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annotate sra_fetch.py @ 2:be22544bfafa draft

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First version of the python script that may work. Whole tool is still not functional.
author Matthew Shirley <mdshw5@gmail.com>
date Wed, 14 Nov 2012 12:07:18 -0500
parents aa7ab53c53bf
children 01dec8611542
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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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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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6 prefix = accession[0:2].uppercase()
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7 middle = accession[3:5]
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8 suffix = accession[6:8]
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10 # NCBI SRA FTP site
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11 ftp = FTP('ftp.ncbi.nlm.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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be22544bfafa First version of the python script that may work. Whole tool is still not functional.
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15 ftp.retrbinary('/sra/sra-instant/reads/ByRun/sra/' +
be22544bfafa First version of the python script that may work. Whole tool is still not functional.
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16 prefix + '/' +
be22544bfafa First version of the python script that may work. Whole tool is still not functional.
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17 prefix + middle + '/' +
be22544bfafa First version of the python script that may work. Whole tool is still not functional.
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18 prefix + middle + suffix + '/' +
be22544bfafa First version of the python script that may work. Whole tool is still not functional.
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19 prefix + middle + suffix + '.sra', sys.stdout)
be22544bfafa First version of the python script that may work. Whole tool is still not functional.
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20 ftp.quit()