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Parsing blast default output to a table file.
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| #!/usr/bin/env python | |
| ''' | |
| #============================================================================= | |
| # FileName: parser_m8_solar.py | |
| # Desc: A script for parsering a blast m8 file to solared blocks; | |
| # Author: tanhao | |
| # Email: tanhao2013@gmail.com | |
| # HomePage: http://buttonwood.github.io | |
| # Version: a.0.1 | |
| # LastChange: 2014-03-19 09:22:07 | |
| # History: 2013-12-27 20:37:43 | |
| #============================================================================= | |
| ''' | |
| import os | |
| import argparse | |
| def total_score(s = [], t = 1): | |
| if t == 1: | |
| return sum([abs(float(i)) for i in s]) | |
| else: | |
| return sum([float(i) for i in s]) | |
| def print_list(l=[]): | |
| #return ";".join([repr(i) for i in l]) | |
| s = '' | |
| for x in l: | |
| s += x +";" | |
| return s | |
| def print_list_tuple(lt): | |
| # l = [(1, 3), (2, 3), (3, 8), (5, 7), (7, 9)] | |
| # print_list_tuple(l) will be 1,3;2,3;3,8;5,7;7,9; | |
| s = '' | |
| for x,y in lt: | |
| s += repr(x)+","+repr(y)+";" | |
| return s | |
| def get_st_ed_list_tuple(lt): | |
| # l = [(1, 3), (2, 3), (3, 8), (5, 7), (7, 9)] | |
| # get_st_ed_list_tuple(l) will return [1,9] | |
| (a,b) = lt[0] | |
| for x,y in lt: | |
| if a > min(x,y): | |
| a = min(x,y) | |
| if b < max(x,y): | |
| b = max(x,y) | |
| return [a,b] | |
| def main(args): | |
| writer = open(args.output, "w") | |
| query = "" | |
| subject = "" | |
| score = [] | |
| iden = [] | |
| q_block = [] | |
| s_block = [] | |
| with open(args.input,'r') as reader: | |
| for line in reader: | |
| fields = line.rstrip("\n").split("\t") | |
| if query == fields[0]: | |
| if subject == fields[1]: | |
| if (int(fields[8]) < int(fields[9])): | |
| score.append("+"+repr(float(fields[-1]))) | |
| else: | |
| score.append("-"+repr(float(fields[-1]))) | |
| iden.append(fields[2]) | |
| q_block.append([int(fields[6]),int(fields[7])]) | |
| s_block.append([int(fields[8]),int(fields[9])]) | |
| else: | |
| if subject: | |
| # print out | |
| text = '' | |
| a, b = get_st_ed_list_tuple(q_block) | |
| text += query + "\t" + repr(a) + "\t" + repr(b) + "\t" | |
| if total_score(score,0) < 0: | |
| text += "-\t" | |
| else: | |
| text += "+\t" | |
| a, b = get_st_ed_list_tuple(s_block) | |
| text += subject + "\t" + repr(a) + "\t" + repr(b) + "\t" | |
| c = len(iden) | |
| text += repr(c) + "\t" + "%.1f" % (total_score(score)) + "\t" | |
| #print text, | |
| #print "%.2f" % (total_score(iden)/c), | |
| text += "%.2f" % (total_score(iden)/c) | |
| text += "\t" + print_list_tuple(q_block) + "\t" + print_list_tuple(s_block) + "\t" | |
| text += print_list(score) + "\t" + print_list(iden) | |
| #print text | |
| #print "\n" | |
| writer.write(text) | |
| writer.write("\n") | |
| subject = fields[1] | |
| score = [] | |
| iden = [] | |
| q_block = [] | |
| s_block = [] | |
| if (int(fields[8]) < int(fields[9])): | |
| score.append("+"+repr(float(fields[-1]))) | |
| else: | |
| score.append("-"+repr(float(fields[-1]))) | |
| iden.append(fields[2]) | |
| q_block.append([int(fields[6]),int(fields[7])]) | |
| s_block.append([int(fields[8]),int(fields[9])]) | |
| else: | |
| if query: | |
| text = '' | |
| a, b = get_st_ed_list_tuple(q_block) | |
| text += query + "\t" + repr(a) + "\t" + repr(b) + "\t" | |
| if total_score(score,0) < 0: | |
| text += "-\t" | |
| else: | |
| text += "+\t" | |
| a, b = get_st_ed_list_tuple(s_block) | |
| text += subject + "\t" + repr(a) + "\t" + repr(b) + "\t" | |
| c = len(iden) | |
| text += repr(c) + "\t" + "%.1f" % (total_score(score)) + "\t" | |
| #print text, | |
| #print "%.2f" % (total_score(iden)/c), | |
| text += "%.2f" % (total_score(iden)/c) | |
| text += "\t" + print_list_tuple(q_block) + "\t" + print_list_tuple(s_block) + "\t" | |
| text += print_list(score) + "\t" + print_list(iden) | |
| #print text | |
| #print "\n" | |
| writer.write(text) | |
| writer.write("\n") | |
| query = fields[0] | |
| subject = fields[1] | |
| score = [] | |
| if (int(fields[8]) < int(fields[9])): | |
| score.append("+"+repr(float(fields[-1]))) | |
| else: | |
| score.append("-"+repr(float(fields[-1]))) | |
| iden = [] | |
| iden.append(fields[2]) | |
| q_block = [] | |
| q_block.append([int(fields[6]),int(fields[7])]) | |
| s_block = [] | |
| s_block.append([int(fields[8]),int(fields[9])]) | |
| if query: | |
| text = '' | |
| a, b = get_st_ed_list_tuple(q_block) | |
| text += query + "\t" + repr(a) + "\t" + repr(b) + "\t" | |
| if total_score(score,0) < 0: | |
| text += "-\t" | |
| else: | |
| text += "+\t" | |
| a, b = get_st_ed_list_tuple(s_block) | |
| text += subject + "\t" + repr(a) + "\t" + repr(b) + "\t" | |
| c = len(iden) | |
| text += repr(c) + "\t" + "%.1f" % (total_score(score)) + "\t" | |
| #print text, | |
| #print "%.2f" % (total_score(iden)/c), | |
| text += "%.2f" % (total_score(iden)/c) | |
| text += "\t" + print_list_tuple(q_block) + "\t" + print_list_tuple(s_block) + "\t" | |
| text += print_list(score) + "\t" + print_list(iden) | |
| #print text | |
| #print "\n" | |
| writer.write(text) | |
| writer.write("\n") | |
| if __name__ == "__main__": | |
| parser = argparse.ArgumentParser( | |
| formatter_class=argparse.RawTextHelpFormatter, | |
| description=""" | |
| A script for parsering a blast m8 file to solared blocks. | |
| input -> blast.m8: | |
| contig-550123 contig-550123 100.00 991 0 0 1 991 1 991 0.0 1875 | |
| contig-550123 contig-5207937 96.70 454 15 0 537 990 1 454 0.0 741 | |
| output -> blast.m8.solar: | |
| contig-999996 332 272 332 - contig-5473656 351 291 351 1 121 272,332; | |
| """) | |
| parser.add_argument( | |
| "-i", "--input", | |
| required=True, | |
| help="input a blast m8 file") | |
| parser.add_argument( | |
| "-o", "--output", | |
| required=True, | |
| help="output a solared file") | |
| args = parser.parse_args() | |
| main(args) |
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| #============================================================================= | |
| # FileName: paser_blast_de_hsp.pl | |
| # Desc: | |
| # Author: tanhao | |
| # Email: tanhao2013@gmail.com | |
| # HomePage: http://buttonwood.github.io | |
| # Version: 0.0.1 | |
| # LastChange: 2014-03-28 17:40:48 | |
| # History: | |
| #============================================================================= | |
| # It may be freely distributed under GNU General Public License. | |
| # | |
| # This script will parse a NCBI blastx output file and output the top | |
| # N hits of each blast search result. | |
| # | |
| # For each hit, the following results are reported: | |
| # Query name, Query length, Query start, Query end, Strand, | |
| # Subject name, Subject length, Subject start, Subject end, | |
| # Bit score, E value, Positives, and Identical | |
| # | |
| # The results are tab-deliminated and ready for import into a spreadsheet | |
| # program for browsing and further analysis. | |
| #============================================================================= | |
| #!/usr/bin/perl -w | |
| use strict; | |
| use Bio::SearchIO; | |
| die ("perl $0 *blast.de\n") unless (@ARGV==1); | |
| my $file = $ARGV[0]; | |
| my $in = new Bio::SearchIO(-format => 'blast', | |
| -file => $file); | |
| print "Query_name\tQuery_length\tQuery_start\tQuery_end\t";#Strand\t"; | |
| print "Subject_name\tSubject_length\tSubject_start\tSubject_end\t"; | |
| print "Hit\tIdentical\tBit_score\tE_value\tConserved\tPositives\n"; | |
| while( my $result = $in->next_result ) { | |
| ## $result is a Bio::Search::Result::ResultI compliant object | |
| while( my $hit = $result->next_hit ) { | |
| ## $hit is a Bio::Search::Hit::HitI compliant object | |
| while( my $hsp = $hit->next_hsp ) { | |
| print $result->query_name, | |
| "\t", $result->query_length, | |
| "\t", $hsp->start('query') . | |
| "\t", $hsp->end('query'), | |
| #"\t", $hsp->strand('query'), | |
| #"\t", $hsp->query->strand, | |
| "\t", $hit->name, | |
| "\t", $hit->length, | |
| "\t", $hsp->start('hit'), | |
| "\t", $hsp->end('hit'), | |
| #"\t", $hsp->strand('hit'), | |
| "\t", $hsp->length('total'), | |
| "\t", $hsp->num_identical, | |
| "\t", $hsp->bits, | |
| "\t", $hsp->significance, | |
| "\t", sprintf("%.2f",($hsp->frac_conserved)*100), | |
| "\t", sprintf("%.2f",($hsp->frac_identical)*100), "\n"; | |
| } | |
| } | |
| } | |
| #************* Float like a butterfly! Stand like a buttonwood! ************* |
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