Mercurial > repos > matt-shirley > sra_tools

annotate sra_fetch.py @ 4:5d7baf38e470 draft

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debugging automatic SRA build and install
author Matt Shirley <mdshw5@gmail.com>
date Mon, 17 Jun 2013 12:48:38 -0400
parents ffdd41766195
children 45031bbf6b27
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ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
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1 from ftplib import FTP
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
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2 import sys
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
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3
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4 # Get accession number from argument
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matt-shirley <mdshw5@gmail.com>
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5 accession = sys.argv[1]
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
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6 outfile = sys.argv[2]
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matt-shirley <mdshw5@gmail.com>
parents:
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7 prefix = accession[0:3]
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matt-shirley <mdshw5@gmail.com>
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8 middle = accession[3:6]
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
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9 suffix = accession[6:9]
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
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ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
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11 # NCBI SRA FTP site
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matt-shirley <mdshw5@gmail.com>
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12 ftp = FTP('ftp-trace.ncbi.nih.gov')
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
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13
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
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14 # Open file and transfer requested SRA as a file
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
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15 # Try to change the working directory until it works
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
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16 sra = open(outfile, 'wb')
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matt-shirley <mdshw5@gmail.com>
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17 ftp.login('ftp')
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
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18 connected = False
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19 while not connected:
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
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20 try:
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
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21 ftp.cwd('/sra/sra-instant/reads/ByRun/sra/' +
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22 prefix + '/' +
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23 prefix + middle + '/' +
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24 prefix + middle + suffix + '/')
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25 connected = True
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
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26 except:
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27 pass
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ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
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29 ftp.retrbinary('RETR ' + prefix + middle + suffix + '.sra', sra.write)
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
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30 ftp.quit()