This will be fixed in the next release. Meanwhile a full or relative path will be fine. Hope this helps, Peter Rice EMBOSS Team From hnorpois at googlemail.com Tue May 15 20:23:59 2012 From: hnorpois at googlemail.com (Hermann Norpois) Date: Tue, 15 May 2012 22:23:59 +0200 Subject: [EMBOSS] jaspscan from the commandline Message-ID: Hello, I tried to execute jaspscan from the command line and got the menu again. This is my syntax: (1) ~/embl/jtest$ jaspscan -sequence sequence.fasta -matrices @matrix_mouse -threshold 89.0 matrix_mouse is a file and looks like this: ma0042.1, ma0090.1 I tried it with upper case as well (MA..., MA...). matrix_mouse is in the same directory like sequence.fasta. It is the directory in which I start jaspscan. If I execute (1) I have to read: Scans DNA sequences for transcription factors Jaspar matrix set C : Core F : Fam P : Phylofacts N : CNE O : POLII S : SPLICE B : PBM L : PBM_HLH H : PBM_HOMEO So jaspscan did not recognise my file matrix_mouse. I tried it with "@matrix_mouse", '@matrix_mouse' etc .. Always the same. Could you please give me a hint concerning the correct syntax? In addition: I would prefer an outputfile with the transcription factors in a list, e.g. like this accessionnumber of input sequence: TFa, TFb etc Thank you very much. Sincerel Hermann From ricepeterm at yahoo.co.uk Wed May 16 07:59:52 2012 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Wed, 16 May 2012 08:59:52 +0100 Subject: [EMBOSS] jaspscan from the commandline In-Reply-To: References: Message-ID: <4FB35E78.2090907@yahoo.co.uk> On 15/05/2012 21:23, Hermann Norpois wrote: > Hello, > > I tried to execute jaspscan from the command line and got the menu again. > This is my syntax: > (1) ~/embl/jtest$ jaspscan -sequence sequence.fasta -matrices @matrix_mouse > -threshold 89.0 > > matrix_mouse is a file and looks like this: > ma0042.1, ma0090.1 > > I tried it with upper case as well (MA..., MA...). > > matrix_mouse is in the same directory like sequence.fasta. It is the > directory in which I start jaspscan. > > If I execute (1) I have to read: > > Scans DNA sequences for transcription factors > Jaspar matrix set > C : Core > F : Fam > P : Phylofacts > N : CNE > O : POLII > S : SPLICE > B : PBM > L : PBM_HLH > H : PBM_HOMEO > > So jaspscan did not recognise my file matrix_mouse. I tried it with > "@matrix_mouse", '@matrix_mouse' etc .. Always the same. Could you please > give me a hint concerning the correct syntax? Your matrix.list file has a list of matrix names (the default is to use all matrices) but you still need to say which matrix set they belong to so jaspscan knows which directory to search. You can simply add -menu c (or whatever section you are searching), or for the default value -auto which defaults all remaining prompted values. > In addition: I would prefer an outputfile with the transcription factors in > a list, e.g. like this > accessionnumber of input sequence: TFa, TFb etc The output is an EMBOSS "report" so you do have a choice of report formats available with the command line qualifier -rformat. For example, you could use -rformat excel and then use excel or any other spreadsheet tool to select the columns you need. We could also add more report formats to the next release, but I am not convinced this one is useful as it removes too much information. However, we may be able to reduce the extra tags included in jaspscan output. We may also be able to provide an applicationn that will post-propcess a standard report format and produce the summary you ask for, again in the next release. Hope this helps Peter Rice EMBOSS Team