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annotate sra_fetch.py @ 3:01dec8611542 draft

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Python script successfully returns SRA archive from accession.
author Matthew Shirley <mdshw5@gmail.com>
date Wed, 14 Nov 2012 13:05:14 -0500
parents be22544bfafa
children f74bbb22bf62
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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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01dec8611542 Python script successfully returns SRA archive from accession.
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6 prefix = accession[0:3]
01dec8611542 Python script successfully returns SRA archive from accession.
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7 middle = accession[3:6]
01dec8611542 Python script successfully returns SRA archive from accession.
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8 suffix = accession[6:9]
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10 # NCBI SRA FTP site
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01dec8611542 Python script successfully returns SRA archive from accession.
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11 ftp = FTP('ftp-trace.ncbi.nih.gov')
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13 # Open stdout and transfer requested SRA as a file
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14 ftp.login()
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01dec8611542 Python script successfully returns SRA archive from accession.
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15 ftp.cwd('/sra/sra-instant/reads/ByRun/sra/' +
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be22544bfafa First version of the python script that may work. Whole tool is still not functional.
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16 prefix + '/' +
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17 prefix + middle + '/' +
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01dec8611542 Python script successfully returns SRA archive from accession.
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18 prefix + middle + suffix + '/')
01dec8611542 Python script successfully returns SRA archive from accession.
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19 ftp.pwd()
01dec8611542 Python script successfully returns SRA archive from accession.
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20 ftp.retrbinary('RETR ' + prefix + middle + suffix + '.sra', sys.stdout)
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be22544bfafa First version of the python script that may work. Whole tool is still not functional.
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21 ftp.quit()