Example #1
0
#!/usr/bin/python
# script for computing small RNA phasing from a bowtie output
# version 1 4-1-2013
# Usage small_RNA_phasing.py <bowtie input> <minsize query> <maxsize query> <min scope> <max scope> <output> <bowtie index>

import sys, subprocess
from smRtools import get_fasta, get_fasta_from_history, antipara, RNAtranslate, SmRNAwindow
from collections import defaultdict

if sys.argv[-1] == "--extract_index":
    geneDic = get_fasta(sys.argv[7])
else:
    geneDic = get_fasta_from_history(sys.argv[7])

objDic = {}

F = open(sys.argv[1], "r")  # F is the bowtie output taken as input
for line in F:
    fields = line.split()
    polarity = fields[1]
    gene = fields[2]
    offset = int(fields[3])
    size = len(fields[4])
    try:
        objDic[gene].addread(polarity, offset, size)
    except KeyError:
        objDic[gene] = SmRNAwindow(gene, geneDic[gene])
        objDic[gene].addread(polarity, offset, size)
F.close()

minquery = int(sys.argv[2])
Example #2
0
#!/usr/bin/python
# script for computing z10 signature from a bowtie genomic output
# version 1 8-5-2012 using SmRNAtools class imported from smRtools
# Usage z10_genome.py <bowtie input> <windowsize> <outputpipi> <outputpisi> <outputsisi> <bowtie index>

import sys, subprocess
from smRtools import get_fasta, antipara, RNAtranslate, SmRNAwindow
from collections import defaultdict
from numpy import mean, std

def split_len(seq, length):
  return [seq[i:i+length] for i in range(0, len(seq), length)]


geneDic = get_fasta (sys.argv[6])
objDic = defaultdict(dict)
windowsize = int(sys.argv[2])

for chrom in geneDic:
  for windowindex, sequencewindow in enumerate (split_len(geneDic[chrom], windowsize)):
    objDic[chrom][windowindex * windowsize] = SmRNAwindow(chrom, sequencewindow, windowindex * windowsize)

F = open (sys.argv[1], "r") # F is the bowtie output taken as input
for line in F:
  fields = line.split()
  polarity = fields[1]
  chrom = fields[2]
  offset = int(fields[3])
  size = len (fields[4])
  objDic[chrom][offset/windowsize*windowsize].addread (polarity, offset, size)
F.close()
Example #3
0
#!/usr/bin/python
# script for computing overlap signatures from a bowtie output
# version 3 17-5-2012 complete refactoring with OOP approach
# Usage pairer.py <bowtie input> <minsize query> <maxsize query> <minsize target> <maxsize target> <output> <output1> <<output2> <<output3> <<output4> <<output5> <<output6> <<bowtie index>

import sys, subprocess
from collections import defaultdict
from smRtools import get_fasta, antipara, RNAtranslate, SmRNAwindow

fasta_dic = get_fasta(sys.argv[13])
objDic = {}
F = open(sys.argv[1], "r")  # F is the bowtie output taken as input

for line in F:
    fields = line.split()
    polarity = fields[1]
    gene = fields[2]
    offset = int(fields[3])
    size = len(fields[4])
    try:
        objDic[gene].addread(polarity, offset, size)
    except KeyError:
        objDic[gene] = SmRNAwindow(gene, fasta_dic[gene])
        objDic[gene].addread(polarity, offset, size)
F.close()

OUT = open(sys.argv[6], "w")

for x in objDic:
    sequence_list = objDic[x].pairer(10, sys.argv[2], sys.argv[3], sys.argv[4],
                                     sys.argv[5])
Example #4
0
#!/usr/bin/python
# script for outputing pairABLE reads from a bowtie output
# version 1 version 3-12-2012
# Usage pairable.py <bowtie input> <minsize query> <maxsize query> <minsize target> <maxsize target> <output> <bowtie index>

import sys, subprocess
from collections import defaultdict
from smRtools import get_fasta, antipara, RNAtranslate, SmRNAwindow

fasta_dic = get_fasta (sys.argv[7])
objDic = {}
F = open (sys.argv[1], "r") # F is the bowtie output taken as input

for line in F:
  fields = line.split()
  polarity = fields[1]
  gene = fields[2]
  offset = int(fields[3])
  size = len (fields[4])
  try:
    objDic[gene].addread (polarity, offset, size)
  except KeyError:
    objDic[gene] = SmRNAwindow(gene, fasta_dic[gene])
    objDic[gene].addread (polarity, offset, size)
F.close()

OUT = open (sys.argv[6], "w")


for x in objDic:
  sequence_list= objDic[x].newpairable_bowtie( 10, sys.argv[2], sys.argv[3], sys.argv[4], sys.argv[5])
Example #5
0
#!/usr/bin/python
# script for computing overlap signatures from a bowtie output
# version 3 17-5-2012 complete refactoring with OOP approach
# Usage pairer.py <bowtie input> <minsize query> <maxsize query> <minsize target> <maxsize target> <output> <output1> <<output2> <<output3> <<output4> <<output5> <<output6> <<bowtie index>

import sys, subprocess
from collections import defaultdict
from smRtools import get_fasta, antipara, RNAtranslate, SmRNAwindow

fasta_dic = get_fasta(sys.argv[13])
objDic = {}
F = open(sys.argv[1], "r")  # F is the bowtie output taken as input

for line in F:
    fields = line.split()
    polarity = fields[1]
    gene = fields[2]
    offset = int(fields[3])
    size = len(fields[4])
    try:
        objDic[gene].addread(polarity, offset, size)
    except KeyError:
        objDic[gene] = SmRNAwindow(gene, fasta_dic[gene])
        objDic[gene].addread(polarity, offset, size)
F.close()

OUT = open(sys.argv[6], "w")


for x in objDic:
    sequence_list = objDic[x].pairer(10, sys.argv[2], sys.argv[3], sys.argv[4], sys.argv[5])