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319 lines
18 KiB
Python
319 lines
18 KiB
Python
#!/usr/bin/env python
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#Guruprasad Ananda
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"""
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Uses SPUTNIK to fetch microsatellites and extracts orthologous repeats from the sputnik output.
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"""
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from galaxy import eggs
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import os
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import re
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import string
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import sys
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import tempfile
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def reverse_complement(text):
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DNA_COMP = string.maketrans( "ACGTacgt", "TGCAtgca" )
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comp = [ch for ch in text.translate(DNA_COMP)]
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comp.reverse()
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return "".join(comp)
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def main():
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if len(sys.argv) != 8:
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print >> sys.stderr, "Insufficient number of arguments."
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sys.exit()
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infile = open(sys.argv[1],'r')
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separation = int(sys.argv[2])
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outfile = sys.argv[3]
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mono_threshold = int(sys.argv[5])
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non_mono_threshold = int(sys.argv[6])
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allow_different_units = int(sys.argv[7])
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print "Min distance = %d bp; Min threshold for mono repeats = %d; Min threshold for non-mono repeats = %d; Allow different motifs = %s" % ( separation, mono_threshold, non_mono_threshold, allow_different_units==1 )
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try:
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fout = open(outfile, "w")
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print >> fout, "#Block\tSeq1_Name\tSeq1_Start\tSeq1_End\tSeq1_Type\tSeq1_Length\tSeq1_RepeatNumber\tSeq1_Unit\tSeq2_Name\tSeq2_Start\tSeq2_End\tSeq2_Type\tSeq2_Length\tSeq2_RepeatNumber\tSeq2_Unit"
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#sputnik_cmd = os.path.join(os.path.split(sys.argv[0])[0], "sputnik")
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sputnik_cmd = "sputnik"
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input = infile.read()
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block_num = 0
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input = input.replace('\r','\n')
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for block in input.split('\n\n'):
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block_num += 1
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tmpin = tempfile.NamedTemporaryFile()
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tmpout = tempfile.NamedTemporaryFile()
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tmpin.write(block.strip())
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cmdline = sputnik_cmd + " " + tmpin.name + " > /dev/null 2>&1 >> " + tmpout.name
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try:
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os.system(cmdline)
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except Exception:
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continue
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sputnik_out = tmpout.read()
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tmpin.close()
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tmpout.close()
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if sputnik_out != "":
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if len(block.split('>')[1:]) != 2: #len(sputnik_out.split('>')):
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continue
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align_block = block.strip().split('>')
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lendict = {'mononucleotide':1, 'dinucleotide':2, 'trinucleotide':3, 'tetranucleotide':4, 'pentanucleotide':5, 'hexanucleotide':6}
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blockdict = {}
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r = 0
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namelist = []
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for k, sput_block in enumerate(sputnik_out.split('>')[1:]):
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whole_seq = ''.join(align_block[k+1].split('\n')[1:]).replace('\n','').strip()
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p = re.compile('\n(\S*nucleotide)')
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repeats = p.split(sput_block.strip())
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repeats_count = len(repeats)
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j = 1
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name = repeats[0].strip()
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try:
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coords = re.search('\d+[-_:]\d+', name).group()
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coords = coords.replace('_', '-').replace(':', '-')
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except Exception:
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coords = '0-0'
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r += 1
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blockdict[r] = {}
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try:
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sp_name = name[:name.index('.')]
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chr_name = name[name.index('.'):name.index('(')]
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namelist.append(sp_name + chr_name)
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except:
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namelist.append(name[:20])
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while j < repeats_count:
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try:
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if repeats[j].strip() not in lendict:
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j += 2
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continue
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if blockdict[r].has_key('types'):
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blockdict[r]['types'].append(repeats[j].strip()) #type of microsat
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else:
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blockdict[r]['types'] = [repeats[j].strip()] #type of microsat
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start = int(repeats[j+1].split('--')[0].split(':')[0].strip())
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#check to see if there are gaps before the start of the repeat, and change the start accordingly
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sgaps = 0
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ch_pos = start - 1
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while ch_pos >= 0:
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if whole_seq[ch_pos] == '-':
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sgaps += 1
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else:
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break #break at the 1st non-gap character
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ch_pos -= 1
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if blockdict[r].has_key('starts'):
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blockdict[r]['starts'].append(start+sgaps) #start co-ords adjusted with alignment co-ords to include GAPS
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else:
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blockdict[r]['starts'] = [start+sgaps]
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end = int(repeats[j+1].split('--')[0].split(':')[1].strip())
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#check to see if there are gaps after the end of the repeat, and change the end accordingly
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egaps = 0
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for ch in whole_seq[end:]:
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if ch == '-':
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egaps += 1
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else:
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break #break at the 1st non-gap character
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if blockdict[r].has_key('ends'):
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blockdict[r]['ends'].append(end+egaps) #end co-ords adjusted with alignment co-ords to include GAPS
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else:
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blockdict[r]['ends'] = [end+egaps]
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repeat_seq = ''.join(repeats[j+1].replace('\r','\n').split('\n')[1:]).strip() #Repeat Sequence
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repeat_len = repeats[j+1].split('--')[1].split()[1].strip()
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gap_count = repeat_seq.count('-')
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#print repeats[j+1].split('--')[1], len(repeat_seq), repeat_len, gap_count
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repeat_len = str(int(repeat_len) - gap_count)
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rel_start = blockdict[r]['starts'][-1]
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gaps_before_start = whole_seq[:rel_start].count('-')
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if blockdict[r].has_key('gaps_before_start'):
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blockdict[r]['gaps_before_start'].append(gaps_before_start) #lengths
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else:
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blockdict[r]['gaps_before_start'] = [gaps_before_start] #lengths
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whole_seq_start = int(coords.split('-')[0])
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if blockdict[r].has_key('whole_seq_start'):
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blockdict[r]['whole_seq_start'].append(whole_seq_start) #lengths
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else:
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blockdict[r]['whole_seq_start'] = [whole_seq_start] #lengths
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if blockdict[r].has_key('lengths'):
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blockdict[r]['lengths'].append(repeat_len) #lengths
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else:
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blockdict[r]['lengths'] = [repeat_len] #lengths
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if blockdict[r].has_key('counts'):
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blockdict[r]['counts'].append(str(int(repeat_len)/lendict[repeats[j].strip()])) #Repeat Unit
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else:
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blockdict[r]['counts'] = [str(int(repeat_len)/lendict[repeats[j].strip()])] #Repeat Unit
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if blockdict[r].has_key('units'):
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blockdict[r]['units'].append(repeat_seq[:lendict[repeats[j].strip()]]) #Repeat Unit
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else:
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blockdict[r]['units'] = [repeat_seq[:lendict[repeats[j].strip()]]] #Repeat Unit
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except Exception:
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pass
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j += 2
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#check the co-ords of all repeats corresponding to a sequence and remove adjacent repeats separated by less than the user-specified 'separation'.
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delete_index_list = []
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for ind, item in enumerate(blockdict[r]['ends']):
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try:
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if blockdict[r]['starts'][ind+1]-item < separation:
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if ind not in delete_index_list:
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delete_index_list.append(ind)
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if ind+1 not in delete_index_list:
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delete_index_list.append(ind+1)
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except Exception:
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pass
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for index in delete_index_list: #mark them for deletion
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try:
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blockdict[r]['starts'][index] = 'marked'
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blockdict[r]['ends'][index] = 'marked'
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blockdict[r]['types'][index] = 'marked'
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blockdict[r]['gaps_before_start'][index] = 'marked'
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blockdict[r]['whole_seq_start'][index] = 'marked'
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blockdict[r]['lengths'][index] = 'marked'
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blockdict[r]['counts'][index] = 'marked'
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blockdict[r]['units'][index] = 'marked'
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except Exception:
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pass
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#remove 'marked' elements from all the lists
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"""
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for key in blockdict[r].keys():
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for elem in blockdict[r][key]:
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if elem == 'marked':
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blockdict[r][key].remove(elem)
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"""
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#print blockdict
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#make sure that the blockdict has keys for both the species
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if (1 not in blockdict) or (2 not in blockdict):
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continue
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visited_2 = [0 for x in range(len(blockdict[2]['starts']))]
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for ind1, coord_s1 in enumerate(blockdict[1]['starts']):
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if coord_s1 == 'marked':
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continue
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coord_e1 = blockdict[1]['ends'][ind1]
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out = []
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for ind2, coord_s2 in enumerate(blockdict[2]['starts']):
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if coord_s2 == 'marked':
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visited_2[ind2] = 1
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continue
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coord_e2 = blockdict[2]['ends'][ind2]
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#skip if the 2 repeats are not of the same type or don't have the same repeating unit.
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if allow_different_units == 0:
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if (blockdict[1]['types'][ind1] != blockdict[2]['types'][ind2]):
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continue
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else:
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if (blockdict[1]['units'][ind1] not in blockdict[2]['units'][ind2]*2) and (reverse_complement(blockdict[1]['units'][ind1]) not in blockdict[2]['units'][ind2]*2):
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continue
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#print >> sys.stderr, (reverse_complement(blockdict[1]['units'][ind1]) not in blockdict[2]['units'][ind2]*2)
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#skip if the repeat number thresholds are not met
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if blockdict[1]['types'][ind1] == 'mononucleotide':
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if (int(blockdict[1]['counts'][ind1]) < mono_threshold):
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continue
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else:
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if (int(blockdict[1]['counts'][ind1]) < non_mono_threshold):
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continue
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if blockdict[2]['types'][ind2] == 'mononucleotide':
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if (int(blockdict[2]['counts'][ind2]) < mono_threshold):
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continue
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else:
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if (int(blockdict[2]['counts'][ind2]) < non_mono_threshold):
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continue
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#print "s1,e1=%s,%s; s2,e2=%s,%s" % ( coord_s1, coord_e1, coord_s2, coord_e2 )
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if (coord_s1 in range(coord_s2, coord_e2)) or (coord_e1 in range(coord_s2, coord_e2)):
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out.append(str(block_num))
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out.append(namelist[0])
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rel_start = blockdict[1]['whole_seq_start'][ind1] + coord_s1 - blockdict[1]['gaps_before_start'][ind1]
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rel_end = rel_start + int(blockdict[1]['lengths'][ind1])
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out.append(str(rel_start))
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out.append(str(rel_end))
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out.append(blockdict[1]['types'][ind1])
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out.append(blockdict[1]['lengths'][ind1])
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out.append(blockdict[1]['counts'][ind1])
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out.append(blockdict[1]['units'][ind1])
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out.append(namelist[1])
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rel_start = blockdict[2]['whole_seq_start'][ind2] + coord_s2 - blockdict[2]['gaps_before_start'][ind2]
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rel_end = rel_start + int(blockdict[2]['lengths'][ind2])
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out.append(str(rel_start))
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out.append(str(rel_end))
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out.append(blockdict[2]['types'][ind2])
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out.append(blockdict[2]['lengths'][ind2])
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out.append(blockdict[2]['counts'][ind2])
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out.append(blockdict[2]['units'][ind2])
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print >> fout, '\t'.join(out)
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visited_2[ind2] = 1
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out = []
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if 0 in visited_2: #there are still some elements in 2nd set which haven't found orthologs yet.
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for ind2, coord_s2 in enumerate(blockdict[2]['starts']):
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if coord_s2 == 'marked':
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continue
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if visited_2[ind] != 0:
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continue
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coord_e2 = blockdict[2]['ends'][ind2]
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out = []
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for ind1, coord_s1 in enumerate(blockdict[1]['starts']):
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if coord_s1 == 'marked':
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continue
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coord_e1 = blockdict[1]['ends'][ind1]
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#skip if the 2 repeats are not of the same type or don't have the same repeating unit.
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if allow_different_units == 0:
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if (blockdict[1]['types'][ind1] != blockdict[2]['types'][ind2]):
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continue
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else:
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if (blockdict[1]['units'][ind1] not in blockdict[2]['units'][ind2]*2):# and reverse_complement(blockdict[1]['units'][ind1]) not in blockdict[2]['units'][ind2]*2:
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continue
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#skip if the repeat number thresholds are not met
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if blockdict[1]['types'][ind1] == 'mononucleotide':
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if (int(blockdict[1]['counts'][ind1]) < mono_threshold):
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continue
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else:
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if (int(blockdict[1]['counts'][ind1]) < non_mono_threshold):
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continue
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if blockdict[2]['types'][ind2] == 'mononucleotide':
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if (int(blockdict[2]['counts'][ind2]) < mono_threshold):
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continue
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else:
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if (int(blockdict[2]['counts'][ind2]) < non_mono_threshold):
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continue
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if (coord_s2 in range(coord_s1, coord_e1)) or (coord_e2 in range(coord_s1, coord_e1)):
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out.append(str(block_num))
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out.append(namelist[0])
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rel_start = blockdict[1]['whole_seq_start'][ind1] + coord_s1 - blockdict[1]['gaps_before_start'][ind1]
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rel_end = rel_start + int(blockdict[1]['lengths'][ind1])
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out.append(str(rel_start))
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out.append(str(rel_end))
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out.append(blockdict[1]['types'][ind1])
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out.append(blockdict[1]['lengths'][ind1])
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out.append(blockdict[1]['counts'][ind1])
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out.append(blockdict[1]['units'][ind1])
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out.append(namelist[1])
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rel_start = blockdict[2]['whole_seq_start'][ind2] + coord_s2 - blockdict[2]['gaps_before_start'][ind2]
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rel_end = rel_start + int(blockdict[2]['lengths'][ind2])
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out.append(str(rel_start))
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out.append(str(rel_end))
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out.append(blockdict[2]['types'][ind2])
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out.append(blockdict[2]['lengths'][ind2])
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out.append(blockdict[2]['counts'][ind2])
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out.append(blockdict[2]['units'][ind2])
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print >> fout, '\t'.join(out)
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visited_2[ind2] = 1
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out = []
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#print >> fout, blockdict
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except Exception, exc:
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print >> sys.stderr, "type(exc),args,exc: %s, %s, %s" % ( type(exc), exc.args, exc )
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if __name__ == "__main__":
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main()
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