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check_gaps.py
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check_gaps.py
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### Boas Pucker ###
### bpucker@cebitec.uni-bielefeld.de ###
import os
# --- end of imports --- #
def load_sequences( multiple_fasta_file ):
"""! @brief load candidate gene IDs from file """
sequences = {}
with open( multiple_fasta_file ) as f:
header = f.readline()[1:].strip().split(' ')[0]
seq = ""
line = f.readline()
while line:
if line[0] == '>':
sequences.update( { header: seq } )
header = line.strip()[1:].split(' ')[0]
seq = ""
else:
seq += line.strip()
line = f.readline()
sequences.update( { header: seq } )
return sequences
def load_gap_positions( gap_file ):
"""! @brief load all gap infos """
gaps = []
with open( gap_file, "r" ) as f:
line = f.readline()
while line:
parts = line.strip().split('\t')
start, end = sorted( map( int, parts[3:] ) )
gaps.append( { 'chr': parts[0], 'start': start, 'end': end } )
line = f.readline()
return gaps
def construct_query_file( gaps, col_seqs, query_file, flank_len ):
"""! @brief construct file with gap flanking sequences """
counter = 0
with open( query_file, "w" ) as out:
for idx, gap in enumerate( gaps ):
if gap['start'] > flank_len and len( col_seqs[ gap['chr'] ] )-gap['end'] > flank_len:
out.write( '>gap' + str( idx ).zfill(2) + '_1\n' + col_seqs[ gap['chr'] ][ gap['start']-flank_len:gap['start'] ] + '\n' )
out.write( '>gap' + str( idx ).zfill(2) + '_2\n' + col_seqs[ gap['chr'] ][ gap['end']:gap['end']+flank_len ] + '\n' )
counter += 1
print "number of query sequences: " + str( counter )
def load_best_blast_hit_per_query( blast_result_file ):
"""! @brief load best BLAST hit """
best_hits = {}
with open( blast_result_file, "r" ) as f:
line = f.readline()
while line:
parts = line.strip().split('\t')
try:
hit = best_hits[ parts[0] ]
if float( parts[-1] ) > hit['score']:
del best_hits[ parts[0] ]
best_hits.update( { parts[0]: { 'chr': parts[1], 'start': int( parts[8] ), 'end': int( parts[9] ), 'score': float( parts[-1] ) } } )
except KeyError:
best_hits.update( { parts[0]: { 'chr': parts[1], 'start': int( parts[8] ), 'end': int( parts[9] ), 'score': float( parts[-1] ) } } )
line = f.readline()
return best_hits
def identify_matching_seqs( best_hits, gaps, new_genome_seqs ):
"""! @brief get matching sequences for all given gaps """
gap_results = []
for idx, gap in enumerate( gaps ):
try:
hit1 = best_hits[ 'gap' + str( idx ).zfill(2) + "_1" ]
hit2 = best_hits[ 'gap' + str( idx ).zfill(2) + "_2" ]
if hit1['chr'] == hit2['chr']:
if hit1['end'] < hit2['start']:
seq_of_interest = new_genome_seqs[ hit1['chr'] ][ hit1['end']:hit2['start'] ]
start = hit1['end']
end = hit2['start']
else:
end, start = sorted( [ hit2['start'], hit1['end'], hit2['end'], hit1['start'] ] )[1:3]
seq_of_interest = new_genome_seqs[ hit1['chr'] ][ start:end ]
if len( seq_of_interest ) > 1 and len( seq_of_interest )<800000:
gap_results.append( { 'id': idx, 'seq': seq_of_interest, 'chr': hit1['chr'], 'start': start, 'end': end } )
else:
print "hits on different sequences! - stopping analysis."
except KeyError:
print gap
return gap_results
if __name__ == '__main__':
gap_file = "TAIR10.gaps.txt"
TAIR10_file = "TAIR10.fa"
new_genome_seq_file = "AthNd1_v2c.fasta"
prefix = "OUTPUT_DIRECTORY"
# --- load gap position data --- #
gaps = load_gap_positions( gap_file )
col_seqs = load_sequences( TAIR10_file )
new_genome_seqs = load_sequences( new_genome_seq_file )
# --- construct_query_file --- #
query_file = prefix + "query.fasta"
construct_query_file( gaps, col_seqs, query_file, flank_len=30000 )
# --- run BLAST --- #
blast_result_file = prefix + "blast_result_file.txt"
blast_db = prefix + "blastdb"
os.popen( "makeblastdb -in " + new_genome_seq_file + " -out " + blast_db + " -dbtype nucl" )
os.popen( "blastn -query " + query_file + " -db " + blast_db + " -out " + blast_result_file + " -outfmt 6 -evalue 0.000000000000000000000000000000000000000000000001 -num_threads 16" )
# --- get gap matching sequences --- #
best_hits = load_best_blast_hit_per_query( blast_result_file )
gap_data = identify_matching_seqs( best_hits, gaps, new_genome_seqs )
# --- save gap matching sequences --- #
print "number of closed gaps: " + str( len( gap_data ) ) + "(total gaps: " + str( len( gaps ) ) + ")"
result_file = prefix + "results.fasta"
with open( result_file, "w" ) as out:
closed_gaps = []
for gap in gap_data:
if not 'N' in gap['seq']:
status = True
for each in closed_gaps:
if each['chr'] == gap['chr']:
if each['start'] < gap['end']:
if each['end'] > gap['start']:
status = False
if status:
closed_gaps.append( gap )
out.write( '>gap' + str( gap['id'] ).zfill( 2 ) + '_' + gap['chr'] + '_' + str( gap['start'] ) + "_" + str( gap['end'] ) + '\n' + gap['seq'] + '\n' )
print "all done!"