# HG changeset patch # User iuc # Date 1467203211 14400 # Node ID e5e9a09ac2de0319a722d2e36431fa0b6525dbb2 # Parent d44c2896957f00700e0555184a4dc097ba991eac Uploaded diff -r d44c2896957f -r e5e9a09ac2de Users/gvk/work/git_workspace/tools-iuc/tools/meme/fimo.xml --- a/Users/gvk/work/git_workspace/tools-iuc/tools/meme/fimo.xml Wed Jun 29 08:24:33 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,294 +0,0 @@ - - - Scan a set of sequences for motifs. - - imagemagick - meme - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - value == True - - - - - - - - - - - - - - - - - - - - - - - - - - - options_type['output_separate_motifs'] == 'no' - - - - - - - - - - - - - options_type['output_separate_motifs'] == 'yes' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -.. class:: warningmark - -**WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted. -Before using, be sure to review, agree, and comply with the license.** - -FIMO scans a sequence database for individual matches to each of the motifs you provide (sample output for motifs and sequences). -The name FIMO stands for 'Find Individual Motif Occurrences'. The program searches a database of sequences for occurrences of -known motifs, treating each motif independently. Motifs must be in MEME Motif Format. You can define the statistical threshold -(p-value) for motifs and whether FIMO scans just the given sequences or their reverse complements (where applicable). - -.. class:: infomark - -For detailed information on FIMO, click here_, or view the license_. - -.. _here: http://meme-suite.org/doc/fimo.html?man_type=web -.. _license: http://meme-suite.org/doc/copyright.html?man_type=web - - - - 10.1093/bioinformatics/btr064 - - diff -r d44c2896957f -r e5e9a09ac2de Users/gvk/work/git_workspace/tools-iuc/tools/meme/fimo_wrapper.py --- a/Users/gvk/work/git_workspace/tools-iuc/tools/meme/fimo_wrapper.py Wed Jun 29 08:24:33 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,193 +0,0 @@ -#!/usr/bin/env python -import argparse -import os -import shutil -import string -import subprocess -import sys -import tempfile - -BUFFSIZE = 1048576 -# Translation table for reverse Complement, with ambiguity codes. -DNA_COMPLEMENT = string.maketrans("ACGTRYKMBDHVacgtrykmbdhv", "TGCAYRMKVHDBtgcayrmkvhdb") - - -def get_stderr(tmp_stderr): - tmp_stderr.seek(0) - stderr = '' - try: - while True: - stderr += tmp_stderr.read(BUFFSIZE) - if not stderr or len(stderr) % BUFFSIZE != 0: - break - except OverflowError: - pass - return stderr - - -def reverse(sequence): - # Reverse sequence string. - return sequence[::-1] - - -def dna_complement(sequence): - # Complement DNA sequence string. - return sequence.translate(DNA_COMPLEMENT) - - -def dna_reverse_complement(sequence): - # Returns the reverse complement of the sequence. - sequence = reverse(sequence) - return dna_complement(sequence) - - -def stop_err(msg): - sys.stderr.write(msg) - sys.exit(1) - -parser = argparse.ArgumentParser() -parser.add_argument('--input_motifs', dest='input_motifs', help='MEME output formatted files for input to fimo') -parser.add_argument('--input_fasta', dest='input_fasta', help='Fassta sequence file') -parser.add_argument('--options_type', dest='options_type', help='Basic or Advance options') -parser.add_argument('--input_psp', dest='input_psp', default=None, help='File containing position specific priors') -parser.add_argument('--input_prior_dist', dest='input_prior_dist', default=None, help='File containing binned distribution of priors') -parser.add_argument('--alpha', dest='alpha', type=float, default=1.0, help='The alpha parameter for calculating position specific priors') -parser.add_argument('--bgfile', dest='bgfile', default=None, help='Background file type, used only if not "default"') -parser.add_argument('--max_strand', action='store_true', help='If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score') -parser.add_argument('--max_stored_scores', dest='max_stored_scores', type=int, help='Maximum score count to store') -parser.add_argument('--motif', dest='motifs', action='append', default=[], help='Specify motif by id') -parser.add_argument('--output_separate_motifs', dest='output_separate_motifs', default='no', help='Output one dataset per motif') -parser.add_argument('--motif_pseudo', dest='motif_pseudo', type=float, default=0.1, help='Pseudocount to add to counts in motif matrix') -parser.add_argument('--no_qvalue', action='store_true', help='Do not compute a q-value for each p-value') -parser.add_argument('--norc', action='store_true', help='Do not score the reverse complement DNA strand') -parser.add_argument('--output_path', dest='output_path', help='Output files directory') -parser.add_argument('--parse_genomic_coord', dest='parse_genomic_coord', default='no', help='Check each sequence header for UCSC style genomic coordinates') -parser.add_argument('--remove_duplicate_coords', dest='remove_duplicate_coords', default='no', help='Remove duplicate entries in unique GFF coordinates') -parser.add_argument('--qv_thresh', action='store_true', help='Use q-values for the output threshold') -parser.add_argument('--thresh', dest='thresh', type=float, help='p-value threshold') -parser.add_argument('--gff_output', dest='gff_output', help='Gff output file') -parser.add_argument('--html_output', dest='html_output', help='HTML output file') -parser.add_argument('--interval_output', dest='interval_output', help='Interval output file') -parser.add_argument('--txt_output', dest='txt_output', help='Text output file') -parser.add_argument('--xml_output', dest='xml_output', help='XML output file') -args = parser.parse_args() - -fimo_cmd_list = ['fimo'] -if args.options_type == 'advanced': - fimo_cmd_list.append('--alpha %4f' % args.alpha) - if args.bgfile is not None: - fimo_cmd_list.append('--bgfile "%s"' % args.bgfile) - if args.max_strand: - fimo_cmd_list.append('--max-strand') - fimo_cmd_list.append('--max-stored-scores %d' % args.max_stored_scores) - if len(args.motifs) > 0: - for motif in args.motifs: - fimo_cmd_list.append('--motif "%s"' % motif) - fimo_cmd_list.append('--motif-pseudo %4f' % args.motif_pseudo) - if args.no_qvalue: - fimo_cmd_list.append('--no-qvalue') - if args.norc: - fimo_cmd_list.append('--norc') - if args.parse_genomic_coord == 'yes': - fimo_cmd_list.append('--parse-genomic-coord') - if args.qv_thresh: - fimo_cmd_list.append('--qv-thresh') - fimo_cmd_list.append('--thresh %4f' % args.thresh) - if args.input_psp is not None: - fimo_cmd_list.append('--psp "%s"' % args.input_psp) - if args.input_prior_dist is not None: - fimo_cmd_list.append('--prior-dist "%s"' % args.input_prior_dist) -fimo_cmd_list.append('--o "%s"' % (args.output_path)) -fimo_cmd_list.append('--verbosity 1') -fimo_cmd_list.append(args.input_motifs) -fimo_cmd_list.append(args.input_fasta) - -fimo_cmd = ' '.join(fimo_cmd_list) - -try: - tmp_stderr = tempfile.NamedTemporaryFile() - proc = subprocess.Popen(args=fimo_cmd, shell=True, stderr=tmp_stderr) - returncode = proc.wait() - if returncode != 0: - stderr = get_stderr(tmp_stderr) - stop_err(stderr) -except Exception, e: - stop_err('Error running FIMO:\n%s' % str(e)) - -shutil.move(os.path.join(args.output_path, 'fimo.txt'), args.txt_output) - -gff_file = os.path.join(args.output_path, 'fimo.gff') -if args.remove_duplicate_coords == 'yes': - tmp_stderr = tempfile.NamedTemporaryFile() - # Identify and eliminating identical motif occurrences. These - # are identical if the combination of chrom, start, end and - # motif id are identical. - cmd = 'sort -k1,1 -k4,4n -k5,5n -k9.1,9.6 -u -o %s %s' % (gff_file, gff_file) - proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, shell=True) - returncode = proc.wait() - if returncode != 0: - stderr = get_stderr(tmp_stderr) - stop_err(stderr) - # Sort GFF output by a combination of chrom, score, start. - cmd = 'sort -k1,1 -k4,4n -k6,6n -o %s %s' % (gff_file, gff_file) - proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, shell=True) - returncode = proc.wait() - if returncode != 0: - stderr = get_stderr(tmp_stderr) - stop_err(stderr) -if args.output_separate_motifs == 'yes': - # Create the collection output directory. - collection_path = (os.path.join(os.getcwd(), 'output')) - # Keep track of motif occurrences. - header_line = None - motif_ids = [] - file_handles = [] - for line in open(gff_file, 'r'): - if line.startswith('#'): - if header_line is None: - header_line = line - continue - items = line.split('\t') - attribute = items[8] - attributes = attribute.split(';') - name = attributes[0] - motif_id = name.split('=')[1] - file_name = os.path.join(collection_path, 'MOTIF%s.gff' % motif_id) - if motif_id in motif_ids: - i = motif_ids.index(motif_id) - fh = file_handles[i] - fh.write(line) - else: - fh = open(file_name, 'wb') - if header_line is not None: - fh.write(header_line) - fh.write(line) - motif_ids.append(motif_id) - file_handles.append(fh) - for file_handle in file_handles: - file_handle.close() -else: - shutil.move(gff_file, args.gff_output) -shutil.move(os.path.join(args.output_path, 'fimo.xml'), args.xml_output) -shutil.move(os.path.join(args.output_path, 'fimo.html'), args.html_output) - -out_file = open(args.interval_output, 'wb') -out_file.write("#%s\n" % "\t".join(("chr", "start", "end", "pattern name", "score", "strand", "matched sequence", "p-value", "q-value"))) -for line in open(args.txt_output): - if line.startswith('#'): - continue - fields = line.rstrip("\n\r").split("\t") - start, end = int(fields[2]), int(fields[3]) - sequence = fields[7] - if start > end: - # Flip start and end and set strand. - start, end = end, start - strand = "-" - # We want sequences relative to strand; FIMO always provides + stranded sequence. - sequence = dna_reverse_complement(sequence) - else: - strand = "+" - # Make 0-based start position. - start -= 1 - out_file.write("%s\n" % "\t".join([fields[1], str(start), str(end), fields[0], fields[4], strand, sequence, fields[5], fields[6]])) -out_file.close() diff -r d44c2896957f -r e5e9a09ac2de fimo.xml --- a/fimo.xml Wed Jun 29 08:24:33 2016 -0400 +++ b/fimo.xml Wed Jun 29 08:26:51 2016 -0400 @@ -117,7 +117,10 @@ - + + + + diff -r d44c2896957f -r e5e9a09ac2de fimo_wrapper.py --- a/fimo_wrapper.py Wed Jun 29 08:24:33 2016 -0400 +++ b/fimo_wrapper.py Wed Jun 29 08:26:51 2016 -0400 @@ -56,13 +56,13 @@ parser.add_argument('--max_strand', action='store_true', help='If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score') parser.add_argument('--max_stored_scores', dest='max_stored_scores', type=int, help='Maximum score count to store') parser.add_argument('--motif', dest='motifs', action='append', default=[], help='Specify motif by id') -parser.add_argument('--output_separate_motifs', default="no", help='Output one dataset per motif') +parser.add_argument('--output_separate_motifs', dest='output_separate_motifs', default='no', help='Output one dataset per motif') parser.add_argument('--motif_pseudo', dest='motif_pseudo', type=float, default=0.1, help='Pseudocount to add to counts in motif matrix') parser.add_argument('--no_qvalue', action='store_true', help='Do not compute a q-value for each p-value') parser.add_argument('--norc', action='store_true', help='Do not score the reverse complement DNA strand') parser.add_argument('--output_path', dest='output_path', help='Output files directory') -parser.add_argument('--parse_genomic_coord', default='no', help='Check each sequence header for UCSC style genomic coordinates') -parser.add_argument('--remove_duplicate_coords', default='no', help='Remove duplicate entries in unique GFF coordinates') +parser.add_argument('--parse_genomic_coord', dest='parse_genomic_coord', default='no', help='Check each sequence header for UCSC style genomic coordinates') +parser.add_argument('--remove_duplicate_coords', dest='remove_duplicate_coords', default='no', help='Remove duplicate entries in unique GFF coordinates') parser.add_argument('--qv_thresh', action='store_true', help='Use q-values for the output threshold') parser.add_argument('--thresh', dest='thresh', type=float, help='p-value threshold') parser.add_argument('--gff_output', dest='gff_output', help='Gff output file') diff -r d44c2896957f -r e5e9a09ac2de meme.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/meme.xml Wed Jun 29 08:26:51 2016 -0400 @@ -0,0 +1,335 @@ + + - Multiple Em for Motif Elicitation + + imagemagick + meme + + + &1 || echo "Error running MEME." + && mv ${html_outfile.files_path}/meme.html ${html_outfile} + && mv ${html_outfile.files_path}/meme.txt ${txt_outfile} + && mv ${html_outfile.files_path}/meme.xml ${xml_outfile} + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + value == True + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: warningmark + +**WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted. +Before using, be sure to review, agree, and comply with the license.** + +If you want to specify sequence weights, you must include them at the top of your input FASTA file. + +MEME discovers novel, ungapped motifs (recurring, fixed-length patterns) in your sequences (sample output from sequences). +MEME splits variable-length patterns into two or more separate motifs. A motif is a sequence pattern that occurs repeatedly +in a group of related sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the +probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns +with variable-length gaps are split by MEME into two or more separate motifs. MEME takes as input a group of sequences and +outputs as many motifs as requested. MEME uses statistical modeling techniques to automatically choose the best width, number +of occurrences, and description for each motif. + +.. class:: infomark + +For detailed information on MEME, click here_, or view the license_. + +.. _here: http://meme-suite.org/doc/meme.html?man_type=web +.. _license: http://meme-suite.org/doc/copyright.html?man_type=web + + + + + @article{Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, + author = {Bailey,Timothy L. and Elkan, Charles}, + title = {Fitting a mixture model by expectation maximization to discover motifs in biopolymers}, + year = {1994}, + eprint = {None}, + url = {http://www.sdsc.edu/~tbailey/papers/ismb94.pdf} + } + + diff -r d44c2896957f -r e5e9a09ac2de test-data/meme_input_1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_input_1.fasta Wed Jun 29 08:26:51 2016 -0400 @@ -0,0 +1,66 @@ +>chr21_19617074_19617124_+ +AAAAATTATTACTAGGGAGGGGGCCGGAACCTCGGGACGTGGGTATATAA +>chr21_26934381_26934431_+ +GCGCCTGGTCGGTTATGAGTCACAAGTGAGTTATAAAAGGGTCGCACGTT +>chr21_28217753_28217803_- +CAAAGGGGAGGAGTGGGGTGGGGGTGGGGGTTTCACTGGTCCACTATAAA +>chr21_31710037_31710087_- +AACACCCAGGTTTCTGAGTATATAATCGCCGCACCAAAGAATTTAATTTT +>chr21_31744582_31744632_- +CCCAGGTCTAAGAGCATATATAACTTGGAGTCCAGACTATGACATTCAAA +>chr21_31768316_31768366_+ +AACGTATATAAATGGTCCTGTCCAGATGTGGCATGCAAACTCAGAATCTT +>chr21_31914206_31914256_- +TGACACCCACTACTTAGAGTATAAAATCATTCTGAGAAGTTAGAGACACC +>chr21_31933633_31933683_- +TCAGAGTATATATAAATGTTCCTGTCCAGTCACAGTCACCAAACTGACCT +>chr21_31962741_31962791_- +ACATATAACTCAGGTTGGATAAAATAATTTGTACAAATCAGGAGAGTCAA +>chr21_31964683_31964733_+ +TCTGATTCACTGAGGCATATAAAAGGCCCTCTGCGGAGAAGTGTCCATAC +>chr21_31973364_31973414_+ +aaacttaaaactctataaacttaaaactCTAGAATCTGATCCTGCTATAC +>chr21_31992870_31992920_+ +CTCATACACTATTGAAGATGTATAAAATTTCATTTGCAGATGGTGACATT +>chr21_32185595_32185645_- +TCACCACCCACCAGAGCTGGGATATATAAAGAAGGTTCTGAGACTAGGAA +>chr21_32202076_32202126_- +TGCCCACCAGCTTGAGGTATAAAAAGCCCTGTACGGGAAGAGACCTTCAT +>chr21_32253899_32253949_- +AGCCCCACCCACCAGCAAGGATATATAAAAGCTCAGGAGTCTGGAGTGAC +>chr21_32410820_32410870_- +TCTACCCCACTAATCACTGAGGATGTATAAAAGTCCCAGGGAAGCTGGTG +>chr21_36411748_36411798_- +ATAGTTCTGTATAGTTTCAGTTGGCATCtaaaaattatataactttattt +>chr21_37838750_37838800_- +gatggttttataaggggcctcaccctcggctcagccctcattcttctcct +>chr21_45705687_45705737_+ +CCGGGGCGGAGCGGCCTTTGCTCTTTGCGTGGTCGCGGGGGTATAACAGC +>chr21_45971413_45971463_- +CAGGCCCTGGGCATATAAAAGCCCCAGCAGCCAACAGGctcacacacaca +>chr21_45978668_45978718_- +CAGAGGGGTATAAAGGTTCCGACCACTCAGAGGCCTGGCACGAtcactca +>chr21_45993530_45993580_+ +CCAAGGAGGAGTATAAAAGCCCCACAAACCCGAGCACCTCACTCACTCGC +>chr21_46020421_46020471_+ +GAGACATATAAAAGCCAACATCCCTGAGCACCTAACACACGGactcactc +>chr21_46031920_46031970_+ +GGAAAATACCCAGGGAGGGTATAAAACCTCAGCAGCCAGGGCACACAAAC +>chr21_46046964_46047014_+ +ACAAGGCCAGGAGGGGTATAAAAGCCTGAGAGCCCCAAGAACctcacaca +>chr21_46057197_46057247_+ +ATTGCTGAGTCTCCTGCTGGGAAAACACAGGCCCTGGGCATATAAAAGCC +>chr21_46086869_46086919_- +GACAGGTGTGCTTCTGTGCTGTGGGGATGCCTGGGCCCAGGTATAAAGGC +>chr21_46102103_46102153_- +AGGTGTGTGCTTCTGTGCTGTGGGGATGCCTGGGTCCAGGTATAAAGGCT +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGCGG +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGCGG +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGCGG +>chr21_47575506_47575556_- +TGAGAAGCCGGTGGGGAGGTGCTGCCGGTGAGCGTATAAAGGCCCTGGCG +>chr21_47575506_47575556_- +TGAGAAGCCGGTGGGGAGGTGCTGCCGGTGAGCGTATAAAGGCCCTGGCG diff -r d44c2896957f -r e5e9a09ac2de test-data/prior30.plib --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prior30.plib Wed Jun 29 08:26:51 2016 -0400 @@ -0,0 +1,275 @@ +Alphabet= ACDEFGHIKLMNPQRSTVWY +NumDistr= 30 +Number= 0 +Mixture= 0.055795 +B= 5.623820 +Alpha= 0.0855491 0.0221831 0.0111063 0.0209959 0.0505726 0.025437 0.0155389 0.132951 0.0247865 0.150287 0.0577239 0.0209317 0.0166629 0.0220905 0.0244295 0.0497608 0.070277 0.157532 0.0102219 0.0309633 +FullUpdate= 1 +QUpdate= 1 +StructID= 0 +Comment= HMM9.4 reestimated in henikoff29.2 + +Number= 1 +Mixture= 0.198333 +B= 0.097240 +Alpha= 0.0562629 0.0329597 0.0692513 0.0385232 0.0400041 0.143573 0.0428939 0.0226244 0.0442102 0.0665467 0.0117853 0.0447655 0.0833299 0.0395825 0.0611271 0.0588852 0.0513472 0.0317153 0.0237865 0.0368161 +FullUpdate= 1 +QUpdate= 1 +StructID= 24 +Comment= Outside + +Number= 2 +Mixture= 0.043566 +B= 1.648336 +Alpha= 0.0144564 0.00845337 0.00785519 0.00864933 0.255959 0.0110815 0.0509526 0.0234533 0.0120443 0.0561967 0.015111 0.0190974 0.00857653 0.0167812 0.0164918 0.0197108 0.0151013 0.0252782 0.050139 0.364613 +FullUpdate= 1 +QUpdate= 1 +StructID= 26 +Comment= Inside + +Number= 3 +Mixture= 0.060170 +B= 2.595432 +Alpha= 0.0452144 0.00587917 0.169731 0.0751478 0.00749471 0.0845832 0.0369819 0.00610072 0.0548186 0.011029 0.00382749 0.212785 0.0206532 0.0416705 0.0280716 0.117267 0.0533742 0.00943157 0.00216149 0.0137784 +FullUpdate= 1 +QUpdate= 1 +StructID= 19 +Comment= Outside Alpha + +Number= 4 +Mixture= 0.065466 +B= 3.112271 +Alpha= 0.0361167 0.0049157 0.0134924 0.0461325 0.00557631 0.0209043 0.0302551 0.016425 0.307554 0.0338255 0.0139435 0.0360733 0.0127659 0.0873761 0.222668 0.0369042 0.0354442 0.0228891 0.00434827 0.0123906 +FullUpdate= 1 +QUpdate= 1 +StructID= 21 +Comment= Outside Beta + +Number= 5 +Mixture= 0.067614 +B= 2.053644 +Alpha= 0.0194362 0.00765176 0.00188738 0.00372898 0.0849894 0.00421787 0.00400459 0.152735 0.00407958 0.4568 0.106051 0.00304386 0.00545956 0.00900935 0.00605071 0.00519029 0.016255 0.0861045 0.00787965 0.0154248 +FullUpdate= 1 +QUpdate= 1 +StructID= 22 +Comment= Inside alpha + +Number= 6 +Mixture= 0.080724 +B= 2.138987 +Alpha= 0.0423172 0.0153891 0.00409306 0.00565735 0.0197117 0.00590607 0.00139926 0.307863 0.00544884 0.115721 0.0285808 0.00522771 0.00474851 0.00328193 0.00351054 0.00892385 0.0348922 0.380003 0.00117673 0.00614917 +FullUpdate= 1 +QUpdate= 1 +StructID= 23 +Comment= Inside beta + +Number= 7 +Mixture= 0.051030 +B= 3.878926 +Alpha= 0.0548123 0.000759746 0.144127 0.46019 0.00249502 0.0192754 0.0106535 0.00938765 0.0562429 0.0163148 0.00717389 0.0245612 0.0177482 0.0744802 0.0199233 0.0323535 0.0257651 0.018574 0.00087086 0.00429088 +FullUpdate= 1 +QUpdate= 1 +StructID= 23 +Comment= Alpha helix + +Number= 8 +Mixture= 0.103529 +B= 1.486325 +Alpha= 0.315754 0.0384546 0.0116388 0.0133665 0.0111126 0.107921 0.00752325 0.0154885 0.0111281 0.0231087 0.011626 0.0228375 0.0304785 0.0166632 0.0156345 0.186379 0.0954421 0.0546691 0.00351538 0.00725682 +FullUpdate= 1 +QUpdate= 1 +StructID= 23 +Comment= Beta strand + +Number= 9 +Mixture= 0.062940 +B= 8.221215 +Alpha= 0.0869919 0.00672577 0.0600995 0.10763 0.0153489 0.0378086 0.0325335 0.023388 0.113765 0.041623 0.0196906 0.0625344 0.0262599 0.0788667 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