mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-19 10:51:34 +08:00
63 lines
1.4 KiB
Python
63 lines
1.4 KiB
Python
#!/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()
|