Mercurial > repos > mheinzl > fsd_bvsa
changeset 8:238a71241876 draft
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_beforevsafter commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
| author | mheinzl |
|---|---|
| date | Mon, 08 Oct 2018 05:55:14 -0400 |
| parents | c357ce2783a4 |
| children | e486f84adbec |
| files | fsd_beforevsafter.py fsd_beforevsafter.xml test-data/Test_data.tabular test-data/Test_data_DCS.fasta test-data/Test_data_regions.txt test-data/Test_data_trimming.fasta test-data/output_file.pdf test-data/output_file.tabular |
| diffstat | 8 files changed, 268 insertions(+), 123 deletions(-) [+] |
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--- a/fsd_beforevsafter.py Wed May 23 15:04:39 2018 -0400 +++ b/fsd_beforevsafter.py Mon Oct 08 05:55:14 2018 -0400 @@ -1,5 +1,4 @@ #!/usr/bin/env python - # Family size distribution of DCS from various steps of the Galaxy pipeline # # Author: Monika Heinzl, Johannes-Kepler University Linz (Austria) @@ -10,25 +9,27 @@ # a FASTA file with tags after trimming as input (optional). # The program produces a plot which shows the distribution of family sizes of the DCS from the input files and # a CSV file with the data of the plot. - -# USAGE: python FSD before vs after_no_refF1.3_FINAL.py --inputFile_SSCS filenameSSCS --inputName1 filenameSSCS --makeDCS filenameMakeDCS --afterTrimming filenameAfterTrimming -- alignedTags filenameTagsRefGenome -# --sep "characterWhichSeparatesCSVFile" --output_csv outptufile_name_csv --output_pdf outptufile_name_pdf - +# USAGE: python FSD before vs after_no_refF1.3_FINAL.py --inputFile_SSCS filenameSSCS --inputName1 filenameSSCS --makeDCS filenameMakeDCS --afterTrimming filenameAfterTrimming -- alignedTags filenameTagsRefGenome +# --output_tabular outptufile_name_tabular --output_pdf outptufile_name_pdf -import numpy -import matplotlib.pyplot as plt -from collections import Counter -from Bio import SeqIO import argparse import sys -import os +from collections import Counter + +import matplotlib.pyplot as plt +import numpy +from Bio import SeqIO from matplotlib.backends.backend_pdf import PdfPages +plt.switch_backend('agg') + + def readFileReferenceFree(file, delim): with open(file, 'r') as dest_f: data_array = numpy.genfromtxt(dest_f, skip_header=0, delimiter=delim, comments='#', dtype='string') return(data_array) + def readFasta(file): tag_consensus = [] fs_consensus = [] @@ -38,10 +39,11 @@ line = record.description a, b = line.split(" ") fs1, fs2 = b.split("-") - fs_consensus.extend([fs1,fs2]) + fs_consensus.extend([fs1, fs2]) fs_consensus = numpy.array(fs_consensus).astype(int) return(tag_consensus, fs_consensus) + def make_argparser(): parser = argparse.ArgumentParser(description='Analysis of read loss in duplex sequencing data') parser.add_argument('--inputFile_SSCS', @@ -49,18 +51,17 @@ parser.add_argument('--inputName1') parser.add_argument('--makeDCS', help='FASTA File with information about tag and family size in the header.') - parser.add_argument('--afterTrimming',default=None, + parser.add_argument('--afterTrimming', default=None, help='FASTA File with information about tag and family size in the header.') - parser.add_argument('--alignedTags',default=None, + parser.add_argument('--alignedTags', default=None, help=' TXT file with tags aligned to the reference genome and family size.') parser.add_argument('--output_pdf', default="data.pdf", type=str, - help='Name of the pdf and csv file.') - parser.add_argument('--output_csv', default="data.csv", type=str, - help='Name of the pdf and csv file.') - parser.add_argument('--sep', default=",", - help='Separator in the csv file.') + help='Name of the pdf and tabular file.') + parser.add_argument('--output_tabular', default="data.tabular", type=str, + help='Name of the pdf and tabular file.') return parser + def compare_read_families_read_loss(argv): parser = make_argparser() args = parser.parse_args(argv[1:]) @@ -70,16 +71,12 @@ makeConsensus = args.makeDCS afterTrimming = args.afterTrimming ref_genome = args.alignedTags - title_file = args.output_csv + title_file = args.output_tabular title_file2 = args.output_pdf - sep = args.sep - - if type(sep) is not str or len(sep)>1: - print("Error: --sep must be a single character.") - exit(4) + sep = "\t" with open(title_file, "w") as output_file, PdfPages(title_file2) as pdf: - ### PLOT ### + # PLOT plt.rc('figure', figsize=(11.69, 8.27)) # A4 format plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color plt.rcParams['xtick.labelsize'] = 14 @@ -92,7 +89,7 @@ colors = [] labels = [] -### data with tags of SSCS +# data with tags of SSCS data_array = readFileReferenceFree(SSCS_file, "\t") seq = numpy.array(data_array[:, 1]) tags = numpy.array(data_array[:, 2]) @@ -107,7 +104,7 @@ seqDic_ab = dict(zip(all_ab, quant_ab_sscs)) seqDic_ba = dict(zip(all_ba, quant_ba_sscs)) - ### get tags of the SSCS which form a DCS + # get tags of the SSCS which form a DCS # group large family sizes bigFamilies = numpy.where(quant > 20)[0] quant[bigFamilies] = 22 @@ -139,9 +136,9 @@ plt.text(0.55, 0.14, legend1, size=11, transform=plt.gcf().transFigure) plt.text(0.88, 0.14, legend2, size=11, transform=plt.gcf().transFigure) -## data make DCS +# data make DCS tag_consensus, fs_consensus = readFasta(makeConsensus) - ### group large family sizes in the plot of fasta files + # group large family sizes in the plot of fasta files bigFamilies = numpy.where(fs_consensus > 20)[0] fs_consensus[bigFamilies] = 22 list1.append(fs_consensus) @@ -152,7 +149,7 @@ plt.text(0.55, 0.11, legend3, size=11, transform=plt.gcf().transFigure) plt.text(0.88, 0.11, legend4, size=11, transform=plt.gcf().transFigure) -### data after trimming +# data after trimming if afterTrimming != str(None): tag_trimming, fs_trimming = readFasta(afterTrimming) bigFamilies = numpy.where(fs_trimming > 20)[0] @@ -165,10 +162,10 @@ plt.text(0.55, 0.09, legend5, size=11, transform=plt.gcf().transFigure) plt.text(0.88, 0.09, legend6, size=11, transform=plt.gcf().transFigure) -### data of tags aligned to reference genome +# data of tags aligned to reference genome if ref_genome != str(None): mut_array = readFileReferenceFree(ref_genome, " ") - ### use only unique tags that were alignment to the reference genome + # use only unique tags that were alignment to the reference genome seq_mut, seqMut_index = numpy.unique(numpy.array(mut_array[:, 1]), return_index=True) # get family sizes @@ -194,7 +191,6 @@ plt.text(0.55, 0.07, legend7, size=11, transform=plt.gcf().transFigure) plt.text(0.88, 0.07, legend8, size=11, transform=plt.gcf().transFigure) - counts = plt.hist(list1, bins=range(-1, maximumX + 1), stacked=False, label=labels, color=colors, align="left", alpha=1, edgecolor="black", linewidth=1) ticks = numpy.arange(0, maximumX, 1) @@ -248,60 +244,41 @@ if afterTrimming == str(None) and ref_genome == str(None): if afterTrimming == str(None): - output_file.write( - "{}before SSCS buidling{}after DCS building\n".format(sep, sep)) + output_file.write("{}before SSCS buidling{}after DCS building\n".format(sep, sep)) elif ref_genome == str(None): - output_file.write( - "{}before SSCS building{}atfer DCS building\n".format(sep, sep)) + output_file.write("{}before SSCS building{}atfer DCS building\n".format(sep, sep)) - for fs, sscs, dcs in zip(counts[1][2:len(counts[1])], counts[0][0][2:len(counts[0][0])], - counts[0][1][2:len(counts[0][1])]): + for fs, sscs, dcs in zip(counts[1][2:len(counts[1])], counts[0][0][2:len(counts[0][0])], counts[0][1][2:len(counts[0][1])]): if fs == 21: fs = ">20" else: fs = "={}".format(fs) - output_file.write( - "FS{}{}{}{}{}\n".format(fs, sep, int(sscs), sep, int(dcs))) - output_file.write( - "sum{}{}{}{}\n".format(sep, int(sum(counts[0][0])), sep, int(sum(counts[0][1])))) + output_file.write("FS{}{}{}{}{}\n".format(fs, sep, int(sscs), sep, int(dcs))) + output_file.write("sum{}{}{}{}\n".format(sep, int(sum(counts[0][0])), sep, int(sum(counts[0][1])))) elif afterTrimming == str(None) or ref_genome == str(None): if afterTrimming == str(None): - output_file.write( - "{}before SSCS buidling{}after DCS building{}after alignment to reference\n".format(sep, sep, sep)) + output_file.write("{}before SSCS buidling{}after DCS building{}after alignment to reference\n".format(sep, sep, sep)) elif ref_genome == str(None): - output_file.write( - "{}before SSCS building{}atfer DCS building{}after trimming\n".format(sep, sep, sep)) + output_file.write("{}before SSCS building{}atfer DCS building{}after trimming\n".format(sep, sep, sep)) - for fs, sscs, dcs, reference in zip(counts[1][2:len(counts[1])], counts[0][0][2:len(counts[0][0])], - counts[0][1][2:len(counts[0][1])],counts[0][2][2:len(counts[0][2])]): + for fs, sscs, dcs, reference in zip(counts[1][2:len(counts[1])], counts[0][0][2:len(counts[0][0])], counts[0][1][2:len(counts[0][1])], counts[0][2][2:len(counts[0][2])]): if fs == 21: fs = ">20" else: fs = "={}".format(fs) - output_file.write( - "FS{}{}{}{}{}{}{}\n".format(fs, sep, int(sscs), sep, int(dcs), sep, int(reference))) - output_file.write( - "sum{}{}{}{}{}{}\n".format(sep, int(sum(counts[0][0])), sep, int(sum(counts[0][1])), sep, int(sum(counts[0][2])))) + output_file.write("FS{}{}{}{}{}{}{}\n".format(fs, sep, int(sscs), sep, int(dcs), sep, int(reference))) + output_file.write("sum{}{}{}{}{}{}\n".format(sep, int(sum(counts[0][0])), sep, int(sum(counts[0][1])), sep, int(sum(counts[0][2])))) else: - output_file.write( - "{}before SSCS building{}after DCS building{}after trimming{}after alignment to reference\n".format( - sep, sep, sep, sep)) - for fs, sscs, dcs, trim, reference in zip(counts[1][2:len(counts[1])], counts[0][0][2:len(counts[0][0])], - counts[0][1][2:len(counts[0][1])], - counts[0][2][2:len(counts[0][2])], - counts[0][3][2:len(counts[0][3])]): + output_file.write("{}before SSCS building{}after DCS building{}after trimming{}after alignment to reference\n".format(sep, sep, sep, sep)) + for fs, sscs, dcs, trim, reference in zip(counts[1][2:len(counts[1])], counts[0][0][2:len(counts[0][0])], counts[0][1][2:len(counts[0][1])], counts[0][2][2:len(counts[0][2])], counts[0][3][2:len(counts[0][3])]): if fs == 21: fs = ">20" else: fs = "={}".format(fs) - output_file.write( - "FS{}{}{}{}{}{}{}{}{}\n".format(fs, sep, int(sscs), sep, int(dcs), sep, int(trim), sep, - int(reference))) - output_file.write( - "sum{}{}{}{}{}{}{}{}\n".format(sep, int(sum(counts[0][0])), sep, int(sum(counts[0][1])), sep, - int(sum(counts[0][2])), sep, int(sum(counts[0][3])))) + output_file.write("FS{}{}{}{}{}{}{}{}{}\n".format(fs, sep, int(sscs), sep, int(dcs), sep, int(trim), sep, int(reference))) + output_file.write("sum{}{}{}{}{}{}{}{}\n".format(sep, int(sum(counts[0][0])), sep, int(sum(counts[0][1])), sep, int(sum(counts[0][2])), sep, int(sum(counts[0][3])))) output_file.write("\n\nIn the plot, the family sizes of ab and ba strands and of both duplex tags were used.\nWhereas the total numbers indicate only the single count of the formed duplex tags.\n") output_file.write("total nr. of tags (unique, FS>=1){}{}\n".format(sep, len(seq_unique_FS))) @@ -316,5 +293,6 @@ print("Files successfully created!") + if __name__ == '__main__': - sys.exit(compare_read_families_read_loss(sys.argv)) + sys.exit(compare_read_families_read_loss(sys.argv))
--- a/fsd_beforevsafter.xml Wed May 23 15:04:39 2018 -0400 +++ b/fsd_beforevsafter.xml Mon Oct 08 05:55:14 2018 -0400 @@ -1,90 +1,78 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="fsd_beforevsafter" name="Duplex Sequencing Analysis: fsd_beforevsafter" version="0.0.9"> +<tool id="fsd_beforevsafter" name="FSD Before/After" version="1.0.0"> + <description>: Family Size Distribution of duplex sequecning tags during DuNovo analysis</description> <requirements> <!-- galaxy version 16.04 --> <requirement type="package" version="2.7">python</requirement> <requirement type="package" version="1.4">matplotlib</requirement> <requirement type="package" version="1.71">biopython</requirement> - </requirements> - <description>Family size distribution (FSD) of tags from various steps of the Du Novo pipeline</description> <command> - python2 $__tool_directory__/fsd_beforevsafter.py --inputFile_SSCS "$file1" --inputName1 "$file1.name" --makeDCS "$makeDCS" --afterTrimming "$afterTrimming" --alignedTags "$alignedTags" --sep $separator --output_pdf $output_pdf --output_csv $output_csv + python2 '$__tool_directory__/fsd_beforevsafter.py' --inputFile_SSCS '$file1' --inputName1 '$file1.name' --makeDCS '$makeDCS' --afterTrimming '$afterTrimming' --alignedTags '$alignedTags' --output_pdf $output_pdf --output_tabular $output_tabular </command> <inputs> <param name="file1" type="data" format="tabular" label="Dataset 1: input tags of whole dataset" optional="false" help="Input in tabular format with the family size, tags and the direction of the strand ('ab' or 'ba') for each family."/> <param name="makeDCS" type="data" format="fasta" label="Dataset 2: tags after making DCSs" help="Input in fasta format with the tags of the reads, which were aligned to DCSs, and their family sizes of both strands (reverse and forward) in the header, as well as the read itself in the next line."/> <param name="afterTrimming" type="data" format="fasta" optional="true" label="Dataset 3: tags after trimming" help="Input in fasta format with the tags of the reads, which were not filtered out after trimming, and their family sizes of both strands (reverse and forward) in the header, as well as the read itself in the next following line."/> - <param name="alignedTags" type="data" format="txt" optional="true" label="Dataset 4: input tags aligned to the reference genome" help="Input in txt format with the regions and the tags, which were aligned to the reference genome."/> - <param name="separator" type="text" label="Separator of the CSV file." help="can be a single character" value=","/> + <param name="alignedTags" type="data" format="txt" optional="true" label="Dataset 4: input tags aligned to the reference genome" help="Input in txt format with the regions of the reference genome and the tags, which were aligned to the reference genome."/> </inputs> <outputs> <data name="output_pdf" format="pdf" /> - <data name="output_csv" format="csv"/> + <data name="output_tabular" format="tabular"/> </outputs> - <help> <![CDATA[ + <tests> + <test> + <param name="file1" value="Test_data.tabular"/> + <param name="makeDCS" value="Test_data_DCS.fasta"/> + <param name="afterTrimming" value="Test_data_trimming.fasta"/> + <param name="alignedTags" value="Test_data_regions.txt"/> + <output name="output_pdf" file="output_file.pdf" lines_diff="183"/> + <output name="output_tabular" file="output_file.tabular"/> + </test> + </tests> + <help><![CDATA[ **What it does** - This tool will create a distribution of family sizes of various datasets obtained from different steps of the Du Novo pipeline. +This tool will create a distribution of family sizes of various datasets obtained from different steps of the Du Novo pipeline. + +----- **Input** - **Dataset 1:** This tools expects a tabular file with the tags of all families, their sizes and information about forward (ab) and reverse (ba) strands. - - +-----+----------------------------+----+ - | 1 | AAAAAAAAAAAATGTTGGAATCTT | ba | - +-----+----------------------------+----+ - | 10 | AAAAAAAAAAAGGCGGTCCACCCC | ab | - +-----+----------------------------+----+ - | 28 | AAAAAAAAAAATGGTATGGACCGA | ab | - +-----+----------------------------+----+ - - - - **Dataset 2:** And a fasta file with all tags and their family sizes of both strands (forward and reverse) in the header and the read itself in the next line is required. This input file can be obtained by Du Novo: make consensus reads. - - - **Dataset 3 (optional):** In addition, the fasta file with all tags, which were not filtered out after trimming, can be given. - For both input files, only one file from both tools are necessary (these tools give for both forward and reverse strands an output file), since both files have the same tags and family sizes, but different reads, which are not required in this tool. +**Dataset 1:** This tools expects a tabular file with the tags of all families, their sizes and information about forward (ab) and reverse (ba) strands.:: + + 1 AAAAAAAAAAAATGTTGGAATCTT ba + 10 AAAAAAAAAAAGGCGGTCCACCCC ab + 28 AAAAAAAAAAATGGTATGGACCGA ab + +**Dataset 2:** A fasta file with all tags and their family sizes of both strands (forward and reverse) in the header and the read itself in the next line is required. This input file can be obtained by the tool "Du Novo: make consensus reads". - +-------------------------------------------+ - | >AAAAAAAAATAGATCATAGACTCT 7-10 | - | | - | CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCACGTG | - +-------------------------------------------+ - | >AAAAAAAAGGCAGAAGATATACGC 11-3 | - | | - | CNCNGGCCCCCCGCTCCGTGCACAGACGNNGCNACTGACAA | - +-------------------------------------------+ - - - +**Dataset 3 (optional):** In addition, the fasta file with all tags, which were not filtered out after trimming, can be given. This file can be obtained by the tool "Sequence Content Trimmer". +For both input files, only one file from both tools are necessary (these tools give for both forward and reverse strands an output file), since both files have the same tags and family sizes, but different reads, which are not required in this tool:: + + >AAAAAAAAATAGATCATAGACTCT 7-10 + CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCACGTG + >AAAAAAAAGGCAGAAGATATACGC 11-3 + CNCNGGCCCCCCGCTCCGTGCACAGACGNNGCNACTGACAA - **Dataset 4 (optional):** Finally, a TXT file with the regions and all tags that were aligned to the reference genome can be given as input. This file can obtained from "Duplex Sequencing Analysis: range2tag" +**Dataset 4 (optional):** Finally, a TXT file with the regions and all tags that were aligned to the reference genome can be given as input. This file can be obtained by the tool "Duplex Sequencing Analysis: range2tag":: - +-----------+------------------------------+ - | 87_636 | AAATCAAAGTATGAATGAAGTTGCCT | - +-----------+------------------------------+ - | 87_636 | AAATTCATAGCATTAATTTCAACGGG | - +-----------+------------------------------+ - | 656_1143 | GGGGCAGCCATATTGGCAATTATCAT | - +-----------+------------------------------+ - + 87_636 AAATCAAAGTATGAATGAAGTTGCCT + 87_636 AAATTCATAGCATTAATTTCAACGGG + 656_1143 GGGGCAGCCATATTGGCAATTATCAT + **Output** - The output is a PDF file with the plot and a CSV with the data of the plot. - - +The output is a PDF file with the plot and a tabular file with the data of the plot. + **About Author** - Author: Monika Heinzl - - Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria - - Contact: monika.heinzl@edumail.at +Author: Monika Heinzl +Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria +Contact: monika.heinzl@edumail.at - ]]> +]]> </help> <citations>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Test_data.tabular Mon Oct 08 05:55:14 2018 -0400 @@ -0,0 +1,32 @@ +10 AAAAAACATCCCAATAAGAAATCA ab +9 AAAAAACATCCCAATAAGAAATCA ba +4 AAAAAAGTCCTTCGACTCAAGCGG ab +5 AAAAAAGTCCTTCGACTCAAGCGG ba +5 AAAAAATAGTTAAGCCGACACACT ab +7 AAAAAATAGTTAAGCCGACACACT ba +7 AAAAAATGTGCCGAACCTTGGCGA ab +10 AAAAAATGTGCCGAACCTTGGCGA ba +7 AAAAACAACATAGCTTGAAAATTT ab +4 AAAAACAACATAGCTTGAAAATTT ba +81 ATTCGGATAATTCGACGCAACATT ab +11 ATTCGGATAATTCGACGCAACATT ba +41 ATTCGTCGACAATACAAAGGGGCC ab +226 ATTCGTCGACAATACAAAGGGGCC ba +6 ATTGCCAGTGTGGGCTGGTTAGTA ab +41 ATTGCCAGTGTGGGCTGGTTAGTA ba +50 ATTTCGCGACCATCCGCCACTTTG ab +332 ATTTCGCGACCATCCGCCACTTTG ba +64 CAAACTTTAGCACAGTGTGTGTCC ab +57 CAAACTTTAGCACAGTGTGTGTCC ba +85 ATAAACGGCCTTCGACATTGTGAC ab +15 ATAAACGGCCTTCGACATTGTGAC ba +11 ATAAAGTCACCTGTGAATACGTTG ab +35 ATAAAGTCACCTGTGAATACGTTG ba +83 ATAAATCGAAACCGTGCCCAACAA ab +63 ATAAATCGAAACCGTGCCCAACAA ba +9 ATTTAGATATTTTCTTCTTTTTCT ab +7 ATTTAGATATTTTCTTCTTTTTCT ba +7 ATTTAGTTATCCGTCGGCGACGAA ab +3 ATTTAGTTATCCGTCGGCGACGAA ba +8 ATTTAGTTTGAATTGCCCTGCGTC ab +9 ATTTAGTTTGAATTGCCCTGCGTC ba \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Test_data_DCS.fasta Mon Oct 08 05:55:14 2018 -0400 @@ -0,0 +1,50 @@ +>AAAAAAGGACCCTACCACCAACGT 8-5 +CTAGGGTACTTTGGGGCACGAAACATTCTAAAAATCTTCATTCAATGCTGGTGGAAGTCAGAACGCCCCCCCTTCTGGCCCAGCACTGACCCCCGGCTGTACCTCCACGCCCTGTCGCCCACGCGGCGCCAACCTGCCCCTGCTGACCCAAGCAGGTGTCCCTGGNGTCCAACGCGTCCATGAGCTNCNACNCNCCACTGGTGCGCNNCGCNNGNCTNNNNNCAGNNNANNNCCNCANNNNNNCCNNNNNCNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNN +>AAAAAAGGATTCCAAATCTCTGGA 3-7 +TACTCCATGCCCCGGGCCACCTGGTAGGCACAGGACACCAGGTCCTTGAAGGTGAGCTGCTCCTCGGGCGGCTTGCAGGTGTCGAAGGAGTAGTCCAGGCCCGGGGGCCGCCGCGCCCGCAGAAACTCCCGCAGGTTACCCTTGGCCGCGTACTCCACCAGCACGTACAGGGNCCCTGGGGACACGGGCTCCTCAGACGGGNTGCCAGGCNCNGGAGGNCCGCNCAGCCGGNNNCCACCGCNNSNNNCCNNNNCCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNN +>AAAAAAGGCCAGTTTAAAAAAACT 37-3 +CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTNGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCNNNTGGGCCTGGCANCCCNNCNGAGGAGCCNGNNNCCNCAGGTCCCCTGTACNNNCTNGTG +>AAAAAAGGCCCAGATCTCTTAAAA 194-31 +CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCGTCTGAGGAGCCCGTGTCCCCAGGGCCCCTGTACGTGCTGGTGGAGTACGCGGCCAAGGGTAACCTGCGGGAGTTTCAGTCATTTTAAG +>AAAAAAGGGGCCTCATGCGTCAGT 4-3 +CTAGGCTCTACATGGTGAGCAGAGACGAGGAGAGGGGAGCCCGCCTGGCTGCAGAGAGGGCTCACACAGCCCAGGACCAGCGTGGGCCGAGGTGGGGCTCCAGGAGGCCTGGCGGGCAGGCAGCTCAGAACCTGGTATCTACTTTCTGTTACCTGTCGCTTGAGCNGGAAGNGGGAGANCTTGTGCACGGTGGNNGANCCNAGGCCTTNCTTGGGGGGNNTGCGNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNGGNNNANNNGNNNNNNNNNNNNNNNNT +>AAAAAAGTCCTTCGACTCAAGCGG 4-5 +GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTNCTGCCAGGTACCGGCNTCTNCTGCTGCTGNNGNNCNNCNNTNNCNNNNNNNNNNTNNCNNNNNNNNNNNN +>AAAAAAGTGGGATCGGGTTGCAGC 11-6 +CTGGGGTCCTGGCTCTGCCCAGTTCCCGCCTCCACCCCTGAAGCCTGAGCTCTGCAGGACACGTACACGTCACTCTGGTGAGTGTAGACTCNGTCAAACAAGGCCTCAGGCGCCATCCACTTCACGGGCAGCCGGCCCTGGGAGGGTGTGGGAAGGCGGTGTTGGCGCCAGGCGTCCTACTGGCATGACCCCCACCCCCGCNCCCCAGGGCCGGGCNCACGTTGGTTGTCTTCTTGNANTAGTCNNNNTNGTGCNCGTNNNNNNNCNNNNNNNNNNNNNCNNNN +>AAAAAATAATTTCGCCCTCGAGTA 16-4 +CTAGGGTACTTTGGGGCACGAAACATTCTAAAAATCTTCATTCAATGCTGGTGGAAGTCAGAACGCCCCCCCTTCTGGCCCAGCACTGACCCCCGGCTGTACCTCCACGCCCTGTCGCCCACGCGGCGCCAACCTGCCCCTGCTGACCCAAGCAGGTGTCCCTGGAGTCCAACGCGTCCATGAGCTCCANCNCACCACTGGNNNGNNTCNCANNGCTNTCNNCAGNNNNNGGCCNNNNNCTGNNCNANNTCNCC +>AAAAAATAGTTAAGCCGACACACT 5-7 +GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGNGTACACCTGCCTGGCGGGCAATTCTATNGGGTTTTCTCATCACTCTGCGTGGNNGGTGGTGCTGCCAGGTACCGGCNTCTGCTGCTNNNGCTGNNCCGCNNNNNNNNNNNNNNNNNGNNNNNNNNNNCN +>AAAAAATCAGAATAGAGCGCTTTC 4-3 +GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGNGGACGCCGGGGAGTANACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGNCTGGTGGNGCTGCCNGNNNCCNNNNNCTNNNNNNNNNGCTNNNNNNNNNTNNNNNNNNNNNNNNNNNCTNNCNNNNNNNN +>AAAAAATCATAAACATTTTAACAA 65-21 +CTAGGGTACTTTGGGGCACGAAACATTCTAAAAATCTTCATTCAATGCTGGTGGAAGTCAGAACGCCCCCCCTTCTGGCCCAGCACTGACCCCCGGCTGTACCTCCACGCCCTGTCGCCCACGTGGCGCCAACCTGCCCCTGCTGACCCAAGCAGGTGTCCCTGGAGTCCAACGCGTCCATGAGCTCCAACACACCACTGGTGCGCATCGCAAGGCTGTCCTCAGGGGAGGGCCCCACGCTGGCCAATGTCTCCNNNCNNGNGCNGCCTGCCNNNNNCAAANGG +>AAAAAATCTTGACTCGGTACACAA 9-3 +CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGMCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCNNCNGAGGAGCCNNNNTCNCCAGGNCCNNTGNANNNNCNGGNGGAGTANNNGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>AAAAAATGACGAACGATTCGTCAT 3-6 +CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGGCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACNNTGGGCACAGGGNCAGGAGNNNNNGCNCAAGNANNNNNNNNNNNNNNNNNNTCNNNNNNNNNNNCNNNNNNNNNNKNNNNNNNNNNNNNNNNNNNCNNNNNNNN +>AAAAAATGTGCCGAACCTTGGCGA 7-10 +CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGGCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGCTCAAGAAGCGGGNNGNNNGNAAGTCNCAGGATTNNNNNCNNNNNTNNNANNTTTGGCNNNNNNNNNNNNANN +>AAAAAATTGAATCCGTGGATATAG 3-8 +CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGNNCCNNNCCNGGCCNNAACGCCCATNTCTTTNCNGCNNNGNNNGANCNGGTGGAGGNNNGACNAGGCGGGNNGTGNNTNNNNMNGNCNNNNNNNNNNNNGNNNNGNGNNNNNNNNNTGTNNNTCMNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>AAAAAATTGCATGCATCGTCCCTG 6-9 +CTAGGGTACTTTGGGGCACGAAACATTCTAAAAATCTTCATTCAATGCTGGTGGAAGTCAGAACGCCCCCCCTTCTGGCCCAGCACTGACCCCCGGCTGTACCTCCACGCCCTGTCGCCCACGCGGCGCCAACCTGCCCCTGCTGACCCAAGCAGGTGTCCCTGGAGTCCAACGCGTCCATGAGCTCCAACACACCACTGGTGCGNATCGCAAGGCTGTCCTCAGGGGNGGNCCNCNNNNTGNCNNATNNCNCCGNGCNNNNGCNNCCTGCNNNNNNCNNNN +>AAAAAATTGGCATTGTGTATGCAT 18-5 +CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCNGNNCNNNNGNNNANNCCGTGNCCCCAGGGNCNNTGNNNNNNNNGGTNNNNNACGNNNNCNANNNTANCCNNNNNNNGT +>AAAAAATTTTCCCACCAAAATTTC 18-3 +CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTNNNGGNTNGGCGGCCCTCCTGGGCCTGGCNGCNCGTCTGAGGNNCCNNNGTCNNCAGGNNNNCNNTNNNNNNNGGNGNNNNANNNNGNNNNGNNNNNNNNNNNNNNNNNNCNGNNNNNNNNNNNN +>AAAAAATTTTTCTTTACCACCTGT 4-4 +CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCAGACAAGGCGCGTGCTGAGGTTCTGAGCCCCCTTCCGCTCCCAGTGGTGCCTGCGGCTCTGGGCCAGGGGCATCCATGGGAGCCCCGTGGGGGGGGGGGCCNGGCNNNNCNNNAACGCCCANNNTNTTTNNANCNNNNGNGNNNNNGNNNNNNNSNNNCNNNNNNNNNNGNNNNNNNNNNNNNCNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>AAAAACAACATAGCTTGAAAATTT 7-4 +CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGGCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCNCAGGGCCAGGAGTGAGGGCNCNAGNAGCNGGACGGNNGTAAGTNNNNNNANTNNNNNNNNTNNNNGCNNNNNTNNNNNNNCNNNNNNNAGN +>AAAAACAACCAACGTTCTATCTCT 18-4 +CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCNNNNGNGGNNNNNGNGTCCCCAGGGCCCCTGNNNNNNNNGGNNGNNNNNNNGGNCNNGNNNNNCNTGNNNNANNNNNNNNNNNNNNNNNNN +>AAAAACAAGATAATTGGCGCCCGT 5-22 +CTGCCATACACCCGTCCCAGGAGCATGTCCACAGAACCCCAGCCACACCCAACATCCGCCACATCCCTGACGGCCCCTAAACCCAGCCGGGCCTCTGACTGGTGGCTGTTTCACCCCCACCACCAAGCCCCCTACAGCCAACGCTGGCCCTCAGCACCACTGACCGGGCCCGAGACAGCTCCCATTTGGGGTCGGCAGGCAGCTCGAGCTCGGANACATTGGCCAGCGTGGNGNNNNNCCCNNNGNNCNNCCNTNNNNNNYNNNNNANNNNNNNNNNNNNNNMNNN +>AAAAACAAGCATCTGTCGACACTA 69-60 +TGCCGCCTGCGCAGCCCCCCCAAGAAAGGCCTGGGCTCCCCCACCGTGCACAAGATCTCCCGCTTCCCGCTCAAGCGACAGGTAACAGAAAGTAGATACCAGGTTCTGAGCTGCCTGCCCGCCAGGCCTCCTGGAGCCCCACCTCGGCCCACGCTGGTCCTGGGCTGTGTGAGCCCTCTCTGCAGCCAGGCGGGCTCCCCTCTCCTCGTCTCTGCTCACCATGTAGAGCCTAGGGAGTCATAGTGTCGACAG +>AAAAACAATCTTAACCGCGATCTA 10-4 +CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCGTCTGAGGNGCCNGNNTCCCCNGGTCCCCTGTNNGTGCTGGNGGANTACNNGGNCNAGGGTNNCCNGCNNNNGNTNNTGNNNGNNNNNNNN +>AAAAACACGCGGACTTTCCGCATT 4-7 +ACTCCATGCCCCGGGCCACCTGGTAGGCACAGGACACCAGGTCCTTGAAGGTGAGCTGCTCCTCGGGCGGCTTGCAGGTGTCGAAGGAGTAGTCCAGGCCCGGGGGCCGCCGCGCCCGCAGAAACTCCCGCAGGTTACCCTTGGCCGCGTACTCCACCAGCACGTACAGGGGCCCTGGGGACACGGGCTCCTCAGACGGGCTGCCAGGCCCAGGNGGGCCGCCCAGCCGGCACCACCGCCGCTACCGCNNCTACCNCCNNNNCGTGCNNNNNNCNNNCAGNNNNNN \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Test_data_regions.txt Mon Oct 08 05:55:14 2018 -0400 @@ -0,0 +1,17 @@ +87_636 AAAAAACATCCCAATAAGAAATCA +87_636 AAAAAAGTCCTTCGACTCAAGCGG +87_636 AAAAAATAGTTAAGCCGACACACT +87_636 AAAAAATGTGCCGAACCTTGGCGA +87_636 AAAAACAACATAGCTTGAAAATTT +656_1143 ATTCGGATAATTCGACGCAACATT +656_1143 ATTCGTCGACAATACAAAGGGGCC +656_1143 ATTGCCAGTGTGGGCTGGTTAGTA +656_1143 ATTTCGCGACCATCCGCCACTTTG +656_1143 CAAACTTTAGCACAGTGTGTGTCC +1141_1564 ATAAACGGCCTTCGACATTGTGAC +1141_1564 ATAAAGTCACCTGTGAATACGTTG +1141_1564 ATAAATCGAAACCGTGCCCAACAA +1892_2398 ATTTAGATATTTTCTTCTTTTTCT +1892_2398 ATTTAGTTATCCGTCGGCGACGAA +1892_2398 ATTTAGTTTGAATTGCCCTGCGTC +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Test_data_trimming.fasta Mon Oct 08 05:55:14 2018 -0400 @@ -0,0 +1,34 @@ +>AAAAAGAAAAACGATGCTTGACCA 4-6 +CTGGGGTCCTGGCTCTGCCCAGTTCCCGCCTCCACCCCTGAAGCCTGAGCTCTGCAGGACACGTACACGTCACTCTGGTGAGTGTAGACTCGGTCAAACAAGGCCTCAGGCGCCATCCACTTCACGGGCAGCCGGCCCTGGGAGGGTGTGGGAAGGCGGTGTTGGCGCCAGGCGTCCTACTGGCATGACCCCCACCCCCGC +>AAAAAGAAAAGTTTGCTTTTTCTT 13-17 +CTCCATGCCCCGGGCCACCTGGTAGGCACAGGACACCAGGTCCTTGAAGGTGAGCTGCTCCTCGGGCGGCTTGCAGGTGTCGAAGGAGTAGTCCAGGCCCGGGGGCCGCCGCGCCCGCAGAAACTCCCGCAGGTTACCCTTGGCCGCGTACTCCACCAGCACGTACAGGGGACCTGGGGACACGGGCTCCTCAGACGGGCTGCCAGGCCCAGGAGGGCCGCCCAGCCGGCACCACCGCCGCT +>AAAAAGAAATGAATTGGTCCTAGA 24-7 +CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCGTNTGAGGAGCC +>AAAAAGACAGCCTGAATTCCTTGT 17-4 +CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGNGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCNCCTGGGCCTGGCAGCCCGTCNGAG +>AAAAAGACGATTACACAATAACCT 16-7 +CTAGGGTACTTTGGGGCACGAAACATTCTAAAAATCTTCATTCAATGCTGGTGGAAGTCAGAACGCCCCCCCTTCTGGCCCAGCACTGACCCCCGGCTGTACCTCCACGCCCTGTCGCCCACGTGGCGCCAACCTGCCCCTGCTGACCCAAGCAGGTGTCCCTGGAGTCCAACGCGTCCATGAGCTCCAACACACCACTGGT +>AAAAAGATACGGGAGGTGAATTGT 75-6 +CTCTGCGTGGCTGGTGGTGCTGCCAGGTACCGGCTTCTGCTGCTGCTGCTGCTCCGCACTGTCTGGGGGACGCTGGCTCGGGACACGCCAAAGCTGCCAGGACGGACGGGAATCCTGTGACTTACGGCCGTCCCGCTTCTTGAGCCCTCACTCCTGGCCCTGTGCCCAGTGTGGGGACAAAGTTGGCCTGGCCCGGTCCTGGTCCCAGAGGGGC +>AAAAAGATATTTTAATCGGCCCGA 7-6 +GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTMTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGC +>AAAAAGATTACACTGAAATCTTTT 25-5 +CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCNTCTGAGGAGCCCNTGTCCCCAGGGCC +>AAAAAGCCATATGGTCGAAGAGAT 13-10 +ACTCCATGCCCCGGGCCACCTGGTAGGCACAGGACACCAGGTCCTTGAAGGTGAGCTGCTCCTCGGGCGGCTTGCAGGTGTCGAAGGAGTAGTCCAGGCCCGGGGGCCGCCGCGCCCGCAGAAACTCCCGCAGGTTACCCTTGGCCGCGTACTCCACCAGCACGTACAGGGGACCTGGGGACACGGGCTCCTCAGACGGGCTGCCAGGCCCAGGAGGGCCGCCCAGCCGGCACCACCGCC +>AAAAAGCGAAAGTGCCCCATATTT 13-16 +CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCNTCTGAGGAGCCCGTGTCCCCAGGGCCCCTGTACGTNCTGGTGG +>AAAAAGCGATTTAACTGAAATTAT 5-4 +CTAGAGGGCCAGACCCTGGAGAGAAGGAGCCCAGCAGAGCCAGCCAGTCCCACACCGCCACCAGGCGCCCGGGAGACACCAGAGCCACAGGAGAGGCCTTTGGGGACCCAGATGGGAAGTGGGCTCGAGGGGGCTGAGGGGGCCCCTCTGGGACCAGGACCGGGCCAGGCCAACTTTGTCCCCACACTGGGCACAGGGCCAGGAGTGAGGGC +>AAAAAGCGGGGTGGCCTTACGCCC 17-10 +CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCGTCTGAGGAGCCCGNGTCCCCAGGGCCNCTGTACGT +>AAAAAGCTCTACCCCCACGAAGCG 5-10 +GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGCCAGGTACCGNCTTCTGCTGCTGCTGC +>AAAAAGGATATGTCTAACATCCCT 15-16 +CTAGGCTCTACATGGTGAGCAGAGACGAGGAGAGGGGAGCCCGCCTGGCTGCAGAGAGGGCTCACACAGCCCAGGACCAGCGTGGGCCGAGGTGGGGCTCCAGGAGGCCTGGCGGGCAGGCAGCTCAGAACCTGGTATCTACTTTCTGTTACCTGTCGCTTGAGCGGGAAGCGGGAGATCTTGTGCACGGTGGGGGAGCCCAGGCCTTTCTTGGGGGGGCTGCGCAGGCGGCAGAGCGTCACAGCCGCCACCACCAGGATGAACAGGAAGAAGCCCACCCCGT +>AAAAAGGTACACCCGAGATGAACT 13-9 +CACAGGCCCCCCGCTCCGTGCACAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGTAGGTGCGGTAGCGGCGGTGGTGCCGGCTGGGCGGCCCTCCTGGGCCTGGCAGCCCGTCTGAGGNGCCCGTGTCCCCAGGTCCCCTGTACGTGCTGGTGGAGTAC +>AAAAAGTAGCTTCGGTTCGGGTCT 12-4 +GATCCTGCCGTGTGGACTCTGTGCGGTGCCCGCAGGGCGGTGCTGGCGCTCGCCTATCGCTCTGCTCTCTCTTTGTAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGANTACACCTGCCTGGCGGGCANTTCTATTGGGTTTTCTCATCACTCTGCGTG +>AAAAAGTAGGGACATAATTGACTT 4-4 +CTGGGGTCCTGGCTCTGCCCAGTTCCCGCCTCCACCCCTGAAGCCTGAGCTCTGCAGGACACGTACACGTCACTCTGGTGAGTGTAGACTCGGTCAAACAAGGCCTCAGGCGCCATCCACTTCACGGGCAGCCGGCCCTGGGAGGGTGTGGGAAGGCGRTGTTGGCGCCAGGCGTCCTACTGGCATGACCCCCACCCCCGCACCCCA \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_file.tabular Mon Oct 08 05:55:14 2018 -0400 @@ -0,0 +1,46 @@ +Dataset: Test_data.tabular + AB BA +max. family size: 85 332 +absolute frequency: 1 1 +relative frequency: 0.062 0.062 + + + +total nr. of reads 1312 + + +Values from family size distribution + before SSCS building after DCS building after trimming after alignment to reference +FS=1 0 0 0 0 +FS=2 0 0 0 0 +FS=3 1 8 0 1 +FS=4 2 10 6 2 +FS=5 2 5 3 2 +FS=6 1 3 3 1 +FS=7 5 5 3 5 +FS=8 1 2 0 1 +FS=9 3 2 1 3 +FS=10 2 2 3 2 +FS=11 2 1 0 2 +FS=12 0 0 1 0 +FS=13 0 0 4 0 +FS=14 0 0 0 0 +FS=15 1 0 1 1 +FS=16 0 1 3 0 +FS=17 0 0 3 0 +FS=18 0 3 0 0 +FS=19 0 0 0 0 +FS=20 0 0 0 0 +FS>20 12 8 3 12 +sum 32 50 34 32 + + +In the plot, the family sizes of ab and ba strands and of both duplex tags were used. +Whereas the total numbers indicate only the single count of the formed duplex tags. +total nr. of tags (unique, FS>=1) 16 +DCS (before SSCS building, FS>=1) 16 +total nr. of tags (unique, FS>=3) 16 +DCS (before SSCS building, FS>=3) 16 +after DCS building 25 +after trimming 17 +after alignment to reference 16