[docs]def save_per_gene(filename, tn_per_gene, reads_per_gene, aliases_designation):
"""Create text file with transposons and reads per gene
NOTE THAT THE TRANSPOSON WITH THE HIGHEST READ COUNT IS IGNORED.
E.G. IF THIS FILE IS COMPARED WITH THE _PERGENE_INSERTIONS.TXT FILE THE
READS DON'T ADD UP (SEE https://groups.google.com/forum/#!category-topic/satayusers/bioinformatics/uaTpKsmgU6Q)
TOO REMOVE THIS HACK, CHANGE THE INITIALIZATION OF THE VARIABLE readpergene
Parameters
----------
filename : str
Path with the filename extension included(e.g "data_file/file.txt")
describing where do you want to store the results.
By default it will be stored in the same location as the bamfile,
with the same basename.
Example, if the bamfile path is data_file/data_1.bam then the file will be data_file/data_1.bam_pergene.txt
tn_per_gene : int
The number of transposons found per gene
reads_per_gene : int
The number of reads found per gene
aliases_designation : dict
Last output of the function read_genes _, _, aliases_designation = read_genes(
gff_file, essential_file, gene_name_file)
"""
with open(filename, "w") as f:
f.write("Gene name\tNumber of transposons per gene\tNumber of reads per gene\n")
for gene in tn_per_gene:
tnpergene = tn_per_gene[gene]
readpergene = reads_per_gene[gene]
if gene in aliases_designation:
gene_alias = aliases_designation.get(gene)[0]
else:
gene_alias = gene
f.write(gene_alias + "\t" + str(tnpergene) + "\t" + str(readpergene) + "\n")
