print msg
LOG.write(msg)
split_info = re.split(" ", orig_search_ids[0])
[orig_protein, orig_gene_name, orig_transcript, orig_gene_location] = [split_info[0], split_info[1], split_info[2], split_info[4]]
msg = "%s id in %s: %s\n" % (seqfile, orig_genome, orig_protein)
print msg
LOG.write(msg)
msg = "gene name in %s: %s\n\n" % (orig_genome, orig_gene_name)
print msg
LOG.write(msg)
orig_seq_file = "orig_seq.fasta"
extract_first_seq(outfile, orig_protein, orig_seq_file)
##################################################################
# blast the query sequence against all of the remaining genomes
#
not_found = []
for genome in genomes:
#forward search
msg = "%s\n" % genome
print msg
LOG.write(msg)
found = 0
found_in_known = 0;
found_in_abinitio = 0
outfile = "tmp.fasta"
output_gene_location = ""
output_protein = ""
###############################
# find the query sequence in the "original" species
# (together with the gene/protein/trnascript entry it belongs to)
known_proteome_f = ensembldb +
orig_search_ids = find_by_blasting("%s%s/%s" % (known_proteome_f, orig_genome, orig_genome), seqfile, working_results_f)
logger("the closest match to %s in %s is %s\n" % (seqfile, orig_genome, orig_search_ids[0]))
split_info = re.split(" ", orig_search_ids[0])
[orig_protein, orig_gene_name, orig_transcript, orig_gene_location] = [split_info[0], split_info[1], split_info[2], split_info[4]]
logger("%s id in %s: %s\n" % (seqfile, orig_genome, orig_protein))
logger("gene name in %s: %s\n\n" % (orig_genome, orig_gene_name))
orig_seq_f = "orig_seq.fasta"
extract_first_seq(working_results_f, orig_protein, orig_seq_f)
###############################
# blast the query sequence against all of the remaining proteomes
#
not_found = []
for species in species_list:
###forward search###
logger("%s\n" % species)
found = 0
found_in_known = 0;
found_in_abinitio = 0
forward_ids = find_by_blasting("%s%s/%s" % (known_proteome_f, species, species), orig_seq_f, working_results_f)
if (len(forward_ids) == 0):
logger("%s not found in %s, \"known\" sequences\n\n" % (seqfile, species))
