VNc@sddddgZddlZddlmZmZddlZddlZddlZddlmZej drej dZ nd Z e e_ iZ iZ iad Zd d Zd Zd dZd dZd dZd dZddd dZd dddZd ddZdZddZdd dZdd dZd d dZed dZd ddZ d d d!Z!eed dd"Z"eeed dd#Z#eeed dd$Z$d eedd%Z%d&Z&d'Z'd d(Z(d d)Z)d d*Z*d d+Z+d d,Z,d d-Z-d d.Z.d d/Z/d0d1Z0d d d d d ed2Z1d d d d dd ed3Z2dS(4tmotifthomologytgeneinfotproteiniN(tGenometgeneDB(tenvirontCISTEMATIC_TEMPs/tmpcCsb|tkrTy2dtj}tjt|||t| %s s%s iN(topentwriteRtclose(R tgenesR\RatoutputFilePathtoutFiletgeneR.((sS/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/core/__init__.pyt retrieveAlls   $cCsd|d|d|f}|S(s; write a fasta formated seq with geneID in the header. s > %s-%s %s ii((R.tseqt fastaString((sS/woldlab/castor/data00/home/georgi/code/erange-4.0a-BAM/cistematic/core/__init__.pytfastascCsDt|dt||}|tjkr@|jt|s\ $        o'$    !