comparison smRtools.py @ 1:ca3845fb0b31 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 70312b58ba246c07e70cdbd0a097f274f1386d09

0:b996480cd604

# version 1 7-5-2012 unification of the SmRNAwindow class

import sys, subprocess
from collections import defaultdict
from numpy import mean, median, std
from scipy import stats

def get_fasta (index="/home/galaxy/galaxy-dist/bowtie/5.37_Dmel/5.37_Dmel"):
  '''This function will return a dictionary containing fasta identifiers as keys and the
  sequence as values. Index must be the path to a fasta file.'''
  p = subprocess.Popen(args=["bowtie-inspect","-a", "0", index], stdout=subprocess.PIPE, stderr=subprocess.STDOUT) # bowtie-inspect outputs sequences on single lines

    Rbarycenter = (weigthAverage (reverseTuppleList) - upstream_coord) / window_size
    return Fbarycenter, Rbarycenter

  def correlation_mapper (self, reference, window_size):
    '''to map correlation with a sliding window 26-2-2013'''
    if window_size > self.size:
      return []
    F=open(reference, "r")
    reference_forward = []
    reference_reverse = []

1:ca3845fb0b31

# version 1 7-5-2012 unification of the SmRNAwindow class

import sys, subprocess
from collections import defaultdict
from numpy import mean, median, std
##Disable scipy import temporarily, as no working scipy on toolshed.
##from scipy import stats

def get_fasta (index="/home/galaxy/galaxy-dist/bowtie/5.37_Dmel/5.37_Dmel"):
  '''This function will return a dictionary containing fasta identifiers as keys and the
  sequence as values. Index must be the path to a fasta file.'''
  p = subprocess.Popen(args=["bowtie-inspect","-a", "0", index], stdout=subprocess.PIPE, stderr=subprocess.STDOUT) # bowtie-inspect outputs sequences on single lines

    Rbarycenter = (weigthAverage (reverseTuppleList) - upstream_coord) / window_size
    return Fbarycenter, Rbarycenter

  def correlation_mapper (self, reference, window_size):
    '''to map correlation with a sliding window 26-2-2013'''
    from scipy import stats

    if window_size > self.size:
      return []
    F=open(reference, "r")
    reference_forward = []
    reference_reverse = []