Mercurial > repos > matt-shirley > sra_fetch

annotate sra_fetch.py @ 8:61d634d123c0 draft

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Added datatypes_conf and sra class.
author matt-shirley <mdshw5@gmail.com>
date Sun, 18 Nov 2012 17:12:24 -0500
parents d7708f338c82
children
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aa7ab53c53bf Started working on the python FTP script.
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1 from ftplib import FTP
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be22544bfafa First version of the python script that may work. Whole tool is still not functional.
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2 import sys
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4 # Get accession number from argument
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5 accession = sys.argv[1]
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f74bbb22bf62 Fixed typos in python script.
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6 outfile = sys.argv[2]
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01dec8611542 Python script successfully returns SRA archive from accession.
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7 prefix = accession[0:3]
01dec8611542 Python script successfully returns SRA archive from accession.
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8 middle = accession[3:6]
01dec8611542 Python script successfully returns SRA archive from accession.
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9 suffix = accession[6:9]
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be22544bfafa First version of the python script that may work. Whole tool is still not functional.
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11 # NCBI SRA FTP site
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01dec8611542 Python script successfully returns SRA archive from accession.
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12 ftp = FTP('ftp-trace.ncbi.nih.gov')
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14 # Open file and transfer requested SRA as a file
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15 # Try to change the working directory until it works
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16 sra = open(outfile, 'wb')
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17 ftp.login('ftp')
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18 connected = False
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19 while not connected:
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20 try:
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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
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26 except:
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27 pass
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29 ftp.retrbinary('RETR ' + prefix + middle + suffix + '.sra', sra.write)
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30 ftp.quit()