Mercurial > repos > matt-shirley > sra_tools

changeset 1:75d914fa5711 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Moving repository to testtoolshed for now.
author matt-shirley
date Tue, 27 Nov 2012 13:43:03 -0500
parents cdcc400dcafc
children
files datatypes_conf.xml fastq_dump.xml sam_dump.xml sra.py sra_fetch.py sra_fetch.xml
diffstat 6 files changed, 0 insertions(+), 168 deletions(-) [+]
line wrap: on
line diff
--- a/datatypes_conf.xml	Tue Nov 27 13:31:09 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<datatypes>
-  <datatype_files>
-    <datatype_file name="sra.py"/>
-  </datatype_files>
-  <registration>
-    <datatype extension="sra" type="galaxy.datatypes.binary:Sra" display_in_upload="true"/>
-  </registration>
-  <sniffers>
-    <sniffer type="galaxy.datatypes.binary:Sra"/>
-  </sniffers>
-</datatypes>
\ No newline at end of file
--- a/fastq_dump.xml	Tue Nov 27 13:31:09 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-<tool id="fastq_dump" name="Extract fastq" version="1.0.0">
-  <description> format reads from NCBI SRA.</description>
-  <command>./fastq-dump --log-level fatal --report never --accession '${input.name}' --stdout $split $aligned '$input' > $output </command>
-  <version_string>fastq-dump --version</version_string>
-  <inputs>
-    <param format="sra" name="input" type="data" label="sra archive"/>
-    <param format="text" name="split" type="select" value="">
-      <label>Split read pairs</label>
-      <option value="">No</option>
-      <option value="--split-spot">Yes</option>
-    </param>
-    <param format="text" name="aligned" type="select" value="">
-      <label>Specify alignment</label>
-      <option value="">All</option>
-      <option value="--aligned">Only aligned</option>
-      <option value="--unaligned">Only unaligned</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="fastqsanger" name="output"/>
-  </outputs>
-  <stdio>
-    <exit_code range="127" level="fatal" description="Cannot find fastq-dump binary"/>
-  </stdio>
-  <requirements>
-    <requirement type="binary">fastq-dump</requirement>
-  </requirements>
-  <help>
-    This tool extracts fastqsanger reads from SRA archives using fastq-dump. The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
-  </help>
-</tool>
--- a/sam_dump.xml	Tue Nov 27 13:31:09 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-<tool id="sam_dump" name="Extract SAM" version="1.0.0">
-  <description> format reads from NCBI SRA.</description>
-  <command>sam-dump $header $aligned $primary '$input' > $output</command>
-  <version_string>sam-dump --version</version_string>
-  <inputs>
-    <param format="sra" name="input" type="data" label="sra archive"/>
-    <param format="text" name="header" type="select" value="">
-      <label>Output SAM header</label>
-      <option value="--header">Yes</option>
-      <option value="--no-header">No</option>
-    </param>
-    <param format="text" name="aligned" type="select" value="">
-      <label>Output unaligned reads</label>
-      <option value="">No</option>
-      <option value="--unaligned">Yes</option>
-    </param>
-    <param format="text" name="primary" type="select" value="">
-      <label>Output only primary aligments</label>
-      <option value="">No</option>
-      <option value="--primary">Yes</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="sam" name="output"/>
-  </outputs>
-  <requirements>
-    <requirement type="binary">sam-dump</requirement>
-  </requirements>
-  <help>
-    This tool extracts SAM format reads from SRA archives using sam-dump. The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
-Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
-  </help>
-</tool>
--- a/sra.py	Tue Nov 27 13:31:09 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-"""
-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)
--- a/sra_fetch.py	Tue Nov 27 13:31:09 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-from ftplib import FTP
-import sys
-
-# Get accession number from argument
-accession = sys.argv[1]
-outfile = sys.argv[2]
-prefix = accession[0:3]
-middle = accession[3:6]
-suffix = accession[6:9]
-
-# NCBI SRA FTP site
-ftp = FTP('ftp-trace.ncbi.nih.gov')
-
-# Open file and transfer requested SRA as a file
-# Try to change the working directory until it works
-sra = open(outfile, 'wb')
-ftp.login('ftp')
-connected = False
-while not connected:
-    try:
-        ftp.cwd('/sra/sra-instant/reads/ByRun/sra/' + 
-                prefix + '/' +
-                prefix + middle + '/' +
-                prefix + middle + suffix + '/')
-        connected = True
-    except:
-        pass
-        
-ftp.retrbinary('RETR ' + prefix + middle + suffix + '.sra', sra.write)
-ftp.quit()
--- a/sra_fetch.xml	Tue Nov 27 13:31:09 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-<tool id="sra_fetch" name="Fetch SRA" version="1.0.0">
-  <description> by accession from NCBI SRA.</description>
-  <command interpreter="python">sra_fetch.py '$accession' '$output'</command>
-  <inputs>
-    <param name="accession" size="13" type="text" value="SRR000001" label="SRA run accession"/>
-  </inputs>
-  <outputs>
-    <data format="sra" name="output" label="Fetch ${accession.value}"/>
-  </outputs>
-  <requirements>
-    <requirement type="python">sra_fetch.py</requirement>
-  </requirements>
-  <help>
-    This tool fetches SRA archives from NCBI over FTP using the python ftplib.
-  </help>
-</tool>