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