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The following scripts are used to integrate BAC data into
current agp and tpf contig/gap files:

limit_bac_output.pl:

this file is used to select biased the BLAST
information that is of importance to you. You can
specify the parameters of the search near the top
of the file.

The script requires in input of the BLAST results to
be searched and a file containing two columns: first
the BAC id and second the correct BAC length.



bac_chr_position.pl:

Able to input options. -d for the folder containing the
current agp and tpf files, and -t for a transformation
file. The transformation file contins two colums first
of BAC ID and second of GenBank ID. This gives output
as many BAC IDs, put in the print (can be output wiht
">" to a error file), are not in current transformation
file (mainly chromosome 8). In this case file uses
original BAC ID.

This script requires an input of the BAC data to be
integrated (from limit_bac_output.pl), and a folder
containing both the current agp and tpf files for
chromosomes of interest (use all chromosomes if you
do not know which your BAC information will map to).
It is possible to input BLAST information not from
BACS, and the script should run this similarly,
however this has yet to be tested.

This script looks at each chromosome individually,
taking the BAC information mapping to the chromosome
and adding it to the chromosome information. After
all BACs have been checked the start positions are
used to sort the data After sorting is completed,
orientation information is added and BACs are
used to replace current contigs and gaps where
possible.

A standard error output is generated when an unknown
gap is removed by a BAC, as the estimated length of
all such gaps is 100bp. These locations will need to
be tested to find the correct gap length, and test if
the BAC truly spans the gap. The following data start
and end positions as well as contained information
will need to be corrected accordingly. Until more
information is known the script assumes 100bp to be
the correct length of such gaps.

The script will automatically create a new folder in the
location the program is called. Within this folder there
will be new agp and tpf files created for each chromosome
named the same as the input files. The output files will
contain the BACs associated with the given chromosome, as
well as all the BAC and contained information.


itag2annotate.pl:

This file is to integrate .gff3 files to annotation for
Genbank. It currently is not working correctly, it will
not note the multiple elements of a given type, and needs
work, possibly re-writing.
##########################################
##########NOT WORKING CORRECTLY###########
##########################################
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