Mercurial > repos > rnateam > graphclust_preprocessing
changeset 11:c0c9d19bc7b2 draft
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
| author | rnateam |
|---|---|
| date | Tue, 18 Jul 2017 01:43:49 -0400 |
| parents | 16bcaef3dc1e |
| children | 8a1786cdcf95 |
| files | preprocessing.xml splitSHAPE.py splitStockholm.py test-data/sample_4_alignment_data_split.stk test-data/sample_4_all.stk test-data/sample_4_representatives.fa |
| diffstat | 6 files changed, 1005 insertions(+), 8 deletions(-) [+] |
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--- a/preprocessing.xml Thu Jun 01 12:11:37 2017 -0400 +++ b/preprocessing.xml Tue Jul 18 01:43:49 2017 -0400 @@ -1,7 +1,8 @@ -<tool id="preproc" name="Preprocessing" version="0.2"> +<tool id="preproc" name="Preprocessing" version="0.3"> <requirements> - <requirement type="package" version="0.1.12">graphclust-wrappers</requirement> + <requirement type="package" version="0.3.1">graphclust-wrappers</requirement> <requirement type="package" version="3.0">zip</requirement> + <requirement type="package" version="1.70">biopython</requirement> </requirements> <stdio> @@ -19,13 +20,22 @@ && python '$__tool_directory__/splitSHAPE.py' '$SHAPEdata' - $max_length + #end if + + #if $AlignmentData: + && + python '$__tool_directory__/splitStockholm.py' + '$AlignmentData' + + #end if + ]]> </command> <inputs> <param type="data" name="fastaFile" format="fasta" /> <param type="data" name="SHAPEdata" format="txt" optional="true" label="SHAPE data"/> + <param type="data" name="AlignmentData" format="stockholm" optional="true" label="Alignments file"/> <param name="max_length" type="integer" value="10000" size="5" label="window size"/> <param name="in_winShift" type="integer" value="100" size="5" label="window shift in percent"/> <param name="min_seq_length" type="integer" value="5" size="5" label="minimum sequence length"/> @@ -36,7 +46,8 @@ <data name="data.names" format="txt" from_work_dir="FASTA/data.names" label="data.names"/> <data name="data.fasta.scan" format="fasta" from_work_dir="FASTA/data.fasta.scan" label="data.fasta.scan"/> <data name="FASTA" format="zip" from_work_dir="FASTA.zip" label="FASTA.ZIP"/> - <data name="shape_data_split" format="txt" from_work_dir="shape_data_split.react" label="SHAPE data splited"/> + <data name="shape_data_split" format="txt" from_work_dir="shape_data_split.react" label="SHAPE.data.split"/> + <data name="alignment_data_split" format="stockholm" from_work_dir="alignment_data_split.stk" label="alignments.data.stk"/> </outputs> <tests> <test> @@ -57,6 +68,14 @@ <param name="in_winShift" value="50"/> <param name="min_seq_length" value="5"/> <output name="shape_data_split" file="sample_3_shape_data_split.react" /> + </test> + <test> + <param name="fastaFile" value="sample_4_representatives.fa"/> + <param name="AlignmentData" value="sample_4_all.stk"/> + <param name="max_length" value="50"/> + <param name="in_winShift" value="50"/> + <param name="min_seq_length" value="5"/> + <output name="alignment_data_split" file="sample_4_alignment_data_split.stk" /> </test> </tests> <help>
--- a/splitSHAPE.py Thu Jun 01 12:11:37 2017 -0400 +++ b/splitSHAPE.py Tue Jul 18 01:43:49 2017 -0400 @@ -3,7 +3,6 @@ import sys shape_file = sys.argv[1] -win_size = int(sys.argv[2]) pattern = re.compile("^>.*$") toWrite = "" @@ -18,9 +17,9 @@ name_file = "FASTA/data.names" array_all_chunks = [] with open(name_file, 'r') as f: - content = f.read() - lines = content.split('\n')[:-1] - for line in lines: + for line in f: + if len(line.strip()) == 0: + continue seq_id.append(int(line.split()[0])) seq_string.append(line.split()[1]) orig_id_srt = line.split()[3]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/splitStockholm.py Tue Jul 18 01:43:49 2017 -0400 @@ -0,0 +1,91 @@ +#!/usr/bin/env python + +######## +# This script reads multiple alignments merged in single stockholm file +# and splits the alignment blocks according to data.names table +# The first sequence of each alignment file assumed to match to names table entries +# Author: M. Miladi +######## +import os +import re +import sys + +from Bio import AlignIO, SeqIO +try: + from StringIO import StringIO +except ImportError: + from io import StringIO + +stk_file = sys.argv[1] +print ("Parsing and splitting stk file:{}".format(stk_file)) +target_f = "alignment_data_split.stk" +pattern = re.compile("^>.*$") +toWriteID = "" + +count_for_id = 1 +seq_counter = 0 +new_id = "" + +seq_id = [] +seq_string = [] +orig_id = [] +name_file = "FASTA/data.names" +array_all_chunks = [] +with open(name_file, 'r') as f: + for line in f: + if len(line.strip()) == 0: + continue + seq_id.append(int(line.split()[0])) + seq_string.append(line.split()[1]) + orig_id_srt = line.split()[3] + orig_id_srt = orig_id_srt.rsplit('_',1)[0] + orig_id.append(orig_id_srt) + + + +with open(stk_file) as stk_in: + alignments = AlignIO.parse(stk_in, "stockholm")#, alphabet=IUPAC.ambiguous_rna) + alignments_dic = {(a[0].id):a for a in alignments} + + +regx_gaps = '[-.~_]' # valid gap symbols all be converted to "-" +str_gaps = '-.~_' # valid gap symbols all be converted to "-" + + +chunks = [] +with open(target_f, 'w') as out_stk_handle: + for i in range(len(orig_id)): + + #---------------------- + # We need to map ungapped positions of the chunks to gapped positions of first sequence + gap_count = 0 + ungap_ind = 0 + dic_gap_counts = dict() + cur_alignment = alignments_dic[orig_id[i]] + for c in cur_alignment[0].seq: + #print ungap_ind + if c in str_gaps: + gap_count += 1 + else: + dic_gap_counts[ungap_ind] = gap_count + ungap_ind += 1 + ID = str(seq_id[i]) + " " + seq_string[i] + chunks = re.findall(r'\d+', seq_string[i]) + print (ID,chunks) + + index_start, index_end =int(chunks[1])-1, int(chunks[2])-1 + subalign = cur_alignment[:, index_start + dic_gap_counts[index_start]: + index_end+dic_gap_counts[index_end]+1] + + #---------------------- + # BioPython does not handel the GF ID entry for alignment + # So we add entry in the second line manually + siotmp = StringIO() + AlignIO.write(subalign, siotmp, format="stockholm") + stk_lines = siotmp.getvalue().split('\n') + out_stk_handle.write('{}\n'.format(stk_lines[0])) + out_stk_handle.write('#=GF ID {}\n'.format(ID)) + out_stk_handle.writelines('\n'.join(stk_lines[1:])) + #print out_stk_handle.getvalue() + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_4_alignment_data_split.stk Tue Jul 18 01:43:49 2017 -0400 @@ -0,0 +1,798 @@ +# STOCKHOLM 1.0 +#=GF ID 1 SEQ1#1#50#+ +#=GF SQ 5 +ath1 TAACTCGGAAGTTGTCGATTGAACAAACTTGAGGTTTTGTCGTTTCCACG +#=GS ath1 AC ath1 +#=GS ath1 DE ath1 +bol1 TTACTTTGAAGTTGTCAACTAGGCAACCGCGAGGTTTTGTCTCCTTGACG +#=GS bol1 AC bol1 +#=GS bol1 DE bol1 +bna1 TTACTTTGAAGTTGTCAACTAGGCAACCGCGAGGTTTTGTCTCCTTGACG +#=GS bna1 AC bna1 +#=GS bna1 DE bna1 +bra1 TTACTCGGAAGTTGTCAACTAGGGAACCGCGAGGTTTTGTCGCCTTGACG +#=GS bra1 AC bra1 +#=GS bra1 DE bra1 +aly1 TTACTCGGAAGTTGTCGATTGAACAAACTTGAGGTTTTATCGTCTTCACA +#=GS aly1 AC aly1 +#=GS aly1 DE aly1 +// +# STOCKHOLM 1.0 +#=GF ID 2 SEQ1#26#75#+ +#=GF SQ 5 +ath1 AACTTGAGGTTTTGTCGTTTCCACG---------GCTGTCGTAGACGGTGGCAGCTGCT +#=GS ath1 AC ath1 +#=GS ath1 DE ath1 +bol1 ACCGCGAGGTTTTGTCTCCTTGACGGTCTTCAACACCGCTGTTGATGGTGGTGGCACG- +#=GS bol1 AC bol1 +#=GS bol1 DE bol1 +bna1 ACCGCGAGGTTTTGTCTCCTTGACGGTCTTCAACACCGCTGTTGATGGTGGCGGCACG- +#=GS bna1 AC bna1 +#=GS bna1 DE bna1 +bra1 ACCGCGAGGTTTTGTCGCCTTGACGGTCTTCAACACCGTCGTCGATGGT---GGCACG- +#=GS bra1 AC bra1 +#=GS bra1 DE bra1 +aly1 AACTTGAGGTTTTATCGTCTTCACATCTCTCACCGCCGCCGGAGACGGTGGCTGCTGCT +#=GS aly1 AC aly1 +#=GS aly1 DE aly1 +// +# STOCKHOLM 1.0 +#=GF ID 3 SEQ1#51#100#+ +#=GF SQ 5 +ath1 GCTGTCGTAGACGGTGGCAGCTGCTGCTGCAGCGGTTGATGATAGTGGTA +#=GS ath1 AC ath1 +#=GS ath1 DE ath1 +bol1 ACCGCTGTTGATGGTGGTGGCACG---TGTAACGTTTGGTGGTTATAGTA +#=GS bol1 AC bol1 +#=GS bol1 DE bol1 +bna1 ACCGCTGTTGATGGTGGCGGCACG---TGTAACGTTTGATGGTTATAGTA +#=GS bna1 AC bna1 +#=GS bna1 DE bna1 +bra1 ACCGTCGTCGATGGT---GGCACG---------------TGATTATAGTA +#=GS bra1 AC bra1 +#=GS bra1 DE bra1 +aly1 GCCGCCGGAGACGGTGGCTGCTGCTGCTGCAGCGGTTGATGAGAGTAGTA +#=GS aly1 AC aly1 +#=GS aly1 DE aly1 +// +# STOCKHOLM 1.0 +#=GF ID 4 SEQ1#62#111#+ +#=GF SQ 5 +ath1 CGGTGGCAGCTGCTGCTGCAGCGGTTGATGATAGTGGTAGGCGGAGAAGT +#=GS ath1 AC ath1 +#=GS ath1 DE ath1 +bol1 TGGTGGTGGCACG---TGTAACGTTTGGTGGTTATAGTAAGCTGTCAAGT +#=GS bol1 AC bol1 +#=GS bol1 DE bol1 +bna1 TGGTGGCGGCACG---TGTAACGTTTGATGGTTATAGTAAGCTGTCAAGT +#=GS bna1 AC bna1 +#=GS bna1 DE bna1 +bra1 TGGT---GGCACG---------------TGATTATAGTATGCGGTCAAGT +#=GS bra1 AC bra1 +#=GS bra1 DE bra1 +aly1 CGGTGGCTGCTGCTGCTGCAGCGGTTGATGAGAGTAGTAGGCGGAGAAGT +#=GS aly1 AC aly1 +#=GS aly1 DE aly1 +// +# STOCKHOLM 1.0 +#=GF ID 5 SEQ2#1#50#+ +#=GF SQ 5 +ath2 GGTCGAGAAAGGAACCGGCAATATCGAACCGGAAAAATCCGAGATAACCA +#=GS ath2 AC ath2 +#=GS ath2 DE ath2 +bol2 AGCAGAGAACGGAACCGGTAGAATTGAACCGGTTGAACCGGAGCTGACCA +#=GS bol2 AC bol2 +#=GS bol2 DE bol2 +bna2 AGCAGAGAACGGAACCGGTAGAATTGAACCGGTTGAACCGGAGCTGACCA +#=GS bna2 AC bna2 +#=GS bna2 DE bna2 +bra2 AGCAGAGAACGGAACCGGTAAAATCGAACCGGTTGAACCGGAGCTGACCA +#=GS bra2 AC bra2 +#=GS bra2 DE bra2 +aly2 GGTCGAGAAAGGAACCGGCAAAATCGAACCGGAAACATTCGAGCTAACCA +#=GS aly2 AC aly2 +#=GS aly2 DE aly2 +// +# STOCKHOLM 1.0 +#=GF ID 6 SEQ2#26#75#+ +#=GF SQ 5 +ath2 GAACCGGAAAAATCCGAGATAACCACGTTTTGCATAAACTGGTACATAAG +#=GS ath2 AC ath2 +#=GS ath2 DE ath2 +bol2 GAACCGGTTGAACCGGAGCTGACCACGTTTTGCATAAACTGGTACAAAAG +#=GS bol2 AC bol2 +#=GS bol2 DE bol2 +bna2 GAACCGGTTGAACCGGAGCTGACCACGTTTTGCATAAACTGGTACAAAAG +#=GS bna2 AC bna2 +#=GS bna2 DE bna2 +bra2 GAACCGGTTGAACCGGAGCTGACCACGTTCTGCATAAACTGGTACAAAAG +#=GS bra2 AC bra2 +#=GS bra2 DE bra2 +aly2 GAACCGGAAACATTCGAGCTAACCACGTTTTGCATAAACTGGTACATAAG +#=GS aly2 AC aly2 +#=GS aly2 DE aly2 +// +# STOCKHOLM 1.0 +#=GF ID 7 SEQ2#51#100#+ +#=GF SQ 5 +ath2 CGTTTTGCATAAACTGGTACATAAGCAGAACGTCACCGTTAACCAAAGCC +#=GS ath2 AC ath2 +#=GS ath2 DE ath2 +bol2 CGTTTTGCATAAACTGGTACAAAAGCAAGACATCGCCGTTCACCAACGCC +#=GS bol2 AC bol2 +#=GS bol2 DE bol2 +bna2 CGTTTTGCATAAACTGGTACAAAAGCAAGACATCGCCGTTCACCAGCGCC +#=GS bna2 AC bna2 +#=GS bna2 DE bna2 +bra2 CGTTCTGCATAAACTGGTACAAAAGCAAGACATCGCCGTTCACCAACGCC +#=GS bra2 AC bra2 +#=GS bra2 DE bra2 +aly2 CGTTTTGCATAAACTGGTACATAAGCAAAACGTCACCGTTAACCAAAGCC +#=GS aly2 AC aly2 +#=GS aly2 DE aly2 +// +# STOCKHOLM 1.0 +#=GF ID 8 SEQ2#71#120#+ +#=GF SQ 5 +ath2 ATAAGCAGAACGTCACCGTTAACCAAAGCCATGTCCTTAAACCGGTCTCG +#=GS ath2 AC ath2 +#=GS ath2 DE ath2 +bol2 AAAAGCAAGACATCGCCGTTCACCAACGCCATGTCTTTAAACCGGTCTCG +#=GS bol2 AC bol2 +#=GS bol2 DE bol2 +bna2 AAAAGCAAGACATCGCCGTTCACCAGCGCCATGTCTTTAAACCGGTCTCG +#=GS bna2 AC bna2 +#=GS bna2 DE bna2 +bra2 AAAAGCAAGACATCGCCGTTCACCAACGCCATGTCTTTAAACCGGTCTCG +#=GS bra2 AC bra2 +#=GS bra2 DE bra2 +aly2 ATAAGCAAAACGTCACCGTTAACCAAAGCCACGTCCTTAAACCGGTCTCG +#=GS aly2 AC aly2 +#=GS aly2 DE aly2 +// +# STOCKHOLM 1.0 +#=GF ID 9 SEQ3#1#50#+ +#=GF SQ 5 +ath3 CTGCACCATCTCCAAACAGAGCAGCTCCAACTAGGTCGTACGGACGCGCT +#=GS ath3 AC ath3 +#=GS ath3 DE ath3 +bna3 CCGCACCGTCCCCGAACAAAGCTGCCCCGACCAGGTCGTAAGGGCGAGCT +#=GS bna3 AC bna3 +#=GS bna3 DE bna3 +bol3 CCGCACCGTCCCCGAACAAAGCTGCCCCGACCAGGTCGTAAGAGCGAGCT +#=GS bol3 AC bol3 +#=GS bol3 DE bol3 +bra3 CTGCACCGTCCCCGAACAAAGCTGCCCCGACCAGGTCGTAAGGGCGAGCT +#=GS bra3 AC bra3 +#=GS bra3 DE bra3 +aly3 CTGCACCATCTCCAAACAGAGCAGCTCCAACTAGGTCGTACGGACGAGCT +#=GS aly3 AC aly3 +#=GS aly3 DE aly3 +// +# STOCKHOLM 1.0 +#=GF ID 10 SEQ3#26#75#+ +#=GF SQ 5 +ath3 TCCAACTAGGTCGTACGGACGCGCTTTGTTTGGTGGCCGAAATCCGAGAA +#=GS ath3 AC ath3 +#=GS ath3 DE ath3 +bna3 CCCGACCAGGTCGTAAGGGCGAGCTTTGTTCGGTGGTCGGAACCCGAGGA +#=GS bna3 AC bna3 +#=GS bna3 DE bna3 +bol3 CCCGACCAGGTCGTAAGAGCGAGCTTTGTTCGGTGGTCGGAACCCGAGGA +#=GS bol3 AC bol3 +#=GS bol3 DE bol3 +bra3 CCCGACCAGGTCGTAAGGGCGAGCTTTGTTCGGTGGTCGGAACCCGAGGA +#=GS bra3 AC bra3 +#=GS bra3 DE bra3 +aly3 TCCAACTAGGTCGTACGGACGAGCTTTGTTTGGTGGGCGAAACCCGAGAA +#=GS aly3 AC aly3 +#=GS aly3 DE aly3 +// +# STOCKHOLM 1.0 +#=GF ID 11 SEQ3#51#100#+ +#=GF SQ 5 +ath3 TTGTTTGGTGGCCGAAATCCGAGAATGGTGGTTTCAGAGGTTGTGAGCAG +#=GS ath3 AC ath3 +#=GS ath3 DE ath3 +bna3 TTGTTCGGTGGTCGGAACCCGAGGATGGTGGTTTCAGAGGTTGTGAGGAG +#=GS bna3 AC bna3 +#=GS bna3 DE bna3 +bol3 TTGTTCGGTGGTCGGAACCCGAGGATGGTGGTTTCAGAGGTTGTGAGGAG +#=GS bol3 AC bol3 +#=GS bol3 DE bol3 +bra3 TTGTTCGGTGGTCGGAACCCGAGGATGGTGGTTTCAGAGGTTGTGAGGAG +#=GS bra3 AC bra3 +#=GS bra3 DE bra3 +aly3 TTGTTTGGTGGGCGAAACCCGAGAATGGTGGTTTCAGAGGTTGTGAGCAG +#=GS aly3 AC aly3 +#=GS aly3 DE aly3 +// +# STOCKHOLM 1.0 +#=GF ID 12 SEQ3#76#125#+ +#=GF SQ 5 +ath3 TGGTGGTTTCAGAGGTTGTGAGCAGAACACGGCTTCCGGGGTTGTTCTCA +#=GS ath3 AC ath3 +#=GS ath3 DE ath3 +bna3 TGGTGGTTTCAGAGGTTGTGAGGAGCACACGGCTTCCGGGGTTGTTCTCG +#=GS bna3 AC bna3 +#=GS bna3 DE bna3 +bol3 TGGTGGTTTCAGAGGTTGTGAGGAGCACACGGCTTCCGGGGTTGTTCTCG +#=GS bol3 AC bol3 +#=GS bol3 DE bol3 +bra3 TGGTGGTTTCAGAGGTTGTGAGGAGAACACGGCTTCCGGGGTTGTTCTCA +#=GS bra3 AC bra3 +#=GS bra3 DE bra3 +aly3 TGGTGGTTTCAGAGGTTGTGAGCAGAACACGGCTTCCCGGGTTGTTCTCA +#=GS aly3 AC aly3 +#=GS aly3 DE aly3 +// +# STOCKHOLM 1.0 +#=GF ID 13 SEQ3#101#150#+ +#=GF SQ 5 +ath3 AACACGGCTTCCGGGGTTGTTCTCAGCAATGTCTTTGGCCACACGGAGGC +#=GS ath3 AC ath3 +#=GS ath3 DE ath3 +bna3 CACACGGCTTCCGGGGTTGTTCTCGGCTATGTCTTTGGCGACACGGAGGC +#=GS bna3 AC bna3 +#=GS bna3 DE bna3 +bol3 CACACGGCTTCCGGGGTTGTTCTCGGCTATGTCTTTGGCGACACGGAGGC +#=GS bol3 AC bol3 +#=GS bol3 DE bol3 +bra3 AACACGGCTTCCGGGGTTGTTCTCAGCGATGTCTTTGGCCACACGGAGGC +#=GS bra3 AC bra3 +#=GS bra3 DE bra3 +aly3 AACACGGCTTCCCGGGTTGTTCTCAGCAATGTCTTTGGCCACACGGAGGC +#=GS aly3 AC aly3 +#=GS aly3 DE aly3 +// +# STOCKHOLM 1.0 +#=GF ID 14 SEQ3#126#175#+ +#=GF SQ 5 +ath3 GCAATGTCTTTGGCCACACGGAGGCCAGTCACACCTCCGTAGCATCCCAG +#=GS ath3 AC ath3 +#=GS ath3 DE ath3 +bna3 GCTATGTCTTTGGCGACACGGAGGCCTGTTACGCCTCCGTAGCAGCCTAG +#=GS bna3 AC bna3 +#=GS bna3 DE bna3 +bol3 GCTATGTCTTTGGCGACACGGAGGCCTGTTACGCCTCCGTAGCAGCCTAG +#=GS bol3 AC bol3 +#=GS bol3 DE bol3 +bra3 GCGATGTCTTTGGCCACACGGAGGCCTGTTACGCCTCCGTAGCAGCCTAG +#=GS bra3 AC bra3 +#=GS bra3 DE bra3 +aly3 GCAATGTCTTTGGCCACACGGAGGCCAGTCACACCTCCGTAGCATCCCAG +#=GS aly3 AC aly3 +#=GS aly3 DE aly3 +// +# STOCKHOLM 1.0 +#=GF ID 15 SEQ3#151#200#+ +#=GF SQ 5 +ath3 CAGTCACACCTCCGTAGCATCCCAGAAAATACAGCATCACTCTGTTCACG +#=GS ath3 AC ath3 +#=GS ath3 DE ath3 +bna3 CTGTTACGCCTCCGTAGCAGCCTAGAAAATAAAGCATCACTCTGTTCACG +#=GS bna3 AC bna3 +#=GS bna3 DE bna3 +bol3 CTGTTACGCCTCCGTAGCAGCCTAGAAAGTAAAGCATTACTCTGTTCACG +#=GS bol3 AC bol3 +#=GS bol3 DE bol3 +bra3 CTGTTACGCCTCCGTAGCAGCCTAGAAAATAAAGCATTACTCTGTTCACG +#=GS bra3 AC bra3 +#=GS bra3 DE bra3 +aly3 CAGTCACACCTCCGTAGCATCCCAGAAAATACAGCATCACTCTGTTCACG +#=GS aly3 AC aly3 +#=GS aly3 DE aly3 +// +# STOCKHOLM 1.0 +#=GF ID 16 SEQ3#176#225#+ +#=GF SQ 5 +ath3 AAAATACAGCATCACTCTGTTCACGTCATTCCTCAGGCCTAGCTTTGCTG +#=GS ath3 AC ath3 +#=GS ath3 DE ath3 +bna3 AAAATAAAGCATCACTCTGTTCACGTCGTTCTTTAAGCCTAGCTTGGCGG +#=GS bna3 AC bna3 +#=GS bna3 DE bna3 +bol3 AAAGTAAAGCATTACTCTGTTCACGTCGCTCTTTAGGCCTAGCTTGGCTG +#=GS bol3 AC bol3 +#=GS bol3 DE bol3 +bra3 AAAATAAAGCATTACTCTGTTCACGTCGCTCTTTAGGCCTAGCTTGGCTG +#=GS bra3 AC bra3 +#=GS bra3 DE bra3 +aly3 AAAATACAGCATCACTCTGTTCACGTCATTCCTCAGGCCTAGCTTTGCTG +#=GS aly3 AC aly3 +#=GS aly3 DE aly3 +// +# STOCKHOLM 1.0 +#=GF ID 17 SEQ3#191#240#+ +#=GF SQ 5 +ath3 TCTGTTCACGTCATTCCTCAGGCCTAGCTTTGCTGAGAGGTAAAGGTCAC +#=GS ath3 AC ath3 +#=GS ath3 DE ath3 +bna3 TCTGTTCACGTCGTTCTTTAAGCCTAGCTTGGCGGAGAGGTAAAGGTCAC +#=GS bna3 AC bna3 +#=GS bna3 DE bna3 +bol3 TCTGTTCACGTCGCTCTTTAGGCCTAGCTTGGCTGAGAGGTAAAGGTCGC +#=GS bol3 AC bol3 +#=GS bol3 DE bol3 +bra3 TCTGTTCACGTCGCTCTTTAGGCCTAGCTTGGCTGAGAGGTAAAGGTCGC +#=GS bra3 AC bra3 +#=GS bra3 DE bra3 +aly3 TCTGTTCACGTCATTCCTCAGGCCTAGCTTTGCTGAGAGGTAAAGGTCAC +#=GS aly3 AC aly3 +#=GS aly3 DE aly3 +// +# STOCKHOLM 1.0 +#=GF ID 18 SEQ4#1#50#+ +#=GF SQ 5 +ath4 A----------TGAAGGAGGACTACTTACGAGTGTTGGAAGCGGCAGCGGCAGTGACCGC +#=GS ath4 AC ath4 +#=GS ath4 DE ath4 +bna4 ATATATAGCCTTGGAGAAGG--TACGTACGAGTGTTGAAAGCGGTTGCGGCAGTGCCCGC +#=GS bna4 AC bna4 +#=GS bna4 DE bna4 +bol4 ATATATAGCCTTGGAGAAGG--TACGTACGAGTGTTGAAAGCGGTTGCGGCAGTGCCCGC +#=GS bol4 AC bol4 +#=GS bol4 DE bol4 +bra4 ATATATGGCCTAGGAGAAGG--TACGTACGAGTGTTGAAAGCGGTTGCGGCAGTGCCCGC +#=GS bra4 AC bra4 +#=GS bra4 DE bra4 +aly4 -----------TAAAGGAGGACTACTTACGAGTGCTGTAAGCGGCAGCGGCAGTGCCCGC +#=GS aly4 AC aly4 +#=GS aly4 DE aly4 +// +# STOCKHOLM 1.0 +#=GF ID 19 SEQ4#26#75#+ +#=GF SQ 5 +ath4 TGGAAGCGGCAGCGGCAGTGACCGCAGCTGAAGAGCTTGTCGGAGAAACC +#=GS ath4 AC ath4 +#=GS ath4 DE ath4 +bna4 TGAAAGCGGTTGCGGCAGTGCCCGCAGCGGAATAGTTTGTCGGAAAATCC +#=GS bna4 AC bna4 +#=GS bna4 DE bna4 +bol4 TGAAAGCGGTTGCGGCAGTGCCCGCAGCGGAATAGTTTGTCGGAAAATCC +#=GS bol4 AC bol4 +#=GS bol4 DE bol4 +bra4 TGAAAGCGGTTGCGGCAGTGCCCGCAGCGGAATAGCTTGTCGGAAAAGCC +#=GS bra4 AC bra4 +#=GS bra4 DE bra4 +aly4 TGTAAGCGGCAGCGGCAGTGCCCGCAGCTGAAGAGCTTGTCGGAGAAACC +#=GS aly4 AC aly4 +#=GS aly4 DE aly4 +// +# STOCKHOLM 1.0 +#=GF ID 20 SEQ4#51#100#+ +#=GF SQ 5 +ath4 AGCTGAAGAGCTTGTCGGAGAAACCGACATCACCGCACATGCAACACACT +#=GS ath4 AC ath4 +#=GS ath4 DE ath4 +bna4 AGCGGAATAGTTTGTCGGAAAATCCGACGTCGCCGCACATGCAGCACACT +#=GS bna4 AC bna4 +#=GS bna4 DE bna4 +bol4 AGCGGAATAGTTTGTCGGAAAATCCGACGTCGCCGCACATGCAGCACACT +#=GS bol4 AC bol4 +#=GS bol4 DE bol4 +bra4 AGCGGAATAGCTTGTCGGAAAAGCCGACGTCGCCGCACATGCAGCACACT +#=GS bra4 AC bra4 +#=GS bra4 DE bra4 +aly4 AGCTGAAGAGCTTGTCGGAGAAACCGACGTCGCCGCACATGCAACATACT +#=GS aly4 AC aly4 +#=GS aly4 DE aly4 +// +# STOCKHOLM 1.0 +#=GF ID 21 SEQ4#61#110#+ +#=GF SQ 5 +ath4 CTTGTCGGAGAAACCGACATCACCGCACATGCAACACACTCTCTCCATGa +#=GS ath4 AC ath4 +#=GS ath4 DE ath4 +bna4 TTTGTCGGAAAATCCGACGTCGCCGCACATGCAGCACACTTTCTCCATGT +#=GS bna4 AC bna4 +#=GS bna4 DE bna4 +bol4 TTTGTCGGAAAATCCGACGTCGCCGCACATGCAGCACACTTTCTCCATGT +#=GS bol4 AC bol4 +#=GS bol4 DE bol4 +bra4 CTTGTCGGAAAAGCCGACGTCGCCGCACATGCAGCACACTTTCTCCATGT +#=GS bra4 AC bra4 +#=GS bra4 DE bra4 +aly4 CTTGTCGGAGAAACCGACGTCGCCGCACATGCAACATACTCTCTCCATGA +#=GS aly4 AC aly4 +#=GS aly4 DE aly4 +// +# STOCKHOLM 1.0 +#=GF ID 22 SEQ5#1#50#+ +#=GF SQ 5 +ath5 AACGGCGTCAAGGATCTCCTTCAAATTCTTGTGCCTTACCACCA-ATTTGG +#=GS ath5 AC ath5 +#=GS ath5 DE ath5 +bra5 GATCGCATCAGCGATCTCTTTCAAATCCCTATGCCTAACGGCGACATCTCC +#=GS bra5 AC bra5 +#=GS bra5 DE bra5 +bol5 GATGGCATCAGCGATCTCTTTCAAATCCCTATGCCTAACGgcgacatctcc +#=GS bol5 AC bol5 +#=GS bol5 DE bol5 +bna5 GATGGCATCAGCGATCTCTTTCAAATCCCTATGCCTAACGGCGACATCTCC +#=GS bna5 AC bna5 +#=GS bna5 DE bna5 +aly5 AACGGCGTCGAGGATCTCCTTCAAATTCTTGTGCCTTACCACCA-ATTTGG +#=GS aly5 AC aly5 +#=GS aly5 DE aly5 +// +# STOCKHOLM 1.0 +#=GF ID 23 SEQ5#26#75#+ +#=GF SQ 5 +ath5 TTCTTGTGCCTTACCACCA-ATTTGGT--------------------CTTGTAGCAGTCGGAAGAAGTGGT +#=GS ath5 AC ath5 +#=GS ath5 DE ath5 +bra5 TCCCTATGCCTAACGGCGACATCTCCT------------CCTCCACCTCTATAGCTACCTGAAAACGTCGT +#=GS bra5 AC bra5 +#=GS bra5 DE bra5 +bol5 TCCCTATGCCTAACGgcgacatctcctcctccgcctccgcctCCGCCTCTATAGCTACCGCAATACGTCGT +#=GS bol5 AC bol5 +#=GS bol5 DE bol5 +bna5 TCCCTATGCCTAACGGCGACATCTCCT------CCTCCGCCTCCGCCTCTATAGCTACCGCAATACGTCGT +#=GS bna5 AC bna5 +#=GS bna5 DE bna5 +aly5 TTCTTGTGCCTTACCACCA-ATTTGGT--------------------CTTGTAGCAGTCGGAAGAAGTGGT +#=GS aly5 AC aly5 +#=GS aly5 DE aly5 +// +# STOCKHOLM 1.0 +#=GF ID 24 SEQ5#44#93#+ +#=GF SQ 5 +ath5 A-ATTTGGT--------------------CTTGTAGCAGTCGGAAGAAGTGGTAACATGGTCAGAGTGCTC +#=GS ath5 AC ath5 +#=GS ath5 DE ath5 +bra5 ACATCTCCT------------CCTCCACCTCTATAGCTACCTGAAAACGTCGTCGCATCATCTGCTTTATC +#=GS bra5 AC bra5 +#=GS bra5 DE bra5 +bol5 acatctcctcctccgcctccgcctCCGCCTCTATAGCTACCGCAATACGTCGTCGCATCATCTTCTTTATC +#=GS bol5 AC bol5 +#=GS bol5 DE bol5 +bna5 ACATCTCCT------CCTCCGCCTCCGCCTCTATAGCTACCGCAATACGTCGTCGCATCATCTTCTTTATC +#=GS bna5 AC bna5 +#=GS bna5 DE bna5 +aly5 A-ATTTGGT--------------------CTTGTAGCAGTCGGAAGAAGTGGTAACATGGTCAGAGTTGTC +#=GS aly5 AC aly5 +#=GS aly5 DE aly5 +// +# STOCKHOLM 1.0 +#=GF ID 25 SEQ6#1#50#+ +#=GF SQ 5 +ath6 TAAAAAATAAAGAAT---CTTACCATCACCACGACTGTTTGTTCTAGCCAACT +#=GS ath6 AC ath6 +#=GS ath6 DE ath6 +bol6 TAAAATGGAGAACCTTTGCTTACCATCGCCACGACGGTTTGTTCTAGGCAACT +#=GS bol6 AC bol6 +#=GS bol6 DE bol6 +bna6 TAAAATGGAGAACCTTTACTTACCATCGCCACGACGGTTTGTTCTAGGCAACT +#=GS bna6 AC bna6 +#=GS bna6 DE bna6 +bra6 TAAAATGGAGAACCTTTACTTACCATCGCCACGACGGTTTGTTCTAGGCAACT +#=GS bra6 AC bra6 +#=GS bra6 DE bra6 +aly6 TaaaaaaaaaaGAAT---GTTACCATCACCACGACTGTTTGTTCTAGCCAACT +#=GS aly6 AC aly6 +#=GS aly6 DE aly6 +// +# STOCKHOLM 1.0 +#=GF ID 26 SEQ6#26#75#+ +#=GF SQ 5 +ath6 CCACGACTGTTTGTTCTAGCCAACTGATAAATAGTGTAGCCTGAAGATGA +#=GS ath6 AC ath6 +#=GS ath6 DE ath6 +bol6 CCACGACGGTTTGTTCTAGGCAACTGGAAAATATTGTAGCCTGCAGTGGC +#=GS bol6 AC bol6 +#=GS bol6 DE bol6 +bna6 CCACGACGGTTTGTTCTAGGCAACTGGAAAATATTGTAGCCTGCAGTGGC +#=GS bna6 AC bna6 +#=GS bna6 DE bna6 +bra6 CCACGACGGTTTGTTCTAGGCAACTGGAAAATATCGTAGCCTGCAGTGGC +#=GS bra6 AC bra6 +#=GS bra6 DE bra6 +aly6 CCACGACTGTTTGTTCTAGCCAACTGGAAAATAGTGTAGCCAGAAGTGCC +#=GS aly6 AC aly6 +#=GS aly6 DE aly6 +// +# STOCKHOLM 1.0 +#=GF ID 27 SEQ6#51#100#+ +#=GF SQ 5 +ath6 GATAAATAGTGTAGCCTGAAGATGAAAGCTGGTGGTGGTACATGTTCACT +#=GS ath6 AC ath6 +#=GS ath6 DE ath6 +bol6 GGAAAATATTGTAGCCTGCAGTGGCAAGGCGATCATGGTACATGTTCACC +#=GS bol6 AC bol6 +#=GS bol6 DE bol6 +bna6 GGAAAATATTGTAGCCTGCAGTGGCAAGGCGATCATGGTACATGTTCACC +#=GS bna6 AC bna6 +#=GS bna6 DE bna6 +bra6 GGAAAATATCGTAGCCTGCAGTGGCAAGGCGATCATGGTACATGTTCGCC +#=GS bra6 AC bra6 +#=GS bra6 DE bra6 +aly6 GGAAAATAGTGTAGCCAGAAGTGCCAAGCTGGTCGTGGTACATGTTGACT +#=GS aly6 AC aly6 +#=GS aly6 DE aly6 +// +# STOCKHOLM 1.0 +#=GF ID 28 SEQ6#68#117#+ +#=GF SQ 5 +ath6 GAAGATGAAAGCTGGTGGTGGTACATGTTCACTAATTCCTCATTCCCAAC +#=GS ath6 AC ath6 +#=GS ath6 DE ath6 +bol6 GCAGTGGCAAGGCGATCATGGTACATGTTCACCAATTCTTCATTTGCAAC +#=GS bol6 AC bol6 +#=GS bol6 DE bol6 +bna6 GCAGTGGCAAGGCGATCATGGTACATGTTCACCAATTCTTCATTTGCAAC +#=GS bna6 AC bna6 +#=GS bna6 DE bna6 +bra6 GCAGTGGCAAGGCGATCATGGTACATGTTCGCCAATTCTTCATTTGCAAC +#=GS bra6 AC bra6 +#=GS bra6 DE bra6 +aly6 GAAGTGCCAAGCTGGTCGTGGTACATGTTGACTAATTCCTCATTCCCAAC +#=GS aly6 AC aly6 +#=GS aly6 DE aly6 +// +# STOCKHOLM 1.0 +#=GF ID 29 SEQ7#1#50#+ +#=GF SQ 5 +ath7 TGGATCTCTGGATCAGCTGTGCGACCAGACGTGGATGATCCAAACGCTAA +#=GS ath7 AC ath7 +#=GS ath7 DE ath7 +bra7 TGAAGCTCCGGGTCAGCAGTTCGGCCGGACGTTGATGATCCAAACGCTAA +#=GS bra7 AC bra7 +#=GS bra7 DE bra7 +bol7 TGAAGCTCCGGATCAGCAGCTCGGCCGGACGTTGAAGATCCAAACGCTAA +#=GS bol7 AC bol7 +#=GS bol7 DE bol7 +bna7 TGAAGCTCCGGATCAGCAGCTCGGCCGGACGTTGAAGATCCAAACGCTAA +#=GS bna7 AC bna7 +#=GS bna7 DE bna7 +aly7 TGGATCTCTGGATCAGCGGTGCGGCCAGACGTGGATGATCCAAACGCTAA +#=GS aly7 AC aly7 +#=GS aly7 DE aly7 +// +# STOCKHOLM 1.0 +#=GF ID 30 SEQ7#26#75#+ +#=GF SQ 5 +ath7 CAGACGTGGATGATCCAAACGCTAAACGCCTTTGAGCGATTGGTCGAACA +#=GS ath7 AC ath7 +#=GS ath7 DE ath7 +bra7 CGGACGTTGATGATCCAAACGCTAAACTCCTTTGAACGACTGGTCGGACG +#=GS bra7 AC bra7 +#=GS bra7 DE bra7 +bol7 CGGACGTTGAAGATCCAAACGCTAAACGACTTTGAGCGACTGGTCGGACG +#=GS bol7 AC bol7 +#=GS bol7 DE bol7 +bna7 CGGACGTTGAAGATCCAAACGCTAAACGACTTTGAGCGACTGGTCGGACG +#=GS bna7 AC bna7 +#=GS bna7 DE bna7 +aly7 CAGACGTGGATGATCCAAACGCTAAACGCCTTTGAGCGATTGGTCGAACA +#=GS aly7 AC aly7 +#=GS aly7 DE aly7 +// +# STOCKHOLM 1.0 +#=GF ID 31 SEQ7#51#100#+ +#=GF SQ 5 +ath7 ACGCCTTTGAGCGATTGGTCGAACACGTGAACGCGCCGCTGAAGCAAACG +#=GS ath7 AC ath7 +#=GS ath7 DE ath7 +bra7 ACTCCTTTGAACGACTGGTCGGACGCGGGAACGCGCCGCTGAAGCAAACG +#=GS bra7 AC bra7 +#=GS bra7 DE bra7 +bol7 ACGACTTTGAGCGACTGGTCGGACGCGGGAACGCGCCGCTGAAGCAAACG +#=GS bol7 AC bol7 +#=GS bol7 DE bol7 +bna7 ACGACTTTGAGCGACTGGTCGGACGCGGGAACGCGCCGCTGAAGCAAACG +#=GS bna7 AC bna7 +#=GS bna7 DE bna7 +aly7 ACGCCTTTGAGCGATTGGTCGAACACGGGAACGCGCCGCAGAAGCAAACG +#=GS aly7 AC aly7 +#=GS aly7 DE aly7 +// +# STOCKHOLM 1.0 +#=GF ID 32 SEQ7#68#117#+ +#=GF SQ 5 +ath7 GTCGAACACGTGAACGCGCCGCTGAAGCAAACGCTAATAATCGGGATTG---C +#=GS ath7 AC ath7 +#=GS ath7 DE ath7 +bra7 GTCGGACGCGGGAACGCGCCGCTGAAGCAAACGCTAATAATCGGGACTGCATC +#=GS bra7 AC bra7 +#=GS bra7 DE bra7 +bol7 GTCGGACGCGGGAACGCGCCGCTGAAGCAAACGCTAATAATCGGGACTGCATC +#=GS bol7 AC bol7 +#=GS bol7 DE bol7 +bna7 GTCGGACGCGGGAACGCGCCGCTGAAGCAAACGCTAATAATCGGGACTGCATC +#=GS bna7 AC bna7 +#=GS bna7 DE bna7 +aly7 GTCGAACACGGGAACGCGCCGCAGAAGCAAACGCTAATAATCGGGATTGCATC +#=GS aly7 AC aly7 +#=GS aly7 DE aly7 +// +# STOCKHOLM 1.0 +#=GF ID 33 SEQ8#1#50#+ +#=GF SQ 5 +ath8 TTGCTCTTCTAAACTCGGTCGGGGAGTATCGTCTACGATTTCTTCCGCCG +#=GS ath8 AC ath8 +#=GS ath8 DE ath8 +bra8 TTGCTCTTCTAAACTTGACCGTGGTTGTTCATCGACGATTTCTTCTGCCG +#=GS bra8 AC bra8 +#=GS bra8 DE bra8 +bol8 TtgttgtTctaaacttgaccgtggttGTTCGTCGACGATTTCTTCTGCCG +#=GS bol8 AC bol8 +#=GS bol8 DE bol8 +bna8 TTGTTGTTCTAAACTTGACCGTGGTTGTTCGTCGACGATTTCTTCTGCCG +#=GS bna8 AC bna8 +#=GS bna8 DE bna8 +aly8 TTGCTCTTCTAAACTCGGTCGTGGGGTGTCGTCTACGATTTCATCCGCCG +#=GS aly8 AC aly8 +#=GS aly8 DE aly8 +// +# STOCKHOLM 1.0 +#=GF ID 34 SEQ8#26#75#+ +#=GF SQ 5 +ath8 GTATCGTCTACGATTTCTTCCGCCGCCGTTTTAGGGTTTGCAACATCATC +#=GS ath8 AC ath8 +#=GS ath8 DE ath8 +bra8 TGTTCATCGACGATTTCTTCTGCCGCCGTCTTAGGGTTCGCTACATCATC +#=GS bra8 AC bra8 +#=GS bra8 DE bra8 +bol8 tGTTCGTCGACGATTTCTTCTGCCGCCGTCTTAGGGTTCGCCACGTCATC +#=GS bol8 AC bol8 +#=GS bol8 DE bol8 +bna8 TGTTCGTCGACGATTTCTTCTGCCGCCGTCTTAGGGTTCGCCACGTCATC +#=GS bna8 AC bna8 +#=GS bna8 DE bna8 +aly8 GTGTCGTCTACGATTTCATCCGCCGCCGTTTTAGGGTTTGCAACATCATC +#=GS aly8 AC aly8 +#=GS aly8 DE aly8 +// +# STOCKHOLM 1.0 +#=GF ID 35 SEQ8#51#100#+ +#=GF SQ 5 +ath8 CCGTTTTAGGGTTTGCAACATCATCCATACCCTGAAACACAAGCAATCAC +#=GS ath8 AC ath8 +#=GS ath8 DE ath8 +bra8 CCGTCTTAGGGTTCGCTACATCATCCATACCCTGAAGCATAATCAATCAC +#=GS bra8 AC bra8 +#=GS bra8 DE bra8 +bol8 CCGTCTTAGGGTTCGCCACGTCATCCATACCCTGAAGCATAATCAATAAC +#=GS bol8 AC bol8 +#=GS bol8 DE bol8 +bna8 CCGTCTTAGGGTTCGCCACGTCATCCATACCCTGAAGCATAATCAATAAC +#=GS bna8 AC bna8 +#=GS bna8 DE bna8 +aly8 CCGTTTTAGGGTTTGCAACATCATCCATAACCTGAAACACAAGGAATCAC +#=GS aly8 AC aly8 +#=GS aly8 DE aly8 +// +# STOCKHOLM 1.0 +#=GF ID 36 SEQ8#68#117#+ +#=GF SQ 5 +ath8 ACATCATCCATACCCTGAAACACAAGCAATCACCAAAA---ACTTAAACAAAG +#=GS ath8 AC ath8 +#=GS ath8 DE ath8 +bra8 ACATCATCCATACCCTGAAGCATAATCAATCACAAAACAATATTT-AAAAGAG +#=GS bra8 AC bra8 +#=GS bra8 DE bra8 +bol8 ACGTCATCCATACCCTGAAGCATAATCAATAACAAAACAATATTT-AAAAGA- +#=GS bol8 AC bol8 +#=GS bol8 DE bol8 +bna8 ACGTCATCCATACCCTGAAGCATAATCAATAACAAAACAATATTT-AAAAGA- +#=GS bna8 AC bna8 +#=GS bna8 DE bna8 +aly8 ACATCATCCATAACCTGAAACACAAGGAATCAC--------ACTT-AACAGAG +#=GS aly8 AC aly8 +#=GS aly8 DE aly8 +// +# STOCKHOLM 1.0 +#=GF ID 37 SEQ9#1#50#+ +#=GF SQ 5 +ath9 CGTAGAAAAGGCTTGACCGCAAAATGGATATATTATATGTACCTATGAGT +#=GS ath9 AC ath9 +#=GS ath9 DE ath9 +bna9 C-TACCAAATGC--AAAGATAAGGCAAA------------ACCTATGAGT +#=GS bna9 AC bna9 +#=GS bna9 DE bna9 +bol9 C-TACCAAATGC--AAAGATAAGGCAAA------------ACCTATGAGT +#=GS bol9 AC bol9 +#=GS bol9 DE bol9 +bra9 C-TACCAAATGC--AAAGATAAGGCAAA------------ACCTATGAGT +#=GS bra9 AC bra9 +#=GS bra9 DE bra9 +aly9 CATAGAAAAGGCTTGACCACAAACTGGA-----TATATATACCTATGAGT +#=GS aly9 AC aly9 +#=GS aly9 DE aly9 +// +# STOCKHOLM 1.0 +#=GF ID 38 SEQ9#26#75#+ +#=GF SQ 5 +ath9 GGATATATTATATGTACCTATGAGTTTTTCGAGCTTTGTTTGAAGTAGTA +#=GS ath9 AC ath9 +#=GS ath9 DE ath9 +bna9 AAA------------ACCTATGAGTTTCTCGAGCTTTGTTTGAAGTAGTA +#=GS bna9 AC bna9 +#=GS bna9 DE bna9 +bol9 AAA------------ACCTATGAGTTTCTCGAGCTTTGTTTGAAGTAGTA +#=GS bol9 AC bol9 +#=GS bol9 DE bol9 +bra9 AAA------------ACCTATGAGTTTCTCGAGCTTTGTTTGAAGAAGTA +#=GS bra9 AC bra9 +#=GS bra9 DE bra9 +aly9 GGA-----TATATATACCTATGAGTTTTTCGAGCTTTGTTTGAAGTAGTA +#=GS aly9 AC aly9 +#=GS aly9 DE aly9 +// +# STOCKHOLM 1.0 +#=GF ID 39 SEQ9#51#100#+ +#=GF SQ 5 +ath9 TTTTCGAGCTTTGTTTGAAGTAGTAATCCTC---TCTACAATATTGAAGCCAA +#=GS ath9 AC ath9 +#=GS ath9 DE ath9 +bna9 TTCTCGAGCTTTGTTTGAAGTAGTAATCCTCTTCCCTGTAATATTCAAGCAAA +#=GS bna9 AC bna9 +#=GS bna9 DE bna9 +bol9 TTCTCGAGCTTTGTTTGAAGTAGTAATCCTCTTCCCTGTAATATTCAAGCAAA +#=GS bol9 AC bol9 +#=GS bol9 DE bol9 +bra9 TTCTCGAGCTTTGTTTGAAGAAGTAATCCTCTTCCCTATAATATCCAAGCAAA +#=GS bra9 AC bra9 +#=GS bra9 DE bra9 +aly9 TTTTCGAGCTTTGTTTGAAGTAGTAATCCTC---CCTAAAATATTGAAGCCAA +#=GS aly9 AC aly9 +#=GS aly9 DE aly9 +// +# STOCKHOLM 1.0 +#=GF ID 40 SEQ9#76#125#+ +#=GF SQ 5 +ath9 ATCCTC---TCTACAATATTGAAGCCAA-CTATGGTCAAACCACAATCAAATTC +#=GS ath9 AC ath9 +#=GS ath9 DE ath9 +bna9 ATCCTCTTCCCTGTAATATTCAAGCAAAGCTGTGAGTAAACTACAACC------ +#=GS bna9 AC bna9 +#=GS bna9 DE bna9 +bol9 ATCCTCTTCCCTGTAATATTCAAGCAAAGCTGTGAGTAAACTACAACC------ +#=GS bol9 AC bol9 +#=GS bol9 DE bol9 +bra9 ATCCTCTTCCCTATAATATCCAAGCAAAGCTGTGAGTAAACTGCAACC------ +#=GS bra9 AC bra9 +#=GS bra9 DE bra9 +aly9 ATCCTC---CCTAAAATATTGAAGCCAA-CTACTGTCAAACCACAATAAATTTC +#=GS aly9 AC aly9 +#=GS aly9 DE aly9 +// +# STOCKHOLM 1.0 +#=GF ID 41 SEQ9#101#150#+ +#=GF SQ 5 +ath9 CTATGGTCAAACCACAATCAAATTCCCTATAGCTCCTCaaaaaaaaCTAC +#=GS ath9 AC ath9 +#=GS ath9 DE ath9 +bna9 CTGTGAGTAAACTACAACC----------TATTTGGGCAAA--------- +#=GS bna9 AC bna9 +#=GS bna9 DE bna9 +bol9 CTGTGAGTAAACTACAACC----------TATTTGGGCAAA--------- +#=GS bol9 AC bol9 +#=GS bol9 DE bol9 +bra9 CTGTGAGTAAACTGCAACC----------TAATTGGGCAAA--------- +#=GS bra9 AC bra9 +#=GS bra9 DE bra9 +aly9 CTACTGTCAAACCACAATAAATTTCCCTATAGCTCCTCAAA--------- +#=GS aly9 AC aly9 +#=GS aly9 DE aly9 +// +# STOCKHOLM 1.0 +#=GF ID 42 SEQ9#107#156#+ +#=GF SQ 5 +ath9 TCAAACCACAATCAAATTCCCTATAGCTCCTCaaaaaaaaCTACTCAAGC +#=GS ath9 AC ath9 +#=GS ath9 DE ath9 +bna9 GTAAACTACAACC----------TATTTGGGCAAA--------------- +#=GS bna9 AC bna9 +#=GS bna9 DE bna9 +bol9 GTAAACTACAACC----------TATTTGGGCAAA--------------- +#=GS bol9 AC bol9 +#=GS bol9 DE bol9 +bra9 GTAAACTGCAACC----------TAATTGGGCAAA--------------- +#=GS bra9 AC bra9 +#=GS bra9 DE bra9 +aly9 TCAAACCACAATAAATTTCCCTATAGCTCCTCAAA--------------- +#=GS aly9 AC aly9 +#=GS aly9 DE aly9 +//
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_4_all.stk Tue Jul 18 01:43:49 2017 -0400 @@ -0,0 +1,72 @@ +# STOCKHOLM 1.0 +#=GF SQ 5 +ath1 TAACTCGGAAGTTGTCGATTGAACAAACTTGAGGTTTTGTCGTTTCCACG---------GCTGTCGTAGACGGTGGCAGCTGCTGCTGCAGCGGTTGATGATAGTGGTAGGCGGAGAAGT +bol1 TTACTTTGAAGTTGTCAACTAGGCAACCGCGAGGTTTTGTCTCCTTGACGGTCTTCAACACCGCTGTTGATGGTGGTGGCACG---TGTAACGTTTGGTGGTTATAGTAAGCTGTCAAGT +bna1 TTACTTTGAAGTTGTCAACTAGGCAACCGCGAGGTTTTGTCTCCTTGACGGTCTTCAACACCGCTGTTGATGGTGGCGGCACG---TGTAACGTTTGATGGTTATAGTAAGCTGTCAAGT +bra1 TTACTCGGAAGTTGTCAACTAGGGAACCGCGAGGTTTTGTCGCCTTGACGGTCTTCAACACCGTCGTCGATGGT---GGCACG---------------TGATTATAGTATGCGGTCAAGT +aly1 TTACTCGGAAGTTGTCGATTGAACAAACTTGAGGTTTTATCGTCTTCACATCTCTCACCGCCGCCGGAGACGGTGGCTGCTGCTGCTGCAGCGGTTGATGAGAGTAGTAGGCGGAGAAGT +// +# STOCKHOLM 1.0 +#=GF SQ 5 +ath2 GGTCGAGAAAGGAACCGGCAATATCGAACCGGAAAAATCCGAGATAACCACGTTTTGCATAAACTGGTACATAAGCAGAACGTCACCGTTAACCAAAGCCATGTCCTTAAACCGGTCTCG +bol2 AGCAGAGAACGGAACCGGTAGAATTGAACCGGTTGAACCGGAGCTGACCACGTTTTGCATAAACTGGTACAAAAGCAAGACATCGCCGTTCACCAACGCCATGTCTTTAAACCGGTCTCG +bna2 AGCAGAGAACGGAACCGGTAGAATTGAACCGGTTGAACCGGAGCTGACCACGTTTTGCATAAACTGGTACAAAAGCAAGACATCGCCGTTCACCAGCGCCATGTCTTTAAACCGGTCTCG +bra2 AGCAGAGAACGGAACCGGTAAAATCGAACCGGTTGAACCGGAGCTGACCACGTTCTGCATAAACTGGTACAAAAGCAAGACATCGCCGTTCACCAACGCCATGTCTTTAAACCGGTCTCG +aly2 GGTCGAGAAAGGAACCGGCAAAATCGAACCGGAAACATTCGAGCTAACCACGTTTTGCATAAACTGGTACATAAGCAAAACGTCACCGTTAACCAAAGCCACGTCCTTAAACCGGTCTCG +// +# STOCKHOLM 1.0 +#=GF SQ 5 +ath3 CTGCACCATCTCCAAACAGAGCAGCTCCAACTAGGTCGTACGGACGCGCTTTGTTTGGTGGCCGAAATCCGAGAATGGTGGTTTCAGAGGTTGTGAGCAGAACACGGCTTCCGGGGTTGTTCTCAGCAATGTCTTTGGCCACACGGAGGCCAGTCACACCTCCGTAGCATCCCAGAAAATACAGCATCACTCTGTTCACGTCATTCCTCAGGCCTAGCTTTGCTGAGAGGTAAAGGTCAC +bna3 CCGCACCGTCCCCGAACAAAGCTGCCCCGACCAGGTCGTAAGGGCGAGCTTTGTTCGGTGGTCGGAACCCGAGGATGGTGGTTTCAGAGGTTGTGAGGAGCACACGGCTTCCGGGGTTGTTCTCGGCTATGTCTTTGGCGACACGGAGGCCTGTTACGCCTCCGTAGCAGCCTAGAAAATAAAGCATCACTCTGTTCACGTCGTTCTTTAAGCCTAGCTTGGCGGAGAGGTAAAGGTCAC +bol3 CCGCACCGTCCCCGAACAAAGCTGCCCCGACCAGGTCGTAAGAGCGAGCTTTGTTCGGTGGTCGGAACCCGAGGATGGTGGTTTCAGAGGTTGTGAGGAGCACACGGCTTCCGGGGTTGTTCTCGGCTATGTCTTTGGCGACACGGAGGCCTGTTACGCCTCCGTAGCAGCCTAGAAAGTAAAGCATTACTCTGTTCACGTCGCTCTTTAGGCCTAGCTTGGCTGAGAGGTAAAGGTCGC +bra3 CTGCACCGTCCCCGAACAAAGCTGCCCCGACCAGGTCGTAAGGGCGAGCTTTGTTCGGTGGTCGGAACCCGAGGATGGTGGTTTCAGAGGTTGTGAGGAGAACACGGCTTCCGGGGTTGTTCTCAGCGATGTCTTTGGCCACACGGAGGCCTGTTACGCCTCCGTAGCAGCCTAGAAAATAAAGCATTACTCTGTTCACGTCGCTCTTTAGGCCTAGCTTGGCTGAGAGGTAAAGGTCGC +aly3 CTGCACCATCTCCAAACAGAGCAGCTCCAACTAGGTCGTACGGACGAGCTTTGTTTGGTGGGCGAAACCCGAGAATGGTGGTTTCAGAGGTTGTGAGCAGAACACGGCTTCCCGGGTTGTTCTCAGCAATGTCTTTGGCCACACGGAGGCCAGTCACACCTCCGTAGCATCCCAGAAAATACAGCATCACTCTGTTCACGTCATTCCTCAGGCCTAGCTTTGCTGAGAGGTAAAGGTCAC +// +# STOCKHOLM 1.0 +#=GF SQ 5 +ath4 A----------TGAAGGAGGACTACTTACGAGTGTTGGAAGCGGCAGCGGCAGTGACCGCAGCTGAAGAGCTTGTCGGAGAAACCGACATCACCGCACATGCAACACACTCTCTCCATGa +bna4 ATATATAGCCTTGGAGAAGG--TACGTACGAGTGTTGAAAGCGGTTGCGGCAGTGCCCGCAGCGGAATAGTTTGTCGGAAAATCCGACGTCGCCGCACATGCAGCACACTTTCTCCATGT +bol4 ATATATAGCCTTGGAGAAGG--TACGTACGAGTGTTGAAAGCGGTTGCGGCAGTGCCCGCAGCGGAATAGTTTGTCGGAAAATCCGACGTCGCCGCACATGCAGCACACTTTCTCCATGT +bra4 ATATATGGCCTAGGAGAAGG--TACGTACGAGTGTTGAAAGCGGTTGCGGCAGTGCCCGCAGCGGAATAGCTTGTCGGAAAAGCCGACGTCGCCGCACATGCAGCACACTTTCTCCATGT +aly4 -----------TAAAGGAGGACTACTTACGAGTGCTGTAAGCGGCAGCGGCAGTGCCCGCAGCTGAAGAGCTTGTCGGAGAAACCGACGTCGCCGCACATGCAACATACTCTCTCCATGA +// +# STOCKHOLM 1.0 +#=GF SQ 5 +ath5 AACGGCGTCAAGGATCTCCTTCAAATTCTTGTGCCTTACCACCA-ATTTGGT--------------------CTTGTAGCAGTCGGAAGAAGTGGTAACATGGTCAGAGTGCTC +bra5 GATCGCATCAGCGATCTCTTTCAAATCCCTATGCCTAACGGCGACATCTCCT------------CCTCCACCTCTATAGCTACCTGAAAACGTCGTCGCATCATCTGCTTTATC +bol5 GATGGCATCAGCGATCTCTTTCAAATCCCTATGCCTAACGgcgacatctcctcctccgcctccgcctCCGCCTCTATAGCTACCGCAATACGTCGTCGCATCATCTTCTTTATC +bna5 GATGGCATCAGCGATCTCTTTCAAATCCCTATGCCTAACGGCGACATCTCCT------CCTCCGCCTCCGCCTCTATAGCTACCGCAATACGTCGTCGCATCATCTTCTTTATC +aly5 AACGGCGTCGAGGATCTCCTTCAAATTCTTGTGCCTTACCACCA-ATTTGGT--------------------CTTGTAGCAGTCGGAAGAAGTGGTAACATGGTCAGAGTTGTC +// +# STOCKHOLM 1.0 +#=GF SQ 5 +ath6 TAAAAAATAAAGAAT---CTTACCATCACCACGACTGTTTGTTCTAGCCAACTGATAAATAGTGTAGCCTGAAGATGAAAGCTGGTGGTGGTACATGTTCACTAATTCCTCATTCCCAAC +bol6 TAAAATGGAGAACCTTTGCTTACCATCGCCACGACGGTTTGTTCTAGGCAACTGGAAAATATTGTAGCCTGCAGTGGCAAGGCGATCATGGTACATGTTCACCAATTCTTCATTTGCAAC +bna6 TAAAATGGAGAACCTTTACTTACCATCGCCACGACGGTTTGTTCTAGGCAACTGGAAAATATTGTAGCCTGCAGTGGCAAGGCGATCATGGTACATGTTCACCAATTCTTCATTTGCAAC +bra6 TAAAATGGAGAACCTTTACTTACCATCGCCACGACGGTTTGTTCTAGGCAACTGGAAAATATCGTAGCCTGCAGTGGCAAGGCGATCATGGTACATGTTCGCCAATTCTTCATTTGCAAC +aly6 TaaaaaaaaaaGAAT---GTTACCATCACCACGACTGTTTGTTCTAGCCAACTGGAAAATAGTGTAGCCAGAAGTGCCAAGCTGGTCGTGGTACATGTTGACTAATTCCTCATTCCCAAC +// +# STOCKHOLM 1.0 +#=GF SQ 5 +ath7 TGGATCTCTGGATCAGCTGTGCGACCAGACGTGGATGATCCAAACGCTAAACGCCTTTGAGCGATTGGTCGAACACGTGAACGCGCCGCTGAAGCAAACGCTAATAATCGGGATTG---C +bra7 TGAAGCTCCGGGTCAGCAGTTCGGCCGGACGTTGATGATCCAAACGCTAAACTCCTTTGAACGACTGGTCGGACGCGGGAACGCGCCGCTGAAGCAAACGCTAATAATCGGGACTGCATC +bol7 TGAAGCTCCGGATCAGCAGCTCGGCCGGACGTTGAAGATCCAAACGCTAAACGACTTTGAGCGACTGGTCGGACGCGGGAACGCGCCGCTGAAGCAAACGCTAATAATCGGGACTGCATC +bna7 TGAAGCTCCGGATCAGCAGCTCGGCCGGACGTTGAAGATCCAAACGCTAAACGACTTTGAGCGACTGGTCGGACGCGGGAACGCGCCGCTGAAGCAAACGCTAATAATCGGGACTGCATC +aly7 TGGATCTCTGGATCAGCGGTGCGGCCAGACGTGGATGATCCAAACGCTAAACGCCTTTGAGCGATTGGTCGAACACGGGAACGCGCCGCAGAAGCAAACGCTAATAATCGGGATTGCATC +// +# STOCKHOLM 1.0 +#=GF SQ 5 +ath8 TTGCTCTTCTAAACTCGGTCGGGGAGTATCGTCTACGATTTCTTCCGCCGCCGTTTTAGGGTTTGCAACATCATCCATACCCTGAAACACAAGCAATCACCAAAA---ACTTAAACAAAG +bra8 TTGCTCTTCTAAACTTGACCGTGGTTGTTCATCGACGATTTCTTCTGCCGCCGTCTTAGGGTTCGCTACATCATCCATACCCTGAAGCATAATCAATCACAAAACAATATTT-AAAAGAG +bol8 TtgttgtTctaaacttgaccgtggttGTTCGTCGACGATTTCTTCTGCCGCCGTCTTAGGGTTCGCCACGTCATCCATACCCTGAAGCATAATCAATAACAAAACAATATTT-AAAAGA- +bna8 TTGTTGTTCTAAACTTGACCGTGGTTGTTCGTCGACGATTTCTTCTGCCGCCGTCTTAGGGTTCGCCACGTCATCCATACCCTGAAGCATAATCAATAACAAAACAATATTT-AAAAGA- +aly8 TTGCTCTTCTAAACTCGGTCGTGGGGTGTCGTCTACGATTTCATCCGCCGCCGTTTTAGGGTTTGCAACATCATCCATAACCTGAAACACAAGGAATCAC--------ACTT-AACAGAG +// +# STOCKHOLM 1.0 +#=GF SQ 5 +ath9 CGTAGAAAAGGCTTGACCGCAAAATGGATATATTATATGTACCTATGAGTTTTTCGAGCTTTGTTTGAAGTAGTAATCCTC---TCTACAATATTGAAGCCAA-CTATGGTCAAACCACAATCAAATTCCCTATAGCTCCTCaaaaaaaaCTACTCAAGC +bna9 C-TACCAAATGC--AAAGATAAGGCAAA------------ACCTATGAGTTTCTCGAGCTTTGTTTGAAGTAGTAATCCTCTTCCCTGTAATATTCAAGCAAAGCTGTGAGTAAACTACAACC----------TATTTGGGCAAA--------------- +bol9 C-TACCAAATGC--AAAGATAAGGCAAA------------ACCTATGAGTTTCTCGAGCTTTGTTTGAAGTAGTAATCCTCTTCCCTGTAATATTCAAGCAAAGCTGTGAGTAAACTACAACC----------TATTTGGGCAAA--------------- +bra9 C-TACCAAATGC--AAAGATAAGGCAAA------------ACCTATGAGTTTCTCGAGCTTTGTTTGAAGAAGTAATCCTCTTCCCTATAATATCCAAGCAAAGCTGTGAGTAAACTGCAACC----------TAATTGGGCAAA--------------- +aly9 CATAGAAAAGGCTTGACCACAAACTGGA-----TATATATACCTATGAGTTTTTCGAGCTTTGTTTGAAGTAGTAATCCTC---CCTAAAATATTGAAGCCAA-CTACTGTCAAACCACAATAAATTTCCCTATAGCTCCTCAAA--------------- +//
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_4_representatives.fa Tue Jul 18 01:43:49 2017 -0400 @@ -0,0 +1,18 @@ +>ath1 +TAACTCGGAAGTTGTCGATTGAACAAACTTGAGGTTTTGTCGTTTCCACGGCTGTCGTAGACGGTGGCAGCTGCTGCTGCAGCGGTTGATGATAGTGGTAGGCGGAGAAGT +>ath2 +GGTCGAGAAAGGAACCGGCAATATCGAACCGGAAAAATCCGAGATAACCACGTTTTGCATAAACTGGTACATAAGCAGAACGTCACCGTTAACCAAAGCCATGTCCTTAAACCGGTCTCG +>ath3 +CTGCACCATCTCCAAACAGAGCAGCTCCAACTAGGTCGTACGGACGCGCTTTGTTTGGTGGCCGAAATCCGAGAATGGTGGTTTCAGAGGTTGTGAGCAGAACACGGCTTCCGGGGTTGTTCTCAGCAATGTCTTTGGCCACACGGAGGCCAGTCACACCTCCGTAGCATCCCAGAAAATACAGCATCACTCTGTTCACGTCATTCCTCAGGCCTAGCTTTGCTGAGAGGTAAAGGTCAC +>ath4 +ATGAAGGAGGACTACTTACGAGTGTTGGAAGCGGCAGCGGCAGTGACCGCAGCTGAAGAGCTTGTCGGAGAAACCGACATCACCGCACATGCAACACACTCTCTCCATGa +>ath5 +AACGGCGTCAAGGATCTCCTTCAAATTCTTGTGCCTTACCACCAATTTGGTCTTGTAGCAGTCGGAAGAAGTGGTAACATGGTCAGAGTGCTC +>ath6 +TAAAAAATAAAGAATCTTACCATCACCACGACTGTTTGTTCTAGCCAACTGATAAATAGTGTAGCCTGAAGATGAAAGCTGGTGGTGGTACATGTTCACTAATTCCTCATTCCCAAC +>ath7 +TGGATCTCTGGATCAGCTGTGCGACCAGACGTGGATGATCCAAACGCTAAACGCCTTTGAGCGATTGGTCGAACACGTGAACGCGCCGCTGAAGCAAACGCTAATAATCGGGATTGC +>ath8 +TTGCTCTTCTAAACTCGGTCGGGGAGTATCGTCTACGATTTCTTCCGCCGCCGTTTTAGGGTTTGCAACATCATCCATACCCTGAAACACAAGCAATCACCAAAAACTTAAACAAAG +>ath9 +CGTAGAAAAGGCTTGACCGCAAAATGGATATATTATATGTACCTATGAGTTTTTCGAGCTTTGTTTGAAGTAGTAATCCTCTCTACAATATTGAAGCCAACTATGGTCAAACCACAATCAAATTCCCTATAGCTCCTCaaaaaaaaCTACTCAAGC