details: http://www.bx.psu.edu/hg/galaxy/rev/842f1883cf53 changeset: 1507:842f1883cf53 user: wychung date: Mon Sep 15 15:04:41 2008 -0400 description: add SHRiMP mapper for short reads analysis.
6 file(s) affected in this change:
test-data/shrimp_phix_anc.fa test-data/shrimp_wrapper_test1.fastq test-data/shrimp_wrapper_test1.out1 tool_conf.xml.sample tools/metag_tools/shrimp_wrapper.py tools/metag_tools/shrimp_wrapper.xml
diffs (853 lines):
diff -r 26825f08d362 -r 842f1883cf53 test-data/shrimp_phix_anc.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/shrimp_phix_anc.fa Mon Sep 15 15:04:41 2008 -0400 @@ -0,0 +1,2 @@ +>PHIX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTT GAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCG CGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTC TTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATG CCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTT GTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA diff -r 26825f08d362 -r 842f1883cf53 test-data/shrimp_wrapper_test1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/shrimp_wrapper_test1.fastq Mon Sep 15 15:04:41 2008 -0400 @@ -0,0 +1,40 @@ +@HWI-EAS91_1_306UPAAXX:6:1:959:874 +GCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCG ++HWI-EAS91_1_306UPAAXX:6:1:959:874 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_306UPAAXX:6:1:1630:1975 +GAAAGAAAATCAGCAACAGTGGCATCGATTTTACGG ++HWI-EAS91_1_306UPAAXX:6:1:1630:1975 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_306UPAAXX:6:1:770:994 +GCAGGCAGCGTGCTGCGAGTCTTTTCGAATGATAAG ++HWI-EAS91_1_306UPAAXX:6:1:770:994 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_306UPAAXX:6:1:1274:306 +GTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGC ++HWI-EAS91_1_306UPAAXX:6:1:1274:306 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh\h +@HWI-EAS91_1_306UPAAXX:6:1:1339:209 +GTTTGGTCAGTTCCATCAACATCATAGCCAGATGCC ++HWI-EAS91_1_306UPAAXX:6:1:1339:209 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_306UPAAXX:6:1:203:1240 +GATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTA ++HWI-EAS91_1_306UPAAXX:6:1:203:1240 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_306UPAAXX:6:1:869:448 +GCTGGCCATCAGTTCGCGGATACCGGCGGCAAACAT ++HWI-EAS91_1_306UPAAXX:6:1:869:448 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhKhhhhhhh +@HWI-EAS91_1_306UPAAXX:6:1:939:928 +GGAGGCCTCCAGCAATCTTGAACACTCATCCTTAAT ++HWI-EAS91_1_306UPAAXX:6:1:939:928 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_306UPAAXX:6:1:1756:1476 +GCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGC ++HWI-EAS91_1_306UPAAXX:6:1:1756:1476 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_306UPAAXX:6:1:1528:181 +GGCTGGTCAGTATTTTACCAATGACCAAATCAAAGA ++HWI-EAS91_1_306UPAAXX:6:1:1528:181 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh diff -r 26825f08d362 -r 842f1883cf53 test-data/shrimp_wrapper_test1.out1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/shrimp_wrapper_test1.out1 Mon Sep 15 15:04:41 2008 -0400 @@ -0,0 +1,7 @@ +#FORMAT: readname contigname strand contigstart contigend readstart readend readlength score editstring +>HWI-EAS91_1_306UPAAXX:6:1:1528:181 PHIX174 + 3644 3679 1 36 36 3600 36 +>HWI-EAS91_1_306UPAAXX:6:1:1756:1476 PHIX174 + 4505 4540 1 36 36 3600 36 +>HWI-EAS91_1_306UPAAXX:6:1:203:1240 PHIX174 + 310 345 1 36 36 3600 36 +>HWI-EAS91_1_306UPAAXX:6:1:1274:306 PHIX174 + 933 968 1 36 36 3600 36 +>HWI-EAS91_1_306UPAAXX:6:1:939:928 PHIX174 - 4458 4493 1 36 36 3600 36 +>HWI-EAS91_1_306UPAAXX:6:1:1339:209 PHIX174 - 1732 1767 1 36 36 3600 36 diff -r 26825f08d362 -r 842f1883cf53 tool_conf.xml.sample --- a/tool_conf.xml.sample Sun Sep 14 14:58:50 2008 -0400 +++ b/tool_conf.xml.sample Mon Sep 15 15:04:41 2008 -0400 @@ -276,6 +276,7 @@ <tool file="metag_tools/blat_coverage_report.xml" /> </section> <section name="Short Read Mapping" id="solexa_tools"> + <tool file="metag_tools/shrimp_wrapper.xml" /> <tool file="sr_mapping/lastz_wrapper.xml" /> <tool file="metag_tools/megablast_wrapper.xml" /> <tool file="metag_tools/megablast_xml_parser.xml" /> diff -r 26825f08d362 -r 842f1883cf53 tools/metag_tools/shrimp_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/metag_tools/shrimp_wrapper.py Mon Sep 15 15:04:41 2008 -0400 @@ -0,0 +1,577 @@ +#! /usr/bin/python + +""" +SHRiMP wrapper + +Inputs: + reference seq and reads + +Outputs: + table of 8 columns: + chrom ref_loc read_id read_loc ref_nuc read_nuc quality coverage + SHRiMP output + +Parameters: + -s Spaced Seed (default: 111111011111) + -n Seed Matches per Window (default: 2) + -t Seed Hit Taboo Length (default: 4) + -9 Seed Generation Taboo Length (default: 0) + -w Seed Window Length (default: 115.00%) + -o Maximum Hits per Read (default: 100) + -r Maximum Read Length (default: 1000) + -d Kmer Std. Deviation Limit (default: -1 [None]) + + -m S-W Match Value (default: 100) + -i S-W Mismatch Value (default: -150) + -g S-W Gap Open Penalty (Reference) (default: -400) + -q S-W Gap Open Penalty (Query) (default: -400) + -e S-W Gap Extend Penalty (Reference) (default: -70) + -f S-W Gap Extend Penalty (Query) (default: -70) + -h S-W Hit Threshold (default: 68.00%) + +Command: +%rmapper -s spaced_seed -n seed_matches_per_window -t seed_hit_taboo_length -9 seed_generation_taboo_length -w seed_window_length -o max_hits_per_read -r max_read_length -d kmer -m sw_match_value -i sw_mismatch_value -g sw_gap_open_ref -q sw_gap_open_query -e sw_gap_ext_ref -f sw_gap_ext_query -h sw_hit_threshold <query> <target> > <output> 2> <log> + +SHRiMP output: +>7:2:1147:982/1 chr3 + 36586562 36586595 2 35 36 2900 3G16G13 +>7:2:1147:982/1 chr3 + 95338194 95338225 4 35 36 2700 9T7C14 +>7:2:587:93/1 chr3 + 14913541 14913577 1 35 36 2960 19--16 + +Testing: +%python shrimp_wrapper.py single ~/Desktop/shrimp_wrapper/phix_anc.fa tmp tmp1 ~/Desktop/shrimp_wrapper/phix.10.solexa.fastq +%python shrimp_wrapper.py paired ~/Desktop/shrimp_wrapper/eca_ref_chrMT.fa tmp tmp1 ~/Desktop/shrimp_wrapper/eca.5.solexa_1.fastq ~/Desktop/shrimp_wrapper/eca.5.solexa_2.fastq + +""" + +import os, sys, tempfile, os.path + +assert sys.version_info[:2] >= (2.4) + +def stop_err( msg ): + + sys.stderr.write( "%s\n" % msg ) + sys.exit() + +def reverse_complement(s): + + complement_dna = {"A":"T", "T":"A", "C":"G", "G":"C", "a":"t", "t":"a", "c":"g", "g":"c", "N":"N", "n":"n" , ".":".", "-":"-"} + reversed_s = [] + for i in s: + reversed_s.append(complement_dna[i]) + reversed_s.reverse() + return "".join(reversed_s) + +def generate_sub_table(result_file, ref_file, score_files, table_outfile, hit_per_read): + + """ + TODO: the cross-over error has not been addressed yet. + """ + + insertion_size = 600 + + all_score_file = score_files.split('&') + + if len(all_score_file) != hit_per_read: stop_err('Un-equal number of files!') + + temp_table_name = tempfile.NamedTemporaryFile().name + temp_table = open(temp_table_name, 'w') + + outfile = open(table_outfile,'w') + + # reference seq: not a single fasta seq + refseq = {} + chrom_cov = {} + seq = '' + + for i, line in enumerate(file(ref_file)): + line = line.rstrip() + if not line or line.startswith('#'): continue + + if line.startswith('>'): + if seq: + if refseq.has_key(title): + pass + else: + refseq[title] = seq + chrom_cov[title] = {} + seq = '' + title = line[1:] + else: + seq += line + if seq: + if not refseq.has_key(title): + refseq[title] = seq + chrom_cov[title] = {} + + # find hits : one end and/or the other + hits = {} + for i, line in enumerate(file(result_file)): + line = line.rstrip() + if not line or line.startswith('#'): continue + + #FORMAT: readname contigname strand contigstart contigend readstart readend readlength score editstring + fields = line.split('\t') + readname = fields[0][1:] + chrom = fields[1] + strand = fields[2] + chrom_start = int(fields[3]) - 1 + chrom_end = int(fields[4]) + read_start = fields[5] + read_end = fields[6] + read_len = fields[7] + score = fields[8] + editstring = fields[9] + + if hit_per_read == 1: + endindex = '1' + else: + readname, endindex = readname.split('/') + + if hits.has_key(readname): + if hits[readname].has_key(endindex): + hits[readname][endindex].append([strand, editstring, chrom_start, chrom_end, read_start, chrom]) + else: + hits[readname][endindex] = [[strand, editstring, chrom_start, chrom_end, read_start, chrom]] + else: + hits[readname] = {} + hits[readname][endindex] = [[strand, editstring, chrom_start, chrom_end, read_start, chrom]] + + # find score : one end and the other end + hits_score = {} + readname = '' + score = '' + for num_score_file in range(len(all_score_file)): + score_file = all_score_file[num_score_file] + for i, line in enumerate(file(score_file)): + line = line.rstrip() + if not line or line.startswith('#'): continue + + if line.startswith('>'): + if score: + if hits.has_key(readname): + if len(hits[readname]) == hit_per_read: + if hits_score.has_key(readname): + if hits_score[readname].has_key(endindex): + pass + else: + hits_score[readname][endindex] = score + else: + hits_score[readname] = {} + hits_score[readname][endindex] = score + score = '' + if hit_per_read == 1: + readname = line[1:] + endindex = '1' + else: + readname, endindex = line[1:].split('/') + else: + score = line + if score: # the last one + if hits.has_key(readname): + if len(hits[readname]) == hit_per_read: + if hits_score.has_key(readname): + if hits_score[readname].has_key(endindex): + pass + else: + hits_score[readname][endindex] = score + else: + hits_score[readname] = {} + hits_score[readname][endindex] = score + + # mutation call to all mappings + for readkey in hits.keys(): + if len(hits[readkey]) != hit_per_read: continue + + matches = [] + match_count = 0 + + if hit_per_read == 1: + matches = [ hits[readkey]['1'] ] + match_count = 1 + else: + end1_data = hits[readkey]['1'] + end2_data = hits[readkey]['2'] + + for i, end1_hit in enumerate(end1_data): + crin_strand = {'+': False, '-': False} + crin_insertSize = {'+': False, '-': False} + + crin_strand[end1_hit[0]] = True + crin_insertSize[end1_hit[0]] = int(end1_hit[2]) + + for j, end2_hit in enumerate(end2_data): + crin_strand[end2_hit[0]] = True + crin_insertSize[end2_hit[0]] = int(end2_hit[2]) + + if end1_hit[-1] != end2_hit[-1] : continue + + if crin_strand['+'] and crin_strand['-']: + if (crin_insertSize['-'] - crin_insertSize['+']) <= insertion_size: + matches.append([end1_hit, end2_hit]) + match_count += 1 + + if match_count == 1: + for x, end_data in enumerate(matches[0]): + + end_strand, end_editstring, end_chr_start, end_chr_end, end_read_start, end_chrom = end_data + end_read_start = int(end_read_start) - 1 + + if end_strand == '-': + refsegment = reverse_complement(refseq[end_chrom][end_chr_start:end_chr_end]) + else: + refsegment = refseq[end_chrom][end_chr_start:end_chr_end] + + match_len = 0 + editindex = 0 + gap_read = 0 + + while editindex < len(end_editstring): + editchr = end_editstring[editindex] + chrA = '' + chrB = '' + locIndex = [] + if editchr.isdigit(): + editcode = '' + while editchr.isdigit() and editindex < len(end_editstring): + editcode += editchr + editindex += 1 + if editindex < len(end_editstring): editchr = end_editstring[editindex] + for baseIndex in range(int(editcode)): + chrA += refsegment[match_len+baseIndex] + chrB = chrA + match_len += int(editcode) + elif editchr == 'x': + # crossover: inserted between the appropriate two bases + # Two sequencing errors: 4x15x6 (25 matches with 2 crossovers) + # Treated as errors in the reads; Do nothing. + editindex += 1 + + elif editchr.isalpha(): + editcode = editchr + editindex += 1 + chrA = refsegment[match_len] + chrB = editcode + match_len += len(editcode) + + elif editchr == '-': + editcode = editchr + editindex += 1 + chrA = refsegment[match_len] + chrB = editcode + match_len += len(editcode) + gap_read += 1 + + elif editchr == '(': + editcode = '' + while editchr != ')' and editindex < len(end_editstring): + if editindex < len(end_editstring): editchr = end_editstring[editindex] + editcode += editchr + editindex += 1 + editcode = editcode[1:-1] + chrA = '-'*len(editcode) + chrB = editcode + + else: + print 'Warning! Unknown symbols', editchr + + if end_strand == '-': + chrA = reverse_complement(chrA) + chrB = reverse_complement(chrB) + + pos_line = '' + rev_line = '' + + for mappingIndex in range(len(chrA)): + # reference + chrAx = chrA[mappingIndex] + # read + chrBx = chrB[mappingIndex] + + if chrAx and chrBx and chrBx.upper() != 'N': + if end_strand == '+': + chrom_loc = end_chr_start+match_len-len(chrA)+mappingIndex + read_loc = end_read_start+match_len-len(chrA)+mappingIndex-gap_read + if chrAx == '-': chrom_loc -= 1 + + if chrBx == '-': + scoreBx = '-1' + else: + scoreBx = hits_score[readkey][str(x+1)].split()[read_loc] + + # 1-based on chrom_loc and read_loc + pos_line = pos_line + '\t'.join([end_chrom, str(chrom_loc+1), readkey+'/'+str(x+1), str(read_loc+1), chrAx, chrBx, scoreBx]) + '\n' + else: + chrom_loc = end_chr_end-match_len+mappingIndex + read_loc = end_read_start+match_len-1-mappingIndex-gap_read + if chrAx == '-': chrom_loc -= 1 + + if chrBx == '-': + scoreBx = '-1' + else: + scoreBx = hits_score[readkey][str(x+1)].split()[read_loc] + + # 1-based on chrom_loc and read_loc + rev_line = '\t'.join([end_chrom, str(chrom_loc+1), readkey+'/'+str(x+1), str(read_loc+1), chrAx, chrBx, scoreBx]) +'\n' + rev_line + + if chrom_cov.has_key(end_chrom): + if chrom_cov[end_chrom].has_key(chrom_loc): + chrom_cov[end_chrom][chrom_loc] += 1 + else: + chrom_cov[end_chrom][chrom_loc] = 1 + else: + chrom_cov[end_chrom] = {} + chrom_cov[end_chrom][chrom_loc] = 1 + + if pos_line: temp_table.write('%s\n' %(pos_line.rstrip('\r\n'))) + if rev_line: temp_table.write('%s\n' %(rev_line.rstrip('\r\n'))) + + temp_table.close() + + # chrom-wide coverage + for i, line in enumerate(open(temp_table_name)): + line = line.rstrip() + if not line or line.startswith('#'): continue + + fields = line.split() + chrom = fields[0] + eachBp = int(fields[1]) + readname = fields[2] + + if hit_per_read == 1: + fields[2] = readname.split('/')[0] + + if chrom_cov[chrom].has_key(eachBp): + outfile.write('%s\t%d\n' %('\t'.join(fields), chrom_cov[chrom][eachBp])) + else: + outfile.write('%s\t%d\n' %('\t'.join(fields), 0)) + + outfile.close() + + if os.path.exists(temp_table_name): os.remove(temp_table_name) + + return True + +def convert_fastqsolexa_to_fasta_qual(infile_name, query_fasta, query_qual): + + outfile_seq = open( query_fasta, 'w' ) + outfile_score = open( query_qual, 'w' ) + + seq_title_startswith = '' + qual_title_startswith = '' + + default_coding_value = 64 + fastq_block_lines = 0 + + for i, line in enumerate( file( infile_name ) ): + line = line.rstrip() + if not line or line.startswith( '#' ): continue + + fastq_block_lines = ( fastq_block_lines + 1 ) % 4 + line_startswith = line[0:1] + + if fastq_block_lines == 1: + # first line is @title_of_seq + if not seq_title_startswith: + seq_title_startswith = line_startswith + + if line_startswith != seq_title_startswith: + outfile_seq.close() + outfile_score.close() + stop_err( 'Invalid fastqsolexa format at line %d: %s.' % ( i + 1, line ) ) + + read_title = line[1:] + outfile_seq.write( '>%s\n' % line[1:] ) + + elif fastq_block_lines == 2: + # second line is nucleotides + read_length = len( line ) + outfile_seq.write( '%s\n' % line ) + + elif fastq_block_lines == 3: + # third line is +title_of_qualityscore ( might be skipped ) + if not qual_title_startswith: + qual_title_startswith = line_startswith + + if line_startswith != qual_title_startswith: + outfile_seq.close() + outfile_score.close() + stop_err( 'Invalid fastqsolexa format at line %d: %s.' % ( i + 1, line ) ) + + quality_title = line[1:] + if quality_title and read_title != quality_title: + outfile_seq.close() + outfile_score.close() + stop_err( 'Invalid fastqsolexa format at line %d: sequence title "%s" differes from score title "%s".' % ( i + 1, read_title, quality_title ) ) + + if not quality_title: + outfile_score.write( '>%s\n' % read_title ) + else: + outfile_score.write( '>%s\n' % line[1:] ) + + else: + # fourth line is quality scores + qual = '' + fastq_integer = True + # peek: ascii or digits? + val = line.split()[0] + try: + check = int( val ) + fastq_integer = True + except: + fastq_integer = False + + if fastq_integer: + # digits + qual = line + else: + # ascii + quality_score_length = len( line ) + if quality_score_length == read_length + 1: + # first char is qual_score_startswith + qual_score_startswith = ord( line[0:1] ) + line = line[1:] + elif quality_score_length == read_length: + qual_score_startswith = default_coding_value + else: + stop_err( 'Invalid fastqsolexa format at line %d: the number of quality scores ( %d ) is not the same as bases ( %d ).' % ( i + 1, quality_score_length, read_length ) ) + + for j, char in enumerate( line ): + score = ord( char ) - qual_score_startswith # 64 + qual = "%s%s " % ( qual, str( score ) ) + + outfile_score.write( '%s\n' % qual ) + + outfile_seq.close() + outfile_score.close() + + return True + +def __main__(): + + # I/O + type_of_reads = sys.argv[1] # single or paired + input_target = sys.argv[2] # fasta + shrimp_outfile = sys.argv[3] # shrimp output + table_outfile = sys.argv[4] # table output + + # SHRiMP parameters: total = 15 + # TODO: put threshold on each of these parameters + if len(sys.argv) == 21 or len(sys.argv) == 22: + spaced_seed = sys.argv[5] + seed_matches_per_window = sys.argv[6] + seed_hit_taboo_length = sys.argv[7] + seed_generation_taboo_length = sys.argv[8] + seed_window_length = sys.argv[9] + max_hits_per_read = sys.argv[10] + max_read_length = sys.argv[11] + kmer = sys.argv[12] + sw_match_value = sys.argv[13] + sw_mismatch_value = sys.argv[14] + sw_gap_open_ref = sys.argv[15] + sw_gap_open_query = sys.argv[16] + sw_gap_ext_ref = sys.argv[17] + sw_gap_ext_query = sys.argv[18] + sw_hit_threshold = sys.argv[19] + + # Single-end parameters + if type_of_reads == 'single': + input_query = sys.argv[20] # single-end + hit_per_read = 1 + query_fasta = tempfile.NamedTemporaryFile().name + query_qual = tempfile.NamedTemporaryFile().name + else: # Paired-end parameters + input_query_end1 = sys.argv[20] # paired-end + input_query_end2 = sys.argv[21] + hit_per_read = 2 + query_fasta_end1 = tempfile.NamedTemporaryFile().name + query_fasta_end2 = tempfile.NamedTemporaryFile().name + query_qual_end1 = tempfile.NamedTemporaryFile().name + query_qual_end2 = tempfile.NamedTemporaryFile().name + else: + spaced_seed = '111111011111' + seed_matches_per_window = '2' + seed_hit_taboo_length = '4' + seed_generation_taboo_length = '0' + seed_window_length = '115.0' + max_hits_per_read = '100' + max_read_length = '1000' + kmer = '-1' + sw_match_value = '100' + sw_mismatch_value = '-150' + sw_gap_open_ref = '-400' + sw_gap_open_query = '-400' + sw_gap_ext_ref = '-70' + sw_gap_ext_query = '-70' + sw_hit_threshold = '68.0' + + # Single-end parameters + if type_of_reads == 'single': + input_query = sys.argv[5] # single-end + hit_per_read = 1 + query_fasta = tempfile.NamedTemporaryFile().name + query_qual = tempfile.NamedTemporaryFile().name + else: # Paired-end parameters + input_query_end1 = sys.argv[5] # paired-end + input_query_end2 = sys.argv[6] + hit_per_read = 2 + query_fasta_end1 = tempfile.NamedTemporaryFile().name + query_fasta_end2 = tempfile.NamedTemporaryFile().name + query_qual_end1 = tempfile.NamedTemporaryFile().name + query_qual_end2 = tempfile.NamedTemporaryFile().name + + + # temp file for shrimp log file + shrimp_log = tempfile.NamedTemporaryFile().name + + # convert fastq to fasta and quality score files + if type_of_reads == 'single': + return_value = convert_fastqsolexa_to_fasta_qual(input_query, query_fasta, query_qual) + else: + return_value = convert_fastqsolexa_to_fasta_qual(input_query_end1, query_fasta_end1, query_qual_end1) + return_value = convert_fastqsolexa_to_fasta_qual(input_query_end2, query_fasta_end2, query_qual_end2) + + # SHRiMP command + if type_of_reads == 'single': + command = ' '.join(['rmapper-ls', '-s', spaced_seed, '-n', seed_matches_per_window, '-t', seed_hit_taboo_length, '-9', seed_generation_taboo_length, '-w', seed_window_length, '-o', max_hits_per_read, '-r', max_read_length, '-d', kmer, '-m', sw_match_value, '-i', sw_mismatch_value, '-g', sw_gap_open_ref, '-q', sw_gap_open_query, '-e', sw_gap_ext_ref, '-f', sw_gap_ext_query, '-h', sw_hit_threshold, query_fasta, input_target, '>', shrimp_outfile, '2>', shrimp_log]) + + try: + os.system(command) + except Exception, e: + if os.path.exists(query_fasta): os.remove(query_fasta) + if os.path.exists(query_qual): os.remove(query_qual) + stop_err(str(e)) + + else: + command_end1 = ' '.join(['rmapper-ls', '-s', spaced_seed, '-n', seed_matches_per_window, '-t', seed_hit_taboo_length, '-9', seed_generation_taboo_length, '-w', seed_window_length, '-o', max_hits_per_read, '-r', max_read_length, '-d', kmer, '-m', sw_match_value, '-i', sw_mismatch_value, '-g', sw_gap_open_ref, '-q', sw_gap_open_query, '-e', sw_gap_ext_ref, '-f', sw_gap_ext_query, '-h', sw_hit_threshold, query_fasta_end1, input_target, '>', shrimp_outfile, '2>', shrimp_log]) + command_end2 = ' '.join(['rmapper-ls', '-s', spaced_seed, '-n', seed_matches_per_window, '-t', seed_hit_taboo_length, '-9', seed_generation_taboo_length, '-w', seed_window_length, '-o', max_hits_per_read, '-r', max_read_length, '-d', kmer, '-m', sw_match_value, '-i', sw_mismatch_value, '-g', sw_gap_open_ref, '-q', sw_gap_open_query, '-e', sw_gap_ext_ref, '-f', sw_gap_ext_query, '-h', sw_hit_threshold, query_fasta_end2, input_target, '>>', shrimp_outfile, '2>>', shrimp_log]) + + try: + os.system(command_end1) + os.system(command_end2) + except Exception, e: + if os.path.exists(query_fasta_end1): os.remove(query_fasta_end1) + if os.path.exists(query_fasta_end2): os.remove(query_fasta_end2) + if os.path.exists(query_qual_end1): os.remove(query_qual_end1) + if os.path.exists(query_qual_end2): os.remove(query_qual_end2) + stop_err(str(e)) + + # convert to table + if type_of_reads == 'single': + return_value = generate_sub_table(shrimp_outfile, input_target, query_qual, table_outfile, hit_per_read) + else: + return_value = generate_sub_table(shrimp_outfile, input_target, query_qual_end1+'&'+query_qual_end2, table_outfile, hit_per_read) + + # remove temp. files + if type_of_reads == 'single': + if os.path.exists(query_fasta): os.remove(query_fasta) + if os.path.exists(query_qual): os.remove(query_qual) + else: + if os.path.exists(query_fasta_end1): os.remove(query_fasta_end1) + if os.path.exists(query_fasta_end2): os.remove(query_fasta_end2) + if os.path.exists(query_qual_end1): os.remove(query_qual_end1) + if os.path.exists(query_qual_end2): os.remove(query_qual_end2) + + if os.path.exists(shrimp_log): os.remove(shrimp_log) + +if __name__ == '__main__': __main__() + diff -r 26825f08d362 -r 842f1883cf53 tools/metag_tools/shrimp_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/metag_tools/shrimp_wrapper.xml Mon Sep 15 15:04:41 2008 -0400 @@ -0,0 +1,196 @@ +<tool id="shrimp_wrapper" name="SHRiMP" version="1.0.0"> + <description>SHort Read Mapping Package</description> + <command interpreter="python"> + #if ($type_of_reads.single_or_paired=="single" and $param.skip_or_full=="skip"):#shrimp_wrapper.py $type_of_reads.single_or_paired $input_target $output1 $output2 $input_query + #elif ($type_of_reads.single_or_paired=="paired" and $param.skip_or_full=="skip"):#shrimp_wrapper.py $type_of_reads.single_or_paired $input_target $output1 $output2 ${type_of_reads.input1} ${type_of_reads.input2} + #elif ($type_of_reads.single_or_paired=="single" and $param.skip_or_full=="full"):#shrimp_wrapper.py $type_of_reads.single_or_paired $input_target $output1 $output2 $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_hit_threshold $input_query + #elif ($type_of_reads.single_or_paired=="paired" and $param.skip_or_full=="full"):#shrimp_wrapper.py $type_of_reads.single_or_paired $input_target $output1 $output2 $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_hit_threshold ${type_of_reads.input1} ${type_of_reads.input2} + #end if + </command> + <inputs> + <page> + <param name="input_target" type="data" format="fasta" label="Reference sequence" /> + <conditional name="type_of_reads"> + <param name="single_or_paired" type="select" label="Single- or Paired-ends"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + </param> + <when value="single"> + <param name="input_query" type="data" format="fastqsolexa" label="Sequence file" /> + </when> + <when value="paired"> + <param name="input1" type="data" format="fastqsolexa" label="One end" /> + <param name="input2" type="data" format="fastqsolexa" label="The other end" /> + </when> + </conditional> + <conditional name="param"> + <param name="skip_or_full" type="select" label="SHRiMP parameter selection"> + <option value="skip">Default setting</option> + <option value="full">Full list</option> + </param> + <when value="skip" /> + <when value="full"> + <param name="spaced_seed" type="text" size="30" value="111111011111" label="Spaced Seed" /> + <param name="seed_matches_per_window" type="integer" size="5" value="2" label="Seed Matches per Window" /> + <param name="seed_hit_taboo_length" type="integer" size="5" value="4" label="Seed Hit Taboo Length" /> + <param name="seed_generation_taboo_length" type="integer" size="5" value="0" label="Seed Generation Taboo Length" /> + <param name="seed_window_length" type="float" size="10" value="115.0" label="Seed Window Length" help="in percentage"/> + <param name="max_hits_per_read" type="integer" size="10" value="100" label="Maximum Hits per Read" /> + <param name="max_read_length" type="integer" size="10" value="1000" label="Maximum Read Length" /> + <param name="kmer" type="integer" size="10" value="-1" label="Kmer Std. Deviation Limit" help="-1 as None"/> + <param name="sw_match_value" type="integer" size="10" value="100" label="S-W Match Value" /> + <param name="sw_mismatch_value" type="integer" size="10" value="-150" label="S-W Mismatch Value" /> + <param name="sw_gap_open_ref" type="integer" size="10" value="-400" label="S-W Gap Open Penalty (Reference)" /> + <param name="sw_gap_open_query" type="integer" size="10" value="-400" label="S-W Gap Open Penalty (Query)" /> + <param name="sw_gap_ext_ref" type="integer" size="10" value="-70" label="S-W Gap Extend Penalty (Reference)" /> + <param name="sw_gap_ext_query" type="integer" size="10" value="-70" label="S-W Gap Extend Penalty (Query)" /> + <param name="sw_hit_threshold" type="float" size="10" value="68.0" label="S-W Hit Threshold" help="in percentage"/> + </when> + </conditional> + </page> + </inputs> + <outputs> + <data name="output1" format="tabular"/> + <data name="output2" format="tabular"/> + </outputs> + <requirements> + <requirement type="binary">SHRiMP_rmapper</requirement> + </requirements> + <tests> + <test> + <param name="single_or_paired" value="single" /> + <param name="skip_or_full" value="skip" /> + <param name="input_target" value="shrimp_phix_anc.fa" ftype="fasta" /> + <param name="input_query" value="shrimp_wrapper_test1.fastq" ftype="fastqsolexa"/> + <output name="output1" file="shrimp_wrapper_test1.out1" /> + </test> + <!-- + <test> + <param name="input1" value="shrimp_wrapper_test2_end1.fastq" ftype="fastqsolexa" /> + <param name="input2" value="shrimp_wrapper_test2_end2.fastq" ftype="fastqsolexa" /> + <param name="single_or_paired" value="paired" /> + <param name="skip_or_full" value="skip" /> + <param name="input_target" value="shrimp_eca_chrMT.fa" ftype="fasta" /> + <output name="output1" file="shrimp_wrapper_test2.out1" /> + </test> + <test> + <param name="single_or_paired" value="single" /> + <param name="skip_or_full" value="full" /> + <param name="input_target" value="shrimp_phix_anc.fa" ftype="fasta" /> + <param name="input_query" value="shrimp_wrapper_test1.fastq" ftype="fastqsolexa"/> + <param name="spaced_seed" value="111111011111" /> + <param name="seed_matches_per_window" value="2" /> + <param name="seed_hit_taboo_length" value="4" /> + <param name="seed_generation_taboo_length" value="0" /> + <param name="seed_window_length" value="115.0" /> + <param name="max_hits_per_read" value="100" /> + <param name="max_read_length" value="1000" /> + <param name="kmer" value="-1" /> + <param name="sw_match_value" value="100" /> + <param name="sw_mismatch_value" value="-150" /> + <param name="sw_gap_open_ref" value="-400" /> + <param name="sw_gap_open_query" value="-400" /> + <param name="sw_gap_ext_ref" value="-70" /> + <param name="sw_gap_ext_query" value="-70" /> + <param name="sw_hit_threshold" value="68.0" /> + <output name="output1" file="shrimp_wrapper_test1.out1" /> + </test> + <test> + <param name="single_or_paired" value="paired" /> + <param name="skip_or_full" value="full" /> + <param name="input_target" value="shrimp_eca_chrMT.fa" ftype="fasta" /> + <param name="spaced_seed" value="111111011111" /> + <param name="seed_matches_per_window" value="2" /> + <param name="seed_hit_taboo_length" value="4" /> + <param name="seed_generation_taboo_length" value="0" /> + <param name="seed_window_length" value="115.0" /> + <param name="max_hits_per_read" value="100" /> + <param name="max_read_length" value="1000" /> + <param name="kmer" value="-1" /> + <param name="sw_match_value" value="100" /> + <param name="sw_mismatch_value" value="-150" /> + <param name="sw_gap_open_ref" value="-400" /> + <param name="sw_gap_open_query" value="-400" /> + <param name="sw_gap_ext_ref" value="-70" /> + <param name="sw_gap_ext_query" value="-70" /> + <param name="sw_hit_threshold" value="68.0" /> + <param name="input1" value="shrimp_wrapper_test2_end1.fastq" ftype="fastqsolexa"/> + <param name="input2" value="shrimp_wrapper_test2_end2.fastq" ftype="fastqsolexa"/> + <output name="output1" file="shrimp_wrapper_test2.out1" /> + </test> + --> + </tests> +<help> + +.. class:: warningmark + +Only nucleotide sequences as query. + +----- + +**What it does** + +Run SHRiMP on letter-space reads. + +----- + +**Example** + +- Input a multiple-fastq file like the following:: + + @seq1 + TACCCGATTTTTTGCTTTCCACTTTATCCTACCCTT + +seq2 + hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh + +- Use default settings (for detail explanations, please see **Parameters** section) + +- Search against your own uploaded file, result will be in the following format:: + + +-------+-------+--------+----------+----------+---------+--------+--------+-------+------------+ + | id | chrom | strand | t.start | t.end | q.start | q.end | length | score | editstring | + +-------+-------+--------+----------+----------+---------+--------+--------+-------+------------+ + | >seq1 | chrMT | + | 14712 | 14747 | 1 | 36 | 36 | 3350 | 24T11 | + +-------+-------+--------+----------+----------+---------+--------+--------+-------+------------+ + +- The result will be formatted Table:: + + +-------+---------+---------+----------+---------+----------+---------+----------+ + | chrom | ref_loc | read_id | read_loc | ref_nuc | read_nuc | quality | coverage | + +-------+---------+---------+----------+---------+----------+---------+----------+ + | chrMT | 14711 | seq1 | 0 | T | T | 40 | 1 | + | chrMT | 14712 | seq1 | 1 | A | A | 40 | 1 | + | chrMT | 14713 | seq1 | 2 | C | C | 40 | 1 | + +-------+---------+---------+----------+---------+----------+---------+----------+ + +----- + +**Parameters** + +Parameter list with default value settings:: + + -s Spaced Seed (default: 111111011111) + -n Seed Matches per Window (default: 2) + -t Seed Hit Taboo Length (default: 4) + -9 Seed Generation Taboo Length (default: 0) + -w Seed Window Length (default: 115.00%) + -o Maximum Hits per Read (default: 100) + -r Maximum Read Length (default: 1000) + -d Kmer Std. Deviation Limit (default: -1 [None]) + + -m S-W Match Value (default: 100) + -i S-W Mismatch Value (default: -150) + -g S-W Gap Open Penalty (Reference) (default: -400) + -q S-W Gap Open Penalty (Query) (default: -400) + -e S-W Gap Extend Penalty (Reference) (default: -70) + -f S-W Gap Extend Penalty (Query) (default: -70) + -h S-W Hit Threshold (default: 68.00%) + +----- + +**Reference** + + **SHRiMP**: Stephen M. Rumble, Michael Brudno, Phil Lacroute, Vladimir Yanovsky, Marc Fiume, Adrian Dalca. shrimp at cs dot toronto dot edu. + +</help> +</tool>