|Output format options|
If you run CloseUp through the closeup.pl script, then you should have elected for plain text, or MySQL output format. The MySQL data will be in a file called filename.mysql (where 'filename' is your original output filename). The plain text parser creates two files: filename_detail.txt; and filename_overview.txt.
If for some reason you do not have these files, you can parse your output file again using closeup2mysql.pl or closeup2txt.pl
The MySQL parser will create information for two tables. This can be sent into your MySQL database by entering
mysql -p database < filename.mysqlThe tables have the following format:
Detailed results lists every marker pair for every collinear run identified. The table has the format:
Results overview lists summary information for each collinear run. There is only one line for each run.
|Plain text tables|
The plain text parser will create two tables in two files.
The tables have the following format:
Detailed results (filename_detail.txt) lists every marker pair for every collinear run identified. Different runs are separated by a line with several "=" signs, the block id number, and the chromosomes between which the collinear run was identified.
The following lines list the marker names involved in the run, and the position on each chromosome. For example
========== id: 65756 BETWEEN Chr 4 and Chr 2 uaz42 52.5 21.0 uaz43 52.5 21.0 uaz45 52.5 21.0 uaz46 52.5 21.0 uaz48 52.5 21.0 uaz69 52.5 24.7lists detailed information for run number 65756, which pairs a region on chromosome 4, with a region on chromosome 2. The six markers involved in the run are listed, with their position on chromosome 4, and 2 respectively (it will always be true that the positions are listed under the relevant chromosome name).
Results overview (filename_overview.txt) lists summary information for each collinear run. There is only one line for each run.