import.py
#!/usr/bin/env python
"""
Script that imports locally stored data as a new dataset for the user
Usage: import id outputfile
"""
from __future__ import print_function
import os
import sys
assert sys.version_info[:2] >= (2, 6)
BUFFER = 1048576
dataid = sys.argv[1]
out_name = sys.argv[2]
id2name = {
"eryth": "ErythPreCRMmm3_cusTrk.txt",
"cishg16": "ReglRegHBBhg16CusTrk.txt",
"cishg17": "ReglRegHBBhg17CusTrk.txt",
"exons": "ExonsKnownGenes_mm3.txt",
"krhg16": "known_regulatory_hg16.bed",
"krhg17": "known_regulatory_hg17.bed",
"tARhg16mmc": "hg16.mouse.t_AR.cold.bed",
"tARhg16mmm": "hg16.mouse.t_AR.medium.bed",
"tARhg16mmh": "hg16.mouse.t_AR.hot.bed",
"tARhg16rnc": "hg16.rat.t_AR.cold.bed",
"tARhg16rnm": "hg16.rat.t_AR.medium.bed",
"tARhg16rnh": "hg16.rat.t_AR.hot.bed",
"phastConsHg16": "phastConsMost_hg16.bed",
"omimhg16": "omimDisorders_hg16.tab",
"omimhg17": "omimDisorders_hg17.tab",
}
fname = id2name.get(dataid, "")
if not fname:
print("Importing invalid data %s" % dataid)
sys.exit()
else:
print("Imported %s" % fname)
# this path is hardcoded
inp_name = os.path.join("database", "import", fname)
try:
inp = open(inp_name)
except Exception:
print("Could not find file %s" % inp_name)
sys.exit()
out = open(out_name, "wt")
while 1:
data = inp.read(BUFFER)
if not data:
break
out.write(data)
inp.close()
out.close()