annotate size_histogram.py @ 0:ef64759eb181 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda

#!/usr/bin/python
# python parser module for size distributions, guided by GFF3
# version 0.9.1 (1-6-2014)
# Usage readmap.py  <1:index source> <2:extraction directive> <3:output pre-mir> <4: output mature miRs> <5:mirbase GFF3>
#                     <6:pathToLatticeDataframe or "dummy_dataframe_path"> <7:Rcode or "dummy_plotCode"> <8:latticePDF or "dummy_latticePDF">
#                     <9:10:11 filePath:FileExt:FileLabel> <.. ad  lib>

import sys, subprocess, argparse
from smRtools import *
from collections import OrderedDict, defaultdict
import os

def Parser():
  the_parser = argparse.ArgumentParser()
  the_parser.add_argument('--output_size_distribution', action="store", type=str, help="size distribution dataframe")
  the_parser.add_argument('--reference_fasta', action="store", type=str, help="output file")
  the_parser.add_argument('--reference_bowtie_index',action='store', help="paths to indexed or fasta references")
  the_parser.add_argument('--input',nargs='+', help="paths to multiple input files")
  the_parser.add_argument('--ext',nargs='+', help="input file type")
  the_parser.add_argument('--label',nargs='+', help="labels of multiple input files")
  the_parser.add_argument('--normalization_factor',nargs='+', type=float, help="Normalization factor for input file")
  the_parser.add_argument('--gff', type=str, help="GFF containing regions of interest")
  the_parser.add_argument('--minquery', type=int, help="Minimum readsize")
  the_parser.add_argument('--maxquery', type=int, help="Maximum readsize")
  the_parser.add_argument('--rcode', type=str, help="R script")
  the_parser.add_argument('--global_size', action="store_true", help="if specified, size distribution is calcilated for the sum of all items")
  the_parser.add_argument('--collapse', action="store_true", help="if specified, forward and reverse reads are collapsed")
  args = the_parser.parse_args()
  return args

args=Parser()
if args.reference_fasta:
  genomeRefFormat = "fastaSource"
  genomeRefFile = args.reference_fasta  
if args.reference_bowtie_index:
  genomeRefFormat = "bowtieIndex"
  genomeRefFile = args.reference_bowtie_index  
size_distribution_file=args.output_size_distribution
minquery=args.minquery
maxquery=args.maxquery
Rcode = args.rcode
filePath=args.input
fileExt=args.ext
fileLabel=args.label
normalization_factor=args.normalization_factor
global_size=args.global_size
collapse=args.collapse

if collapse:
  pol=["both"]
else:
  pol=["F", "R"]

MasterListOfGenomes = OrderedDict()

def process_samples(filePath):
  for i, filePath in enumerate(filePath):
    norm=normalization_factor[i]
    print fileLabel[i]
    MasterListOfGenomes[fileLabel[i]] = HandleSmRNAwindows (alignmentFile=filePath, alignmentFileFormat=fileExt[i], genomeRefFile=genomeRefFile, genomeRefFormat=genomeRefFormat,\
                        biosample=fileLabel[i], size_inf=minquery, size_sup=maxquery, norm=norm)
  return MasterListOfGenomes

def write_size_distribution_dataframe(readDict, size_distribution_file, pol=["both"] ):
  '''refactored on 7-9-2014'''
  with open(size_distribution_file, 'w') as size_distrib:
    print >>size_distrib, "gene\tpolarity\tsize\tcount\tsample"
    for sample in readDict.keys():
      if args.gff:
        dict=readDict[sample]
      else:
        dict=readDict[sample].instanceDict
      for gene in dict.keys():
        histogram = dict[gene].size_histogram()
        for polarity in pol:
          for size, count in histogram[polarity].iteritems():
            print >>size_distrib, "%s\t%s\t%s\t%s\t%s" % (gene, polarity, size, count, sample)

def write_size_distribution_dataframe_global(readDict, size_distribution_file, pol=["both"]):
  with open(size_distribution_file, 'w') as size_distrib:
    print >>size_distrib, "gene\tpolarity\tsize\tcount\tsample"
    for sample in readDict.keys():
      histogram = readDict[sample].size_histogram()
      gene="sample"
      for polarity in pol:
        for size, count in histogram[polarity].iteritems():
          print >>size_distrib, "%s\t%s\t%s\t%s\t%s" % (gene, polarity, size, count, sample)

def gff_item_subinstances(readDict, gff3):
  GFFinstanceDict=OrderedDict()
  with open(gff3) as gff:
    for line in gff:
      if line[0] == "#": continue
      gff_fields = line[:-1].split("\t")
      chrom = gff_fields[0]
      gff_name = gff_fields[-1].split("Name=")[-1].split(";")[0] # to isolate the GFF Name
      item_upstream_coordinate = int(gff_fields[3])
      item_downstream_coordinate = int(gff_fields[4])
      item_polarity = gff_fields[6]
      for sample in readDict.keys():
	if not GFFinstanceDict.has_key(sample):
          GFFinstanceDict[sample]={}
        subinstance=extractsubinstance(item_upstream_coordinate, item_downstream_coordinate, readDict[sample].instanceDict[chrom])
        if item_polarity == '-':
          subinstance.readDict={key*-1:value for key, value in subinstance.readDict.iteritems()}
#          subinstance.readDict.setdefault(key, [])
        subinstance.gene=gff_name
        GFFinstanceDict[sample][gff_name]=subinstance
  return GFFinstanceDict

MasterListOfGenomes=process_samples(filePath)

if args.gff:
  MasterListOfGenomes=gff_item_subinstances(MasterListOfGenomes, args.gff)

if global_size:
  write_size_distribution_dataframe_global(MasterListOfGenomes, size_distribution_file, pol)
else:
  write_size_distribution_dataframe(MasterListOfGenomes, size_distribution_file, pol)

R_command="Rscript "+ Rcode
process = subprocess.Popen(R_command.split())
process.wait()