tabular to bed

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tabular to bed

Matthias Bernt
Dear galaxy-devs,

What would be the galaxy way to convert tabular data (e.g. the tabular
output of BLAST or infernal) into bed or alignments?

For bed it seems like that cutting the columns and using awk to adapt
the positions to the bed definitions and switch coordinates for the
reverse strand matches would do the job.

But, in particular using awk seems to be "end user incompatible" :)

What would be the best idea: Provide a workflow or a tool doing the job?

Initially I had hoped that I can simply change the data type to bed and
assign the columns in the attributes tab (but I forgot about the
coordinate adjustments).

Anyway there has been a problem:
Then the preview in the history shows that the columns are assigned
(except for the score column). It looks like this:

1.Chrom 2 3.Name 4 5 6 7 8.Start 9.End 10.Strand 11 12 13 14 15 16 17 18

But in "Show Data" the columns are still taken as is, e.g. 2nd column is
start ...

When I try to use the File in BedTools Merge it fails with the message
that it is not a bed file.

Thanks for all the help.

Best,
Matthias

--

-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
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Re: tabular to bed

Tiago Macedo
Hi Rui,

Are you trying to set up proftpd (with sftp) to use galaxy user credentials read from a postgresql database? Do you have the postgresql part working on regular ftp?

1- The proftpd version on ubuntu 16.04's repository works fine, you don't need to compile it yourself (unless you really want/have to). An apt install proftpd-basic proftpd-mod-pgsql would do it.

2- The user and group under which proftpd runs are defined in proftpd.conf. You didn't show that part of your file, but it's these two lines:
User                            proftpd
Group                           nogroup

3- I see you're missing:
#Before the <IfModule mod_sftp.c>
LoadModule      mod_sql_postgres.c
LoadModule      mod_sql_passwd.c

AuthPAM                         off

#Within the <IfModule mod_sftp.c>
TLSProtocol TLSv1

I suppose you can specify tls 1.1 or 1.2 here, but never really tried it.

In my setup I also commented out the AuthOrder line.

I guess these changes should do it.


Best,
Tiago





On 16-03-2017 15:58, Matthias Bernt wrote:
Dear galaxy-devs,

What would be the galaxy way to convert tabular data (e.g. the tabular output of BLAST or infernal) into bed or alignments?

For bed it seems like that cutting the columns and using awk to adapt the positions to the bed definitions and switch coordinates for the reverse strand matches would do the job.

But, in particular using awk seems to be "end user incompatible" :)

What would be the best idea: Provide a workflow or a tool doing the job?

Initially I had hoped that I can simply change the data type to bed and assign the columns in the attributes tab (but I forgot about the coordinate adjustments).

Anyway there has been a problem:
Then the preview in the history shows that the columns are assigned (except for the score column). It looks like this:

1.Chrom    2    3.Name    4    5    6    7    8.Start    9.End    10.Strand    11    12    13    14    15    16    17    18

But in "Show Data" the columns are still taken as is, e.g. 2nd column is start ...

When I try to use the File in BedTools Merge it fails with the message that it is not a bed file.

Thanks for all the help.

Best,
Matthias



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
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