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
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