consed2gap



consed2gap: a complete program suite to convert whole CONSED dataset to GAP4 project

consed2gap is a complete program suite to convert as many as possible information from CONSED into the Staden Genome Assembly Program GAP4. It is based mostly on a modified version of the CAFTOOLS which are available free by anonymous FTP from ftp://ftp.sanger.ac.uk/pub/badger.

Availability:
These programs are runnable whithin SPARC Solaris 8, 9 and 10. and LINUX.


Program description:


Download:

Click consed2gap.tgz to get free access to our consed2gap package.
Click align_to_scf_2002.tgz and to download special align_to_scf source (version 2002).
After download install this files into /usr/local/consed2gap:

% gzip -dc consed2gap.tgz | tar xvf -
	You can run directly the following example from consed:
	
	% cd /usr/local/consed2gap/example
	% sh example.sh

 (0) Check arguments ...
   (v) /usr/local/consed2gap/example/edit_dir
   (v) /usr/local/consed2gap/example/chromat_dir
   (v) /usr/local/consed2gap/example/phd_dir
   (v) /usr/local/consed2gap/example/edit_dir/standard.fasta.screen.ace.1
   (v) /usr/local/consed2gap/example/edit_dir/standard.fasta.screen.qual

 (1) Convert all ABD to SCF ...
   BaseCalling (phred)
   /usr/local/consed2gap/example/chromat_dir/djs74-1432.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-1532.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-1802.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-1803.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-1861.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-1871.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-2231.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-2350.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-2361.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-237.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-2516.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-2664.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-2679.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-2689.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-2931.s
   /usr/local/consed2gap/example/chromat_dir/djs74-3174.s
   /usr/local/consed2gap/example/chromat_dir/djs74-423.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-561.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-564.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-690.x1
   /usr/local/consed2gap/example/chromat_dir/djs74-824.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-932.s1
   /usr/local/consed2gap/example/chromat_dir/djs74-996.s2
   /usr/local/consed2gap/example/chromat_dir/djs74-1180.s1

 (2) Convert ACE to CAF ...
     From /usr/local/consed2gap/example/edit_dir/standard.fasta.screen.ace.1
     To   /home/lamarck/bsenf/tmp/mygap4/standard.fasta.screen.caf

 (3) Append BaseQualities from Sequences ...
      =>> /home/lamarck/bsenf/tmp/mygap4/standard.fasta.screen.caf

-r--r--r--  1 bsenf gendev 67509 Aug 30  2004 /usr/local/consed2gap/example/edit_dir/standard.fasta.screen.qual
-rw-rw----  1 bsenf user 144188 May 20 16:05 /home/lamarck/bsenf/tmp/mygap4/standard.fasta.screen.caf

 (4) Creating GAP4 standard.0 ...
     /home/lamarck/bsenf/tmp/mygap4/standard.fasta.screen.caf => /home/lamarck/bsenf/tmp/mygap4/standard.0

Parsed data for 26 sequences
Contig Contig1
Program finished.
	
            
At the end you can run gap4 from the destination directory.
No source files are changed.

% cd $DST
% gap4 STANDARD.0 &



Contact:

If you have any further questions or comments don't hesitate to write us or
contact the author Bernd Senf.



Hints to reversing from GAP4 to CONSED:
In order to convert project backward from GAP to STADEN you should use first the program from CAFTOOLS gap2caf and caf2phd, then run phd2Ace.perl from the CONSED package. This will produce a single ace file that you can use with consed -ace myace.1

% gap2caf ... | caf2phd ... | phd2Ace.perl ...
% consed -ace myace.1