directory of scripts written by me. 
commandline driven
see individual -h for parameters


CPC2fasta.py	transforms CPCs .tab output to fasta format
CPC2gtf.py 	creates a gtf file from cpc .tab and fasta file used as a reference by cpc.
gff2fasta_extractor.py 		extracts fasta sequences + upstrem downstream regions from based on a gff file
intergenic_regions_extractor.py extracts intergenic regions from difference between an orf and an orf + intergenic file (as on Candida genome database)
BLAST_compare.py	compares extracted intergenic regions against a blast database ( preferably orf) and kicks out any overlap
Blast_multifasta compares (BLASTs) a mutltifasta file against a reference Blastdatabase
CPAT2fasta transforms CPAT .tab output to a multi fasta file
Blast2fasta takes a blast output (xml format) and a reference file and returns the fasta sequence (with overheads)
Create_fastq_reads.py Creates fastq reads of fixed lenght 50bp and high quality for an input fasta sequence, amount of reads is an input parameter
Create_mutations.py  creates mutations (SNPs) in a fasta sequence with a given frequency,  used for benchmarking sequence alignments. 	  
Split_fasta_sequences.py  splits fasta sequence into subsequences of defined length