# HG changeset patch
# User cschu
# Date 1435160672 14400
# Node ID 564795b5acae2234aa2f682fa9b45755e441e563
# Parent 9215ffe7d4d5e48a6095b76250edca18e928b58d
Deleted selected files
diff -r 9215ffe7d4d5 -r 564795b5acae candisnp.py
--- a/candisnp.py Wed Jun 24 11:42:40 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,217 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import sys
-import argparse
-import subprocess
-import struct
-import shutil
-import tempfile
-
-import urllib2
-import csv
-import json
-
-
-CANDISNP_SERVER = 'http://candisnp.tsl.ac.uk' #:8080'
-
-CANDI_TESTDATA = {
- "ref": "athalianaTair10",
- "data": [{
- "is_synonymous": "FALSE",
- "change": "E/K",
- "effect": "NON_SYNONYMOUS_CODING",
- "gene": "AT1G01320",
- "allele_freq": 0.291666667,
- "reference_base": "C",
- "position": 126483,
- "chromosome": "1",
- "is_ctga": "TRUE",
- "in_cds": "TRUE",
- "alternate_base": "T",
- },
- ],
-}
-"""
-'is_ctga',
-'effect',
-'change',
-'gene',
-
-"""
-
-
-SNP_DATA_HEADERS = {
- 0: 'chromosome',
- 1: 'position',
- 3: 'reference_base',
- 4: 'alternate_base',
- 7: 'info'
-}
-
-contentHeaders = {
- 'Content-Type': 'application/json',
- 'Accept': 'text/plain'
-}
-
-class SNPEffect(object):
- def __init__(self, string):
- effectAndData = string.strip(')').split('(')
- # sys.stderr.write(str(effectAndData)+'\n')
- self.effect, effectData = effectAndData[0], effectAndData[1]
- effectData = effectData.split('|')
- assert len(effectData) >= 11, 'Invalid effect field %s' % string
- self.impact, self.fClass, changeDist, self.aaChange, self.aaLength, self.gene, self.transcriptBioType, isCoding, self.transcriptID, exonIntronRank, genotypeNumber, warning = (effectData + [''])[:12]
- if self.effect in ('UPSTREAM', 'DOWNSTREAM'):
- self.transcriptDist = changeDist
- self.codonChange = None
- else:
- self.transcriptDist = None
- self.codonChange = changeDist
- self.isCoding = (isCoding == 'CODING')
- self.exonIntronRank = int(exonIntronRank) if exonIntronRank else 'NA'
- self.genotypeNumber = int(genotypeNumber)
- self.warning = warning if warning else None
-
- self.is_synonymous = not self.effect == 'NON_SYNONYMOUS_CODING'
- if self.effect in ('INTRON', 'INTERGENIC'):
- self.in_cds, self.is_synonymous = False, False
- else:
- self.in_cds = True
- try:
- self.change = '%s/%s' % (self.aaChange[0], self.aaChange[-1])
- except:
- self.change = ''
-
-
- pass
- def toDict(self):
- def is_ctga(ref, alt):
- return (ref == 'C' and alt == 'T') or (ref == 'G' and alt == 'A')
- assert hasattr(self, 'is_synonymous'), 'Missing attribute: is_synonymous'
- assert hasattr(self, 'allele_frequency'), 'Missing attribute: allele_frequency'
- assert hasattr(self, 'reference_base'), 'Missing attribute: reference_base'
- assert hasattr(self, 'alternate_base'), 'Missing attribute: alternate_base'
- return { "is_synonymous": str(self.is_synonymous).upper(),
- "change": self.change if self.change else 'NA',
- "effect": self.effect if self.effect else 'NA',
- "gene": self.gene if self.gene else 'NA',
- "allele_freq": self.allele_frequency,
- "reference_base": self.reference_base,
- "position": self.position,
- "chromosome": self.chromosome,
- "is_ctga": str(is_ctga(self.reference_base, self.alternate_base)).upper(),
- "in_cds": str(self.in_cds).upper(),
- "alternate_base": self.alternate_base, }
-
-
- pass
-
-
-
-class AnnotatedSNPEffectFactory(object):
- def __init__(self, *args, **kwargs):
- assert len(args) >= 7, 'Not enough values in args (%s)' % args
- self.log = kwargs['log']
- self.chromosome = args[0]
- self.position = int(args[1])
- self.reference_base = args[3]
- self.alternate_base = args[4]
-
- # info = dict([field.split('=') for field in args[7].strip().split(';')])
- # info = dict(field.split('=') for field in args[7].strip().split(';'))
- info = dict(field.split('=') for field in args[7].strip().split(';') if len(field.split('=')) == 2)
- # self.log.write('***'+str(info.get('EFF', '@@@')+'***\n'))
-
- self.allele_frequency = float(info.get('AF', '0.0'))
- self.effects = [effect
- for effect in info.get('EFF', '').split(',')
- if effect]
- # assert self.effects, 'No effects in info-string %s' % info.get('EF', '')
- pass
-
- def getEffects(self, notWanted=('UPSTREAM', 'DOWNSTREAM', 'FRAME_SHIFT')):
- for effectString in self.effects:
- effect = SNPEffect(effectString)
- if effect.effect not in notWanted:
- for attr in ('chromosome', 'position', 'reference_base', 'alternate_base', 'allele_frequency'):
- setattr(effect, attr, getattr(self, attr))
- yield effect.toDict()
-
-
- pass
- pass
-
-def extractCandiDataFromSnpEffVCF(snpEffVCF, fo):
- snps = []
- for line in snpEffVCF:
- if not line.startswith('#'):
- #fo.write(line)
- asf = AnnotatedSNPEffectFactory(*line.strip().split('\t'), log=fo)
- snpEffects = list(asf.getEffects())
- #fo.write(str(snpEffects)+'\n')
- snps.extend(snpEffects)
- return snps
-
-
-
-def main(argv):
-
- descr = ''
- parser = argparse.ArgumentParser(description=descr)
- parser.add_argument('--ref', help='The snpEff genome reference.')
- parser.add_argument('snpEff_output', type=str, help='The input file.')
- parser.add_argument('candisnp_html', type=str, help='The output file.')
- args = parser.parse_args()
-
- fo = open(args.candisnp_html, 'wb')
- """
- import subprocess
- import urllib2
- response = urllib2.urlopen('http://ruup.xyz:8080/monitors')
- html = response.read()
-
-
- # p = subprocess.Popen(['wget http://ruup.xyz:8080/monitors'], stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
- # fo.write(p.communicate()[0])
- fo.write(html)
- fo.close()
-
- return None
- """
- """
- # This works.
- candiData = CANDI_TESTDATA
- candiMessage = json.dumps(candiData)
- """
- candiData = extractCandiDataFromSnpEffVCF(open(args.snpEff_output), fo)
- candiMessage = json.dumps({'ref': args.ref, 'data': candiData})
-
- request = urllib2.Request(CANDISNP_SERVER + ':8080',
- headers=contentHeaders,
- data=candiMessage)
-
-
- try:
- response = urllib2.urlopen(request)
- candiURL = response.read()
- except urllib2.URLError, e:
- candiURL = ''
- sys.stderr.write(str(e.reason) + '\n')
-
- if candiURL:
- # body = urllib2.urlopen(candiURL)
- # fo.write(body.read())
- #fo.write('' % candiURL)
- #fo.write('' % candiURL)
- fo.write('\n' % candiURL)
- # fo.write('\n' % candiURL)
- else:
- fo.write('I am sorry. CandiSNP does not pick up. Maybe (try it manually?)\n' % CANDISNP_SERVER)
-
- fo.close()
- pass
-
-# main(sys.argv[1:])
-
-if __name__ == '__main__': main(sys.argv[1:])
diff -r 9215ffe7d4d5 -r 564795b5acae candisnp.xml
--- a/candisnp.xml Wed Jun 24 11:42:40 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,40 +0,0 @@
-
-
-
- python
- snpEff
-
- candisnp.py
- #if $snpDb.genomeSrc == 'cached':
- --ref="${snpDb.genomeVersion.fields.key}"
- #end if
- $input
- $candisnp_html
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- A tool to pull in visualisation output from CandiSNP (candisnp.tsl.ac.uk).
-
-
diff -r 9215ffe7d4d5 -r 564795b5acae snpeffv_genomedb.loc.sample
--- a/snpeffv_genomedb.loc.sample Wed Jun 24 11:42:40 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-## Downloaded Databases for SnpEff
-## These are from the list on: http://snpeff.sourceforge.net/download.html
-## the Description field in this sample is "Genome : Version"
-#Key snpeff_version Version Description data_dir path
-#SnpEff4.0_GRCh37.74 SnpEff4.0 GRCh37.74 Homo sapiens : GRCh37.74 /home/galaxy/snpEff/v4_0/data
-#SnpEff4.1_GRCh38.76 SnpEff4.1 GRCh38.76 Homo sapiens : GRCh38.76 /home/galaxy/snpEff/v4_1/data
diff -r 9215ffe7d4d5 -r 564795b5acae tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample Wed Jun 24 11:42:40 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-
-
-
- key, version, value, name, path
-
-
- toolshed.g2.bx.psu.edu
- snpeff
- iuc
- 500832f27cbc
-
-
-
diff -r 9215ffe7d4d5 -r 564795b5acae tool_dependencies.xml
--- a/tool_dependencies.xml Wed Jun 24 11:42:40 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-
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-