sra_tools: sra.py comparison

Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.

comparison

equal deleted inserted replaced

--1:000000000000
+:cdcc400dcafc
+"""
+Sra class
+"""
+import galaxy.datatypes.binary
+from galaxy.datatypes.binary import Binary
+import data, logging, binascii
+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) """
+file_ext = "sra"
+def __init__( self, **kwd ):
+Binary.__init__( self, **kwd )
+def sniff( self, filename ):
+# The first 8 bytes of any NCBI sra file is 'NCIB.sra', and the file is binary. EBI and DDBJ files may differ. For details
+# about the format, see http://www.ncbi.nlm.nih.gov/books/n/helpsra/SRA_Overview_BK/#SRA_Overview_BK.4_SRA_Data_Structure
+try:
+header = open( filename ).read(8)
+if binascii.b2a_hex( header ) == binascii.hexlify( 'NCBI.sra' ):
+return True
+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.blurb = data.nice_size( dataset.get_size() )
+else:
+dataset.peek = 'file does not exist'
+dataset.blurb = 'file purged from disk'
+def display_peek( self, dataset ):
+try:
+return dataset.peek
+except:
+return "Binary sra file (%s)" % ( data.nice_size( dataset.get_size() ) )
+Binary.register_sniffable_binary_format("sra", "sra", Sra)

Mercurial > repos > matt-shirley > sra_tools