Grouping and Deleting Names
Purpose
This function of CDSParser allows the user to specify names that should be treated as the same, like synonyms. For instance, you might want "cyt b", "cyt-b", and "cytochrome b" to be outputted in the same column in the tab-delimited files, or you might want to have the ten longest sequences selected from the coding sequences (CDS) with the names "cyt b", "cyt-b", and "cytochrome b" to be outputted into a FASTA file.
Display
"GROUPS of NAMES" lists after each number the CDS names in one group separated by "||". So in the above example, "1: cyt b || cyt-b || cytochrome b" would represent the user-specified group.
"UNGROUPED NAMES" lists all of the CDS names that have not been grouped or deleted.
"NAMES to be DELETED" lists all of the CDS names that have been deleted. This means that these CDS's will be ignored when tab-delimited files are outputted.
Option 1: Put name(s) into a new or existing group
To create a group, enter in the line numbers of the names you wish to group, separated by a space (e.g. "1 24 45 46"). To add to a group, enter in the line numbers of the names you want to add to the group. Groups can be combined by entering in the line numbers of each. Adding names to a group and combining groups can be done simultaneously. The name of the group that will be outputted as the heading of the columns in the tab-delimited files is the first name added to the group (e.g. the underlined portion of the following: "1: cyt b || cyt-b || cytochrome b").
Option 2: Put all ungrouped names into individual groups
This option converts each name that has not been grouped or deleted into a group. This means that the new groups will be composed of just one name. For example, if "cyt b", "cyt-b", and "cytochrome b" were not grouped or deleted, all such names would be outputted in the miscellaneous column.
Option 3: Remove name(s) from a group
Removing names from a group is useful when a name has accidently been added to a group or no longer belongs in a group. Simply select the group you want to edit by entering its number, and then remove the unwanted name by entering its number. Multiple names cannot be removed from a group simultaneously. If all names are removed from a group, that group will cease to exist. If the first name is removed from a group, then the second name will become the name of the group.
Option 4: Put name(s) into the delete set
This option is like option 1, except that it puts names into the delete set instead of into a group. It also allows multiple names to be added to the delete set instead of into a group. It also allows multiple names to be added to the delete set simultaneously.
Option 5: Put all ungrouped names into the delete set
This option is like option 2, except that it puts all of the names into the delete list instead of putting each name that is not grouped or deleted into a group.
Option 6: Remove name(s) from the delete set
This option is like option 3, except that it allows the user to remove names from the delete set instead of a group.
Option 7: Save current groups to disk
Saving the groups and delete set is very useful when the user needs to restart CDSParser or user a different data set, but wants to use the same groupings. These files are saved with the extension '.grp'. The first line is the delete set and the succeeding lines each represent a group. Names are separated by '~', because the character is not in any of the CDS names.
Option 8: Load group file
This option loads a group file created with the previous option. If a name is not present in the currently uploaded data set, it will not appear in the groups or delete set. However, the name is still present in the group file and will appear when the loaded data set contains that name.