Mercurial > repos > matt-shirley > sra_tools
changeset 12:b77840618b8f draft
debugging SRA datatype
author | Matt Shirley <mdshw5@gmail.com> |
---|---|
date | Mon, 17 Jun 2013 16:05:30 -0400 |
parents | cdba74ec9eca |
children | 45031bbf6b27 |
files | sra.py |
diffstat | 1 files changed, 5 insertions(+), 12 deletions(-) [+] |
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--- a/sra.py Mon Jun 17 14:26:40 2013 -0400 +++ b/sra.py Mon Jun 17 16:05:30 2013 -0400 @@ -2,17 +2,11 @@ Sra class """ -import galaxy.datatypes.binary +import binascii from galaxy.datatypes.binary import Binary -import data, logging, binascii +from galaxy.datatypes.data import Data from galaxy.datatypes.metadata import MetadataElement -from galaxy.datatypes import metadata from galaxy.datatypes.sniff import * -from galaxy import eggs -import pkg_resources -pkg_resources.require( 'bx-python' ) -import os, subprocess, tempfile -import struct class Sra( Binary ): """ Sequence Read Archive (SRA) """ @@ -28,12 +22,13 @@ header = open(filename).read(8) if binascii.b2a_hex(header) == binascii.hexlify('NCBI.sra'): return True - return False + else: + return False except: return False def set_peek(self, dataset, is_multi_byte=False): if not dataset.dataset.purged: - dataset.peek = 'Binary sra file' + dataset.peek = 'Binary SRA file' dataset.blurb = data.nice_size(dataset.get_size()) else: dataset.peek = 'file does not exist' @@ -43,5 +38,3 @@ return dataset.peek except: return 'Binary sra file (%s)' % ( data.nice_size(dataset.get_size())) - -Binary.register_sniffable_binary_format('sra', 'sra', Sra)