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87 lines
2.5 KiB
Python
87 lines
2.5 KiB
Python
#!/usr/bin/env python
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"""
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Script that imports locally stored data as a new dataset for the user
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Usage: import id outputfile
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"""
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from __future__ import print_function
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import sys
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from shutil import copyfile
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assert sys.version_info[:2] >= (2, 6)
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BUFFER = 1048576
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uids = sys.argv[1].split(",")
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out_file1 = sys.argv[2]
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# remove NONE from uids
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have_none = True
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while have_none:
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try:
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uids.remove("None")
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except ValueError:
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have_none = False
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# create dictionary keyed by uid of tuples of (displayName,filePath,build) for all files
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available_files = {}
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try:
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filename = sys.argv[-1]
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for line in open(filename):
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if not line or line[0:1] == "#":
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continue
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fields = line.split("\t")
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try:
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info_type = fields.pop(0)
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if info_type.upper() == "DATA":
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uid = fields.pop(0)
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org_num = fields.pop(0)
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chr_acc = fields.pop(0)
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feature = fields.pop(0)
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filetype = fields.pop(0)
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path = fields.pop(0).replace("\r", "").replace("\n", "")
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file_type = filetype
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build = org_num
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description = uid
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else:
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continue
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except Exception:
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continue
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available_files[uid] = (description, path, build, file_type, chr_acc)
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except Exception:
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print("It appears that the configuration file for this tool is missing.", file=sys.stderr)
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# create list of tuples of (displayName,FileName,build) for desired files
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desired_files = []
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for uid in uids:
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try:
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desired_files.append(available_files[uid])
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except Exception:
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continue
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# copy first file to contents of given output file
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file1_copied = False
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while not file1_copied:
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try:
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first_file = desired_files.pop(0)
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except IndexError:
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print("There were no valid files requested.", file=sys.stderr)
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sys.exit()
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file1_desc, file1_path, file1_build, file1_type, file1_chr_acc = first_file
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try:
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copyfile(file1_path, out_file1)
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print("#File1\t" + file1_desc + "\t" + file1_chr_acc + "\t" + file1_build + "\t" + file1_type)
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file1_copied = True
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except Exception:
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print("The file specified is missing.", file=sys.stderr)
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continue
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# Tell post-process filter where remaining files reside
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for extra_output in desired_files:
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file_desc, file_path, file_build, file_type, file_chr_acc = extra_output
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print("#NewFile\t" + file_desc + "\t" + file_chr_acc + "\t" + file_build + "\t" + file_path + "\t" + file_type)
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