digger

digger annotates the sequences contained in a FASTA file, using BLAST to search for potential germline sequences. It requires an initial reference set for BLAST to use: this could come from a similar species, or a former annotation. Please refer to Annotating the human IGH locus for example usage.

Find functional and nonfunctional genes in an assembly sequence or contigs

usage: digger [-h] [-species SPECIES] [-motif_dir MOTIF_DIR] [-locus LOCUS] [-v_ref V_REF] [-d_ref D_REF] [-j_ref J_REF] [-v_ref_gapped V_REF_GAPPED]
              [-ref_comp REF_COMP] [-sense SENSE] [-keepwf]
              assembly_file output_file

Positional Arguments

assembly_file

File containing one or more sequences to search

output_file

output file (csv)

Named Arguments

-species

use motifs for the specified species provided with the package

-motif_dir

pathname to directory containing motif probability files

-locus

locus (default is IGH)

-v_ref

set of V reference genes to use as starting point for search

-d_ref

set of D reference genes to use as starting point for search

-j_ref

set of J reference genes to use as starting point for search

-v_ref_gapped

IMGT-gapped v-reference set used to determine alignment of novel sequences

-ref_comp

ungapped reference set(s) to compare to: name and reference file separated by comma eg mouse,mouse.fasta (may be repeated multiple times)

-sense

sense in which to read the assembly (forward or reverse) (if omitted will select automatically)

-keepwf

keep working files after processing has completed

Default: False

At least one file containing reference genes must be provided. You can, for example, supply v_ref, d_ref and j_ref, or just v_ref. Digger will annotate whatever genes are discovered with the corresponding set(s). In practice, the sets do not have to be that good a match: BLAST will identify partial matches, and Digger’s logic will extend the match to a full gene, including canonical RSS and leader (using the motif folder).

Digger requires a set of postion-weighted matrices, to identify RSS and leader. It is also possible to specify conserved locations of motifs. This motif data should be stored in a motif folder. Motifs for human and rhesus macaque IG are built in to the package, and may be used with -species by specifying either human or rhesus_macaque. The species is used in conjunction with -locus to determine the correct motifs. Alternatively, -motif_dir can be used to specify custom motifs created outside of the package. Please refer to calc_motifs and to Annotating the rhesus macaque IGH locus for further details on custom motifs.

v_ref_gapped is used to gep v-sequences correctly in order to identify conserved codons and so on. Again these sequences do not need to be that good a match in practice. The sequences must be IMGT aligned with no extraneous codons. Note in particular that IMGT has introduced insertions into macaque alignments in recent years. Sets with these insertions should not be used.

ref_comp allows you to specify that you would like annotated sequences to be compared with sequences in a set. You can include as many different sets as you wish. The output file will contain columns for each of these, listing the closest sequence found and the proximity (%, and number of nucleotides).

If you choose not to specify the sense, Digger will select the sense that elicits the highest number of hits and the highest evalue (results are shown in the output so that you can decide whether it has made the right choice, and whether you wish to annotate in both senses)