Blat module¶
-
biscot.Blat.
blat_phase
(contigs_sequence_dict)[source]¶ Executes Blat and modifies an AGP file based on the mappings found
- Parameters
contigs_sequence_dict (dict(str: str)) – Dict containing contigs FASTA sequences
-
biscot.Blat.
get_agp_changes
(contigs_sequence_dict)[source]¶ Gets the best blat hit and writes what changes have to be made to the AGP file to incorporate the changes
- Parameters
contigs_sequence_dict (dict(str: str)) – Dict containing contigs FASTA sequences
-
biscot.Blat.
mute_agp_file
()[source]¶ Loads an AGP file and a changes file and modifies the AGP file lines to incorporate the changes
-
biscot.Blat.
parse_blat
()[source]¶ Parses the pslReps output file to get various information about the best hit
- Returns
(true if hit found - False otherwise, max score, reference size, contig_1 end, contig_2 end)
- Return type
tuple(bool, int, int, int)
-
biscot.Blat.
run_blat
(contig_1, contig_1_start, contig_1_end, contig_1_orientation, contig_2, contig_2_start, contig_2_end, contig_2_orientation, contigs_sequence_dict)[source]¶ Launches Blat, then sorts the psl file and extracts the best match
- Parameters
contig_1 (str) – Name of the first contig
contig_1_start (int) – Starting position of the sequence to extract
contig_1_end (int) – End position of the sequence to extract
contig_1_orientation (str) – Strand orientation of the first contig
contig_2 (str) – Name of the second contig
contig_2_start (int) – Starting position of the sequence to extract
contig_2_end (int) – End position of the sequence to extract
contig_2_orientation (str) – Strand orientation of the second contig
contigs_sequence_dict (dict(str, str)) – Dict containing the contigs fasta sequence