Mercurial > repos > artbio > small_rna_signatures
changeset 0:3e0ea204d09e draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 4e84386b619a7941f23d175d7fc86aba7990ac36"
| author | artbio |
|---|---|
| date | Tue, 07 Jan 2020 11:59:34 +0000 |
| parents | |
| children | ca2b04cdbf4d |
| files | overlapping_reads.py overlapping_reads.xml signature.py signature.r signature.xml test-data/global.pdf test-data/h.tab test-data/lattice.pdf test-data/paired.fa test-data/paired_2.fa test-data/paired_3.fa test-data/paired_4.fa test-data/sr_bowtie.bam test-data/z.tab |
| diffstat | 14 files changed, 4984 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/overlapping_reads.py Tue Jan 07 11:59:34 2020 +0000 @@ -0,0 +1,166 @@ +import argparse +from collections import defaultdict + +import pysam + + +def Parser(): + the_parser = argparse.ArgumentParser() + the_parser.add_argument( + '--input', action="store", type=str, help="bam alignment file") + the_parser.add_argument( + '--minquery', type=int, + help="Minimum readsize of query reads (nt) - must be an integer") + the_parser.add_argument( + '--maxquery', type=int, + help="Maximum readsize of query reads (nt) - must be an integer") + the_parser.add_argument( + '--mintarget', type=int, + help="Minimum readsize of target reads (nt) - must be an integer") + the_parser.add_argument( + '--maxtarget', type=int, + help="Maximum readsize of target reads (nt) - must be an integer") + the_parser.add_argument( + '--overlap', type=int, + help="Overlap analyzed (nt) - must be an integer") + the_parser.add_argument( + '--output', action="store", type=str, + help="Pairable sequences") + args = the_parser.parse_args() + return args + + +class Map: + + def __init__(self, bam_file, output, minquery=23, maxquery=29, + mintarget=23, maxtarget=29, overlap=10): + self.bam_object = pysam.AlignmentFile(bam_file, 'rb') + self.output = output + self.query_range = range(minquery, maxquery + 1) + self.target_range = range(mintarget, maxtarget + 1) + self.overlap = overlap + self.chromosomes = dict(zip(self.bam_object.references, + self.bam_object.lengths)) + self.alignement_dic = self.index_alignments(self.bam_object) + self.all_query_positions = self.query_positions(self.bam_object, + overlap=self.overlap) + self.readdic = self.make_readdic(self.bam_object) + self.pairing() + + def make_readdic(self, bam_object): + readdic = defaultdict(int) + for read in bam_object.fetch(): + readdic[read.query_sequence] += 1 + return readdic + + def index_alignments(self, bam_object): + ''' + dic[(chrom, pos, polarity)]: [readseq1, readseq2, ...] + the list value is further converted in set + ''' + dic = defaultdict(list) + for chrom in self.chromosomes: + for read in bam_object.fetch(chrom): + if read.is_reverse: + coord = read.reference_end-1 + pol = 'R' + else: + coord = read.reference_start + pol = 'F' + dic[(chrom, coord, pol)].append(read.query_sequence) + for key in dic: + dic[key] = set(dic[key]) + return dic + + def query_positions(self, bam_object, overlap): + all_query_positions = defaultdict(list) + for genomicKey in self.alignement_dic.keys(): + chrom, coord, pol = genomicKey + if pol == 'F' and len(self.alignement_dic[(chrom, + coord+overlap-1, + 'R')]) > 0: + all_query_positions[chrom].append(coord) + for chrom in all_query_positions: + all_query_positions[chrom] = sorted( + list(set(all_query_positions[chrom]))) + return all_query_positions + + def countpairs(self, uppers, lowers): + query_range = self.query_range + target_range = self.target_range + uppers = [seq for seq in uppers if (len(seq) in query_range or len(seq) + in target_range)] + print(uppers) + uppers_expanded = [] + for seq in uppers: + expand = [seq for i in range(self.readdic[seq])] + uppers_expanded.extend(expand) + print(uppers_expanded) + uppers = uppers_expanded + lowers = [seq for seq in lowers if (len(seq) in query_range or len(seq) + in target_range)] + lowers_expanded = [] + for seq in lowers: + expand = [seq for i in range(self.readdic[seq])] + lowers_expanded.extend(expand) + lowers = lowers_expanded + paired = [] + for upread in uppers: + for downread in lowers: + if (len(upread) in query_range and len(downread) in + target_range) or (len(upread) in target_range and + len(downread) in query_range): + paired.append(upread) + lowers.remove(downread) + break + return len(paired) + + def pairing(self): + F = open(self.output, 'w') + query_range = self.query_range + target_range = self.target_range + overlap = self.overlap + stringresult = [] + header_template = '>%s|coord=%s|strand %s|size=%s|nreads=%s\n%s\n' + total_pairs = 0 + print('Chromosome\tNbre of pairs') + for chrom in sorted(self.chromosomes): + number_pairs = 0 + for pos in self.all_query_positions[chrom]: + stringbuffer = [] + uppers = self.alignement_dic[chrom, pos, 'F'] + lowers = self.alignement_dic[chrom, pos+overlap-1, 'R'] + number_pairs += self.countpairs(uppers, lowers) + total_pairs += number_pairs + if uppers and lowers: + for upread in uppers: + for downread in lowers: + if (len(upread) in query_range and len(downread) in + target_range) or (len(upread) in target_range + and len(downread) in + query_range): + stringbuffer.append( + header_template % + (chrom, pos+1, '+', len(upread), + self.readdic[upread], upread)) + stringbuffer.append( + header_template % + (chrom, pos+overlap-len(downread)+1, '-', + len(downread), self.readdic[downread], + self.revcomp(downread))) + stringresult.extend(sorted(set(stringbuffer))) + print('%s\t%s' % (chrom, number_pairs)) + print('Total nbre of pairs that can be simultaneously formed\t%s' + % total_pairs) + F.write(''.join(stringresult)) + + def revcomp(self, sequence): + antidict = {"A": "T", "T": "A", "G": "C", "C": "G", "N": "N"} + revseq = sequence[::-1] + return "".join([antidict[i] for i in revseq]) + + +if __name__ == "__main__": + args = Parser() + mapobj = Map(args.input, args.output, args.minquery, args.maxquery, + args.mintarget, args.maxtarget, args.overlap)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/overlapping_reads.xml Tue Jan 07 11:59:34 2020 +0000 @@ -0,0 +1,132 @@ +<tool id="overlapping_reads" name="Get overlapping reads" version="0.9.6"> + <description /> + <requirements> + <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Tool exception" /> + </stdio> + <command detect_errors="exit_code"><![CDATA[ + samtools index '$input' && + python '$__tool_directory__'/overlapping_reads.py + --input '$input' + --minquery '$minquery' + --maxquery '$maxquery' + --mintarget '$mintarget' + --maxtarget '$maxtarget' + --overlap '$overlap' + --output '$output' + ]]></command> + <inputs> + <param format="bam" label="Compute signature from this bowtie standard output" name="input" type="data" /> + <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" /> + <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" /> + <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" /> + <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" /> + <param help="'10' = 10 nucleotides overlap" label="Overlap (in nt)" name="overlap" size="3" type="integer" value="10" /> + </inputs> + <outputs> + <data format="fasta" label="pairable reads" name="output" /> + </outputs> + <tests> + <test> + <param ftype="bam" name="input" value="sr_bowtie.bam" /> + <param name="minquery" value="23" /> + <param name="maxquery" value="29" /> + <param name="mintarget" value="23" /> + <param name="maxtarget" value="29" /> + <param name="overlap" value="10" /> + <output file="paired.fa" ftype="fasta" name="output" /> + </test> + <test> + <param ftype="bam" name="input" value="sr_bowtie.bam" /> + <param name="minquery" value="20" /> + <param name="maxquery" value="22" /> + <param name="mintarget" value="23" /> + <param name="maxtarget" value="29" /> + <param name="overlap" value="10" /> + <output file="paired_2.fa" ftype="fasta" name="output" /> + </test> + <test> + <param ftype="bam" name="input" value="sr_bowtie.bam" /> + <param name="minquery" value="23" /> + <param name="maxquery" value="29" /> + <param name="mintarget" value="20" /> + <param name="maxtarget" value="22" /> + <param name="overlap" value="10" /> + <output file="paired_3.fa" ftype="fasta" name="output" /> + </test> + <test> + <param ftype="bam" name="input" value="sr_bowtie.bam" /> + <param name="minquery" value="20" /> + <param name="maxquery" value="22" /> + <param name="mintarget" value="20" /> + <param name="maxtarget" value="22" /> + <param name="overlap" value="10" /> + <output file="paired_4.fa" ftype="fasta" name="output" /> + </test> + </tests> + <help> + +**What it does** + +Extract reads with overlap signatures of the specified overlap (in nt) and +return a fasta file of these "pairable" reads. + +See `Antoniewski (2014)`_ for background and details + +.. _Antoniewski (2014): https://link.springer.com/protocol/10.1007%2F978-1-4939-0931-5_12 + +**Input** + +*A **sorted** BAM alignment file.* + +*Query and target sizes:* + +The algorithm search for each *query* reads (of specified size) in the bam alignment if +there are *target* reads (of specified size) that align on the opposite strand with a 10 nt +overlap. + +Searching query reads of 20-22 nt that overlap by 10 nt with target +reads of 23-29 nt is equivalent to searching query reads of 23-29 nt that overlap by 10 nt +with target reads of 20-22 nt. i.e, searching for siRNAs that pair with piRNAs is equivalent +to searching for siRNAs that pairs with piRNAs. In contrast, searching query reads of 20-22 nt +that overlap by 10 nt with target reads of 23-29 nt is different from searching query reads of +23-29 nt that overlap by 10 nt with target reads of 23-29 nt, since the number of "heterotypic" +pairs of reads is likely to be different from the number of "homotypic" pairs of reads. + +*Overlap* +The number of nucleotides by which the pairs of sequences will overlap + + + +**Outputs** + +a fasta file of pairable reads such as : + +>FBgn0000004_17.6|coord=5839|strand -|size=26|nreads=1 + +TTTTCGTCAATTGTGCCAAATAGGTA + +>FBgn0000004_17.6|coord=5855|strand +|size=23|nreads=1 + +TTGACGAAAATGATCGAGTGGAT + + +where FBgn0000004_17.6 stands for the chromosome, 5839 stands for the 1-based read position, +'strand -' stands for lower strand of chromosome, 26 stands for the size of the sequence and +nreads=1 stands for the number of reads of the sequence in the dataset. + +the second sequence in this example corresponds to 1 read that overlap by 10 nt with +1 read of the first sequence. + +The tool also returns in the standard output the numbers of pairs of reads that +can be formed simultaneously in silico. Note that these numbers are distinct from the numbers +of pairs of read alignments (as computed by the small_rna_signature tool) when analysis is +performed with multi-mapping reads. + + </help> + <citations> + <citation type="doi">10.1007/978-1-4939-0931-5_12</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/signature.py Tue Jan 07 11:59:34 2020 +0000 @@ -0,0 +1,231 @@ +import argparse +from collections import defaultdict + +import numpy + +import pysam + + +def Parser(): + the_parser = argparse.ArgumentParser() + the_parser.add_argument( + '--input', action="store", type=str, help="bam alignment file") + the_parser.add_argument( + '--minquery', type=int, + help="Minimum readsize of query reads (nt) - must be an integer") + the_parser.add_argument( + '--maxquery', type=int, + help="Maximum readsize of query reads (nt) - must be an integer") + the_parser.add_argument( + '--mintarget', type=int, + help="Minimum readsize of target reads (nt) - must be an integer") + the_parser.add_argument( + '--maxtarget', type=int, + help="Maximum readsize of target reads (nt) - must be an integer") + the_parser.add_argument( + '--minscope', type=int, + help="Minimum overlap analyzed (nt) - must be an integer") + the_parser.add_argument( + '--maxscope', type=int, + help="Maximum overlap analyzed (nt) - must be an integer") + the_parser.add_argument( + '--output_h', action="store", type=str, + help="h-signature dataframe") + the_parser.add_argument( + '--output_z', action="store", type=str, + help="z-signature dataframe") + args = the_parser.parse_args() + return args + + +class Map: + + def __init__(self, bam_file, minquery=23, maxquery=29, mintarget=23, + maxtarget=29, minscope=1, maxscope=19, output_h='', + output_z=''): + self.bam_object = pysam.AlignmentFile(bam_file, 'rb') + self.query_range = range(minquery, maxquery + 1) + self.target_range = range(mintarget, maxtarget + 1) + self.scope = range(minscope, maxscope + 1) + self.H = open(output_h, 'w') + self.Z = open(output_z, 'w') + self.chromosomes = dict(zip(self.bam_object.references, + self.bam_object.lengths)) + self.map_dict = self.create_map(self.bam_object) + self.query_positions = self.compute_query_positions() + self.Z.write(self.compute_signature_pairs()) + self.H.write(self.compute_signature_h()) + self.H.close() + self.Z.close() + + def create_map(self, bam_object): + ''' + Returns a map_dictionary {(chromosome,read_position,polarity): + [read_length, ...]} + ''' + map_dictionary = defaultdict(list) + # get empty value for start and end of each chromosome + for chrom in self.chromosomes: + map_dictionary[(chrom, 1, 'F')] = [] + map_dictionary[(chrom, self.chromosomes[chrom], 'F')] = [] + for chrom in self.chromosomes: + for read in bam_object.fetch(chrom): + if read.is_reverse: + map_dictionary[(chrom, read.reference_end, + 'R')].append(read.query_alignment_length) + else: + map_dictionary[(chrom, read.reference_start+1, + 'F')].append(read.query_alignment_length) + return map_dictionary + + def compute_query_positions(self): + ''' this method does not filter on read size, just forward reads + that overlap reverse reads in the overlap range''' + all_query_positions = defaultdict(list) + for genomicKey in self.map_dict.keys(): + chrom, coord, pol = genomicKey + for i in self.scope: + if pol == 'F' and len(self.map_dict[chrom, + coord+i-1, + 'R']) > 0: + all_query_positions[chrom].append(coord) + break + for chrom in all_query_positions: + all_query_positions[chrom] = sorted( + list(set(all_query_positions[chrom]))) + return all_query_positions + + def countpairs(self, uppers, lowers): + query_range = self.query_range + target_range = self.target_range + uppers = [size for size in uppers if size in query_range or size in + target_range] + lowers = [size for size in lowers if size in query_range or size in + target_range] + paired = [] + for upread in uppers: + for downread in lowers: + if (upread in query_range and downread in target_range) or ( + upread in target_range and downread in query_range): + paired.append(upread) + lowers.remove(downread) + break + return len(paired) + + def compute_signature_pairs(self): + frequency_table = defaultdict(dict) + scope = self.scope + for chrom in self.chromosomes: + for overlap in scope: + frequency_table[chrom][overlap] = 0 + for chrom in self.query_positions: + for coord in self.query_positions[chrom]: + for overlap in scope: + uppers = self.map_dict[chrom, coord, 'F'] + lowers = self.map_dict[chrom, coord+overlap-1, 'R'] + frequency_table[chrom][overlap] += self.countpairs(uppers, + lowers) + # compute overlaps for all chromosomes merged + for overlap in scope: + accumulator = [] + for chrom in frequency_table: + if chrom != 'all_chromosomes': + accumulator.append(frequency_table[chrom][overlap]) + frequency_table['all_chromosomes'][overlap] = sum(accumulator) + return self.stringify_table(frequency_table) + + def signature_tables(self): + query_range = self.query_range + target_range = self.target_range + Query_table = defaultdict(dict) + Target_table = defaultdict(dict) + for key in self.map_dict: + for size in self.map_dict[key]: + if size in query_range or size in target_range: + if key[2] == 'F': + coordinate = key[1] + else: + coordinate = -key[1] + if size in query_range: + Query_table[key[0]][coordinate] = Query_table[key[0]].get( + coordinate, 0) + 1 + if size in target_range: + Target_table[key[0]][coordinate] = \ + Target_table[key[0]].get(coordinate, 0) + 1 + return Query_table, Target_table + + def compute_signature_h(self): + scope = self.scope + Query_table, Target_table = self.signature_tables() + frequency_table = defaultdict(dict) + for chrom in self.chromosomes: + for overlap in scope: + frequency_table[chrom][overlap] = 0 + for chrom in Query_table: + Total_Query_Numb = 0 + for coord in Query_table[chrom]: + Total_Query_Numb += Query_table[chrom][coord] + for coord in Query_table[chrom]: + local_table = dict([(overlap, 0) for overlap in scope]) + number_of_targets = 0 + for overlap in scope: + local_table[overlap] += Query_table[chrom][coord] * \ + Target_table[chrom].get(-coord - overlap + 1, 0) + number_of_targets += Target_table[chrom].get( + -coord - overlap + 1, 0) + for overlap in scope: + try: + frequency_table[chrom][overlap] += \ + local_table[overlap] / number_of_targets \ + / float(Total_Query_Numb) + except ZeroDivisionError: + continue + # compute overlap probabilities for all chromosomes merged + general_frequency_table = dict([(overlap, 0) for overlap in scope]) + total_aligned_reads = 0 + for chrom in frequency_table: + for overlap in frequency_table[chrom]: + total_aligned_reads += self.bam_object.count(chrom) + for chrom in frequency_table: + for overlap in frequency_table[chrom]: + try: + general_frequency_table[overlap] += \ + frequency_table[chrom][overlap] / total_aligned_reads \ + * self.bam_object.count(chrom) + except ZeroDivisionError: + continue + for overlap in general_frequency_table: + frequency_table['all_chromosomes'][overlap] = \ + general_frequency_table[overlap] + return self.stringify_table(frequency_table) + + def stringify_table(self, frequency_table): + ''' + method both to compute z-score and to return a writable string + ''' + tablestring = [] + for chrom in sorted(frequency_table): + accumulator = [] + for overlap in frequency_table[chrom]: + accumulator.append(frequency_table[chrom][overlap]) + z_mean = numpy.mean(accumulator) + z_std = numpy.std(accumulator) + if z_std == 0: + for overlap in sorted(frequency_table[chrom]): + tablestring.append('%s\t%s\t%s\t%s\n' % ( + chrom, str(overlap), + str(frequency_table[chrom][overlap]), str(0))) + else: + for overlap in sorted(frequency_table[chrom]): + tablestring.append('%s\t%s\t%s\t%s\n' % ( + chrom, str(overlap), + str(frequency_table[chrom][overlap]), + str((frequency_table[chrom][overlap] - z_mean)/z_std))) + return ''.join(tablestring) + + +if __name__ == "__main__": + args = Parser() + mapobj = Map(args.input, args.minquery, args.maxquery, args.mintarget, + args.maxtarget, args.minscope, args.maxscope, args.output_h, + args.output_z)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/signature.r Tue Jan 07 11:59:34 2020 +0000 @@ -0,0 +1,99 @@ +## Setup R error handling to go to stderr +#options(show.error.messages=F, + #error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +warnings() + +library(RColorBrewer) +library(lattice) +library(latticeExtra) +library(grid) +library(gridExtra) +library(optparse) + +option_list <- list( + make_option("--h_dataframe", type="character", help="path to h-signature dataframe"), + make_option("--z_dataframe", type="character", help="path to z-signature dataframe"), + make_option("--plot_method", type = "character", help="How data should be plotted (global or lattice)"), + make_option("--pdf", type = "character", help="path to the pdf file with plots"), + make_option("--title", type = "character", help="Graph Title") + ) + +parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) +args = parse_args(parser) + + + + +# data frames implementation +h_dataframe = read.delim(args$h_dataframe, header=F) +colnames(h_dataframe) = c("chrom", "overlap", "sig", "z-score") +h_dataframe$sig = h_dataframe$sig * 100 # to get probs in % +z_dataframe = read.delim(args$z_dataframe, header=F) +colnames(z_dataframe) = c("chrom", "overlap", "sig", "z-score") + +# functions + globalgraph = function () { + pdf(args$pdf) + par(mfrow=c(2,2),oma = c(0, 0, 3, 0)) + + plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2,3)], + type = "h", main="Numbers of pairs", cex.main=1, xlab="overlap (nt)", + ylab="Numbers of pairs", col="darkslateblue", lwd=4) + + plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2,4)], + type = "l", main="Number of pairs Z-scores", cex.main=1, xlab="overlap (nt)", + ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2) + + plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2,3)], + type = "l", main="Overlap probabilities", cex.main=1, xlab="overlap (nt)", + ylab="Probability [%]", ylim=c(0,50), pch=19, col="darkslateblue", lwd=2) + + plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2,4)], + type = "l", main="Overlap Probability Z-scores", cex.main=1, + xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, + col="darkslateblue", lwd=2) + + mtext(args$title, outer = TRUE, cex=1) + dev.off() + } + + treillisgraph = function (df, ...) { + pdf(args$pdf, paper="special", height=11.69, width=6 ) # 8.2677 + p = xyplot(sig ~ overlap|factor(method, levels=unique(method))+chrom, data = df, + type = "l", + col='darkblue', + cex=0.5, + scales=list(y=list(tick.number=4, relation="free", cex=0.6, rot=0), x=list(cex=0.6, alternating=FALSE)), + xlab = "Overlap", + ylab = "signature (Nbr of pairs / Overlap prob.)", + main = args$title, + par.strip.text=list(cex=.5), + pch=19, lwd =2, + as.table=TRUE, + layout=c(2,12), + newpage = T, + ...) + plot(p) + dev.off() + } + +# main + +if (args$plot_method=="global") { + globalgraph() + } + +if(args$plot_method=="lattice") { + # rearrange dataframes + h_sig = h_dataframe[,c(1,2,3)] + h_sig = cbind(rep("Overlap Prob (%)", length(h_sig[,1])), h_sig) + colnames(h_sig) = c("method", "chrom", "overlap", "sig") + z_pairs = z_dataframe[,c(1,2,3)] + z_pairs = cbind(rep("Nbr of pairs", length(z_pairs[,1])), z_pairs) + colnames(z_pairs) = c("method", "chrom", "overlap", "sig") + lattice_df = rbind(z_pairs, h_sig) + par.settings.treillis=list(strip.background = list( + col = c("lightblue", "lightgreen"))) + + treillisgraph(lattice_df, par.settings=par.settings.treillis) +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/signature.xml Tue Jan 07 11:59:34 2020 +0000 @@ -0,0 +1,124 @@ +<tool id="signature" name="Small RNA Signatures" version="3.2.1"> + <description /> + <requirements> + <requirement type="package" version="1.11.2=py27_0">numpy</requirement> + <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> + <requirement type="package" version="1.6.1=r351h6115d3f_0">r-optparse</requirement> + <requirement type="package" version="0.6_28=r351h6115d3f_0">r-latticeextra</requirement> + <requirement type="package" version="2.3=r351h6115d3f_0">r-gridextra</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Tool exception" /> + </stdio> + <command detect_errors="exit_code"><![CDATA[ + samtools index '$input' && + python '$__tool_directory__'/signature.py + --input '$input' + --minquery '$minquery' + --maxquery '$maxquery' + --mintarget '$mintarget' + --maxtarget '$maxtarget' + --minscope '$minscope' + --maxscope '$maxscope' + --output_h '$h_dataframe' + --output_z '$z_dataframe' && + Rscript '$__tool_directory__'/signature.r + --h_dataframe '$h_dataframe' + --z_dataframe '$z_dataframe' + --plot_method '$plot_method' + --pdf '$pdf' + --title "Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs" + ]]></command> + <inputs> + <param format="bam" label="Compute signature from this bowtie standard output" name="input" type="data" /> + <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" /> + <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" /> + <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" /> + <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" /> + <param help="'1' = 1 nucleotide overlap" label="Minimal relative overlap analyzed" name="minscope" size="3" type="integer" value="1" /> + <param help="'1' = 1 nucleotide overlap" label="Maximal relative overlap analyzed" name="maxscope" size="3" type="integer" value="26" /> + <param help="Signature can be computed globally or by item present in the alignment file" label="Graph type" name="plot_method" type="select"> + <option selected="True" value="global">Global</option> + <option value="lattice">Lattice</option> + </param> + </inputs> + <outputs> + <data format="tabular" label="z-signature data frame" name="z_dataframe"> + <actions> + <action name="column_names" type="metadata" default="Chromosome,Overlap,Number_of_pairs,z-score" /> + </actions> + </data> + <data format="tabular" label="h-signature data frame" name="h_dataframe"> + <actions> + <action name="column_names" type="metadata" default="Chromosome,Overlap,overlap_probability,z-score" /> + </actions> + </data> + <data format="pdf" label="Overlap probabilities" name="pdf" /> + </outputs> + <tests> + <test> + <param ftype="bam" name="input" value="sr_bowtie.bam" /> + <param name="minquery" value="23" /> + <param name="maxquery" value="29" /> + <param name="mintarget" value="23" /> + <param name="maxtarget" value="29" /> + <param name="minscope" value="5" /> + <param name="maxscope" value="15" /> + <param name="plot_method" value="global" /> + <output file="h.tab" ftype="tabular" name="h_dataframe" /> + <output file="z.tab" ftype="tabular" name="z_dataframe" /> + <output file="global.pdf" ftype="pdf" name="pdf" /> + </test> + <test> + <param ftype="bam" name="input" value="sr_bowtie.bam" /> + <param name="minquery" value="23" /> + <param name="maxquery" value="29" /> + <param name="mintarget" value="23" /> + <param name="maxtarget" value="29" /> + <param name="minscope" value="5" /> + <param name="maxscope" value="15" /> + <param name="plot_method" value="lattice" /> + <output file="h.tab" ftype="tabular" name="h_dataframe" /> + <output file="z.tab" ftype="tabular" name="z_dataframe" /> + <output file="lattice.pdf" ftype="pdf" name="pdf" /> + </test> + </tests> + <help> + +**What it does** + +Compute small RNA (piRNA, siRNA, ...) signatures. + +This tool computes (i) the number of pairs **aligned** reads by overlap classes (in nt) and associated z-scores, +and (ii) the ping-pong signal (`Brennecke et al, 2009`_) and associated z-scores. + +**Note** that the number of pairs of aligned reads is disctint from the number of pairs of reads +when these reads can be aligned at multiple positions in the genome. The two values are equal only +when the analysis is restricted to uniquely mapping reads. + +Options set the min and max size of both the query small rna class and the target small rna class, +the range of overlaps (in nt) over which to compute the signatures, and whether the signatures should be reported at +genome-wide level or by item (chromosomes, genes, etc.). For details on computational algorithmes +for piRNA and siRNA signatures, see `Antoniewski (2014)`_. + +.. _Brennecke et al, 2009: http://dx.doi.org/10.1126/science.1165171 +.. _Antoniewski (2014): https://link.springer.com/protocol/10.1007%2F978-1-4939-0931-5_12 + +**Input** + +A **sorted** BAM alignment file. + +**Outputs** + +**Global**: The number of pairs found, the ping-pong signal and the associated z-scores +are computed at genome-wide level and returned in a pdf file. + +**Lattice**: The number of pairs found, the ping-pong signals and the associated z-scores +are computed for each items described in the BAM alignment input and returned in a pdf file as a lattice graph. + + + </help> + <citations> + <citation type="doi">10.1007/978-1-4939-0931-5_12</citation> + </citations> +</tool>
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired.fa Tue Jan 07 11:59:34 2020 +0000 @@ -0,0 +1,668 @@ +>FBgn0000004_17.6|coord=5839|strand -|size=26|nreads=1 +TTTTCGTCAATTGTGCCAAATAGGTA +>FBgn0000004_17.6|coord=5855|strand +|size=23|nreads=1 +TTGACGAAAATGATCGAGTGGAT +>FBgn0000006_412|coord=742|strand -|size=27|nreads=1 +TTCGACCAAACCGGTGGCGTTTGCTGA +>FBgn0000006_412|coord=744|strand -|size=25|nreads=2 +TTCGACCAAACCGGTGGCGTTTGCT +>FBgn0000006_412|coord=745|strand -|size=24|nreads=2 +TTCGACCAAACCGGTGGCGTTTGC +>FBgn0000006_412|coord=759|strand +|size=24|nreads=3 +TTTGGTCGAAAGCTCTAAAGCTAC +>FBgn0000006_412|coord=759|strand +|size=25|nreads=1 +TTTGGTCGAAAGCTCTAAAGCTACA +>FBgn0000006_412|coord=759|strand +|size=27|nreads=3 +TTTGGTCGAAAGCTCTAAAGCTACATG +>FBgn0000006_412|coord=744|strand -|size=26|nreads=2 +TTTCGACCAAACCGGTGGCGTTTGCT +>FBgn0000006_412|coord=745|strand -|size=25|nreads=1 +TTTCGACCAAACCGGTGGCGTTTGC +>FBgn0000006_412|coord=760|strand +|size=26|nreads=6 +TTGGTCGAAAGCTCTAAAGCTACATG +>FBgn0000007_1731|coord=4539|strand -|size=26|nreads=1 +TTGAGAGCAAAGGCCGAATGAGTAAA +>FBgn0000007_1731|coord=4555|strand +|size=24|nreads=1 +TTGCTCTCAATGCGCTGAGTTTGG +>FBgn0000155_roo|coord=2159|strand -|size=27|nreads=1 +TTGGTCAAAAACTCCCAAGTGGCTTCA +>FBgn0000155_roo|coord=2161|strand -|size=25|nreads=1 +TTGGTCAAAAACTCCCAAGTGGCTT +>FBgn0000155_roo|coord=2176|strand +|size=24|nreads=1 +TTTTGACCAAGCGGTATGAGAATA +>FBgn0000155_roo|coord=2675|strand -|size=27|nreads=1 +TTTTTACCAAACGGATGCCTCAGACAT +>FBgn0000155_roo|coord=2676|strand -|size=26|nreads=5 +TTTTTACCAAACGGATGCCTCAGACA +>FBgn0000155_roo|coord=2677|strand -|size=25|nreads=14 +TTTTTACCAAACGGATGCCTCAGAC +>FBgn0000155_roo|coord=2678|strand -|size=24|nreads=14 +TTTTTACCAAACGGATGCCTCAGA +>FBgn0000155_roo|coord=2679|strand -|size=23|nreads=2 +TTTTTACCAAACGGATGCCTCAG +>FBgn0000155_roo|coord=2692|strand +|size=24|nreads=1 +TTGGTAAAAAATGTATAAGTGAGC +>FBgn0000155_roo|coord=2692|strand +|size=27|nreads=1 +TTGGTAAAAAATGTATAAGTGAGCAGC +>FBgn0000155_roo|coord=3132|strand -|size=27|nreads=1 +TTTATTAAAATCGGGGTCGGCTAATTT +>FBgn0000155_roo|coord=3149|strand +|size=26|nreads=1 +TTTTAATAAACCGGGTCGCATTGATT +>FBgn0000155_roo|coord=3225|strand -|size=26|nreads=1 +TTTTGCCCAAGGAGACCGTCTATTTT +>FBgn0000155_roo|coord=3226|strand -|size=25|nreads=1 +TTTTGCCCAAGGAGACCGTCTATTT +>FBgn0000155_roo|coord=3227|strand -|size=24|nreads=2 +TTTTGCCCAAGGAGACCGTCTATT +>FBgn0000155_roo|coord=3228|strand -|size=23|nreads=1 +TTTTGCCCAAGGAGACCGTCTAT +>FBgn0000155_roo|coord=3241|strand +|size=24|nreads=1 +TTGGGCAAAAAACTGATTTCGGGT +>FBgn0000155_roo|coord=3241|strand +|size=27|nreads=1 +TTGGGCAAAAAACTGATTTCGGGTGGA +>FBgn0000155_roo|coord=3241|strand +|size=28|nreads=1 +TTGGGCAAAAAACTGATTTCGGGTGGAT +>FBgn0000155_roo|coord=8639|strand -|size=26|nreads=1 +TTCTGCCAAAGGGCCAGCAAAGCTGA +>FBgn0000155_roo|coord=8639|strand -|size=26|nreads=1 +TTCTGCCAAAGTGCCAGCAAAGCTGA +>FBgn0000155_roo|coord=8655|strand +|size=25|nreads=1 +TTTGGCAGAATGTTCACACATGAAA +>FBgn0000349_copia|coord=653|strand -|size=27|nreads=1 +TTCTCAAGAATCTGACGCGCCGTAATG +>FBgn0000349_copia|coord=657|strand -|size=23|nreads=1 +TTCTCAAGAATCTGACGCGCCGT +>FBgn0000349_copia|coord=670|strand +|size=25|nreads=1 +TTCTTGAGAATTTGGACGCCGTTTA +>FBgn0000349_copia|coord=4614|strand -|size=24|nreads=1 +TTGCAGCAAACCCAATTTGTCTCG +>FBgn0000349_copia|coord=4628|strand +|size=24|nreads=1 +TTTGCTGCAAGACGACCAATCGAA +>FBgn0000349_copia|coord=4628|strand +|size=28|nreads=1 +TTTGCTGCAAGACGACCAATCGAATGCT +>FBgn0000481_Doc|coord=1812|strand -|size=28|nreads=1 +TTTGCATGAACGTCATGAAGTCTTTCAT +>FBgn0000481_Doc|coord=1815|strand -|size=25|nreads=1 +TTTGCATGAACGTCATAAAGTCTTT +>FBgn0000481_Doc|coord=1815|strand -|size=25|nreads=1 +TTTGCATGAACGTCATGAAGTCTTT +>FBgn0000481_Doc|coord=1816|strand -|size=24|nreads=1 +TTTGCATGAAGGTCATGAAGTCTT +>FBgn0000481_Doc|coord=1830|strand +|size=25|nreads=1 +TTCATGCAAAATACTTTGCAAGAGC +>FBgn0000481_Doc|coord=1830|strand +|size=26|nreads=1 +TTCATGCAAAATACTTTGCAAGAGCT +>FBgn0000481_Doc|coord=3531|strand -|size=27|nreads=1 +TTTCTCTAAAGCCAAATTGATGTGTTG +>FBgn0000481_Doc|coord=3532|strand -|size=26|nreads=1 +TTTCTCTAAAGCCAAATTGATGTGTT +>FBgn0000481_Doc|coord=3533|strand -|size=25|nreads=7 +TTTCTCTAAAGCCAAATTGATGTGT +>FBgn0000481_Doc|coord=3534|strand -|size=24|nreads=1 +TTTCTCTAAAGCCAAATTGATGTG +>FBgn0000481_Doc|coord=3535|strand -|size=23|nreads=2 +TTTCTCTAAAGCCAAATTGATGT +>FBgn0000481_Doc|coord=3548|strand +|size=27|nreads=1 +TTTAGAGAAAAACATGGAACCATCGAA +>FBgn0000652_F-element|coord=1546|strand -|size=28|nreads=1 +TTCGAGAAAATTACTTCAGGATTTGTCT +>FBgn0000652_F-element|coord=1546|strand -|size=28|nreads=1 +TTCGGGAAAATTACTTCAGGATTTGTCT +>FBgn0000652_F-element|coord=1547|strand -|size=27|nreads=1 +TTCGGGAAAATTACTTCAGGATTTGTC +>FBgn0000652_F-element|coord=1547|strand -|size=27|nreads=1 +TTTGAGAAAATTACTTCAGGATTTGTC +>FBgn0000652_F-element|coord=1547|strand -|size=27|nreads=74 +TTCGAGAAAATTACTTCAGGATTTGTC +>FBgn0000652_F-element|coord=1548|strand -|size=26|nreads=3 +TTCGAGAAAATTACTTCAGGATTTGT +>FBgn0000652_F-element|coord=1549|strand -|size=25|nreads=1 +TTCGGGAAAATTACTTCAGGATTTG +>FBgn0000652_F-element|coord=1549|strand -|size=25|nreads=22 +TTCGAGAAAATTACTTCAGGATTTG +>FBgn0000652_F-element|coord=1550|strand -|size=24|nreads=2 +TTCGAGAAAATTACTTCAGGATTT +>FBgn0000652_F-element|coord=1551|strand -|size=23|nreads=7 +TTCGAGAAAATTACTTCAGGATT +>FBgn0000652_F-element|coord=1564|strand +|size=23|nreads=2 +TTTTCTCGAAAGCAGCAAGTTTC +>FBgn0000652_F-element|coord=1564|strand +|size=23|nreads=2 +TTTTCTCGAAAGCAGCTAGTTTC +>FBgn0000652_F-element|coord=1564|strand +|size=24|nreads=2 +TTTTCTCGAAAGCAGCAAGTTTCG +>FBgn0000652_F-element|coord=1564|strand +|size=24|nreads=5 +TTTTCTCGAAAGCAGCTAGTTTCG +>FBgn0000652_F-element|coord=1564|strand +|size=25|nreads=1 +TTTTCTCGAAAGCAGCTAGTTTCGC +>FBgn0000652_F-element|coord=3507|strand -|size=27|nreads=1 +TTTCGCGAAATCCAAATTGGTGGGCTG +>FBgn0000652_F-element|coord=3509|strand -|size=25|nreads=6 +TTTCGCGAAATCCAAATTGGTGGGC +>FBgn0000652_F-element|coord=3510|strand -|size=24|nreads=1 +TTTCGCGAAATCCAAATTGGTGGG +>FBgn0000652_F-element|coord=3524|strand +|size=23|nreads=1 +TTTCGCGAAAGCCACGGAACCAT +>FBgn0000652_F-element|coord=3524|strand +|size=24|nreads=1 +TTTCGCGAAAGCCATGGAACCATT +>FBgn0000652_F-element|coord=3524|strand +|size=26|nreads=1 +TTTCGCGAAAGCCATGGAACCATTGA +>FBgn0000652_F-element|coord=3524|strand +|size=27|nreads=1 +TTTCGCGAAAGCCACGGAACCATTGAA +>FBgn0002697_mdg1|coord=4296|strand -|size=27|nreads=1 +TTCTTTGGAAAGAATTTGGGGCTATTT +>FBgn0002697_mdg1|coord=4297|strand -|size=26|nreads=2 +TTCTTTGGAAAGAATTTGGGGCTATT +>FBgn0002697_mdg1|coord=4298|strand -|size=25|nreads=3 +TTCTTTGGAAAGAATTTGGGGCTAT +>FBgn0002697_mdg1|coord=4299|strand -|size=24|nreads=1 +TTCTTTGGAAAGAATTTGGGGCTA +>FBgn0002697_mdg1|coord=4313|strand +|size=25|nreads=1 +TTCCAAAGAATGATGACCCTTGCAT +>FBgn0002697_mdg1|coord=4670|strand -|size=26|nreads=2 +TTTTTACAAAGCCTCGTTAAGTGGCG +>FBgn0002697_mdg1|coord=4671|strand -|size=25|nreads=4 +TTTTTACAAAGCCTCGTTAAGTGGC +>FBgn0002697_mdg1|coord=4672|strand -|size=24|nreads=3 +TTTTTACAAAGCCTCGTTAAGTGG +>FBgn0002697_mdg1|coord=4673|strand -|size=23|nreads=1 +TTTTTACAAAGCCTCGTTAAATG +>FBgn0002697_mdg1|coord=4673|strand -|size=23|nreads=6 +TTTTTACAAAGCCTCGTTAAGTG +>FBgn0002697_mdg1|coord=4686|strand +|size=24|nreads=1 +TTTGTAAAAAGAATGTTCCATTTG +>FBgn0003122_pogo|coord=1305|strand -|size=25|nreads=1 +TTTACCACAATTAACAGCAATGAGC +>FBgn0003122_pogo|coord=1320|strand +|size=25|nreads=1 +TTGTGGTAAATCTACTGTGGAATTT +>FBgn0003122_pogo|coord=1804|strand -|size=25|nreads=1 +TTCCATAGAATTCAAGTTTTGCAAA +>FBgn0003122_pogo|coord=1806|strand -|size=23|nreads=1 +TTCCATAGAATTCAAGTTTTGCA +>FBgn0003122_pogo|coord=1819|strand +|size=26|nreads=3 +TTCTATGGAAGACAAGCTGTTTAATT +>FBgn0003490_springer|coord=1376|strand -|size=24|nreads=1 +TTCCCCACAAGGGACCAGTCCGGT +>FBgn0003490_springer|coord=1390|strand +|size=24|nreads=1 +TTGTGGGGAAACATTGGATGCCGT +>FBgn0003490_springer|coord=4195|strand -|size=23|nreads=1 +TTTTCAACAACGTTGAGTTGTTG +>FBgn0003490_springer|coord=4208|strand +|size=26|nreads=1 +TTGTTGAAGAGCAAGAACCGGAGTCG +>FBgn0003490_springer|coord=5267|strand -|size=27|nreads=7 +TTCTTGTCAAAATCTGGGCGTTTTTGA +>FBgn0003490_springer|coord=5269|strand -|size=25|nreads=1 +TTCTTGTCAAAATCTGGGCGTTTTT +>FBgn0003490_springer|coord=5271|strand -|size=23|nreads=2 +TTCTTGTCAAAATCTGGGCGTTT +>FBgn0003490_springer|coord=5284|strand +|size=24|nreads=6 +TTGACAAGAAAACGAGAGAACGCT +>FBgn0003490_springer|coord=5284|strand +|size=26|nreads=1 +TTGACAAGAAAACGAGAGAACGCTTC +>FBgn0003490_springer|coord=6910|strand -|size=29|nreads=2 +TTTGCTCCAAGTTCTTTTCACTTAAACGG +>FBgn0003490_springer|coord=6929|strand +|size=23|nreads=2 +TTGGAGCAAATCAGGAACTTCGA +>FBgn0003908_R1A1-element|coord=4671|strand -|size=29|nreads=1 +TTTTCGCCAAGGCGCTGCACTCCAAGTCC +>FBgn0003908_R1A1-element|coord=4672|strand -|size=28|nreads=8 +TTTTCGCCAAGGCGCTGCACTCCAAGTC +>FBgn0003908_R1A1-element|coord=4673|strand -|size=27|nreads=1 +TTTTCGCCAAGGCGCTGCACCCCAAGT +>FBgn0003908_R1A1-element|coord=4673|strand -|size=27|nreads=4 +TTTTCGCCAAGGCGCTGCACTCCAAGT +>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=1 +TTTTCGCCAAGGCGCTGCACCCCAAG +>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=1 +TTTTCGTCAAGGCGCTGCACTCCAAG +>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=2 +TTTTCGCCAAGGCGCTGCACTTCAAG +>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=29 +TTTTCGCCAAGGCGCTGCACTCCAAG +>FBgn0003908_R1A1-element|coord=4675|strand -|size=25|nreads=1 +TTTTCGCCAAGGCGCTGCACCCCAA +>FBgn0003908_R1A1-element|coord=4675|strand -|size=25|nreads=1 +TTTTCGCCAAGGCGCTGCACTTCAA +>FBgn0003908_R1A1-element|coord=4675|strand -|size=25|nreads=10 +TTTTCGCCAAGGCGCTGCACTCCAA +>FBgn0003908_R1A1-element|coord=4676|strand -|size=24|nreads=2 +TTTTCGCCAAGGCGCTGCACTTCA +>FBgn0003908_R1A1-element|coord=4676|strand -|size=24|nreads=21 +TTTTCGCCAAGGCGCTGCACTCCA +>FBgn0003908_R1A1-element|coord=4677|strand -|size=23|nreads=12 +TTTTCGCCAAGGCGCTGCACTCC +>FBgn0003908_R1A1-element|coord=4690|strand +|size=23|nreads=8 +TTGGCGAAAACTGGATCTTCGAG +>FBgn0003908_R1A1-element|coord=4690|strand +|size=24|nreads=7 +TTGGCGAAAACTGGATCTTCGAGG +>FBgn0003908_R1A1-element|coord=4690|strand +|size=24|nreads=9 +TTGGCGAAAACTGGATCTTCGAGA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=25|nreads=11 +TTGGCGAAAACTGGATCTTCGAGAG +>FBgn0003908_R1A1-element|coord=4690|strand +|size=25|nreads=12 +TTGGCGAAAACTGGATCTTCGAGGG +>FBgn0003908_R1A1-element|coord=4690|strand +|size=26|nreads=2 +TTGGCGAAAACTGGATCTTCGAGGGA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=26|nreads=6 +TTGGCGAAAACTGGATCTTCGAGAGA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=27|nreads=20 +TTGGCGAAAACTGGATCTTCGAGAGAA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=27|nreads=9 +TTGGCGAAAACTGGATCTTCGAGGGAA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=28|nreads=1 +TTGGCGAAAACTGGATCTTCGAGGGAAT +>FBgn0003908_R1A1-element|coord=4690|strand +|size=28|nreads=4 +TTGGCGAAAACTGGATCTTCGAGAGAAT +>FBgn0004082_Tirant|coord=4197|strand -|size=27|nreads=1 +TTCTAATGAACTCGTAGTGGCCCCCCT +>FBgn0004082_Tirant|coord=4214|strand +|size=25|nreads=1 +TTCATTAGAATGCCGTTTGGCCTCA +>FBgn0005384_3S18|coord=4741|strand -|size=27|nreads=2 +TTGAAGAAAACAGGATTTGCATTGGAA +>FBgn0005384_3S18|coord=4742|strand -|size=26|nreads=2 +TTGAAGAAAACAGGATTTGCATTGGA +>FBgn0005384_3S18|coord=4743|strand -|size=25|nreads=4 +TTGAAGAAAACAGGATTTGCATTGG +>FBgn0005384_3S18|coord=4744|strand -|size=24|nreads=1 +TTGAAGAAAACAGGATTTGCATTG +>FBgn0005384_3S18|coord=4745|strand -|size=23|nreads=2 +TTGAAGAAAACAGGATTTGCATT +>FBgn0005384_3S18|coord=4758|strand +|size=23|nreads=1 +TTTTCTTCAACGAAAGGGCACAA +>FBgn0005384_3S18|coord=4758|strand +|size=28|nreads=1 +TTTTCTTCAACGAAAGGGCACAAGCAAC +>FBgn0005384_3S18|coord=5237|strand -|size=28|nreads=1 +TTTGATCCAAGTATTCGTTTCATATGGA +>FBgn0005384_3S18|coord=5241|strand -|size=24|nreads=1 +TTTGATCCAAGTATTCGTTTCATA +>FBgn0005384_3S18|coord=5241|strand -|size=24|nreads=2 +TTTGATCCAAGTATCCGTTTCATA +>FBgn0005384_3S18|coord=5255|strand +|size=25|nreads=1 +TTGGATCAAAGGCTTTAACGTTTGA +>FBgn0005384_3S18|coord=5255|strand +|size=28|nreads=4 +TTGGATCAAAGGCTTTAACGTTTGAGGA +>FBgn0005673_1360|coord=2038|strand -|size=28|nreads=1 +TTTGTGAAAATTTAAAAATGTGTAGAGA +>FBgn0005673_1360|coord=2042|strand -|size=24|nreads=3 +TTTGTGAAAATTTAAAAATGTGTA +>FBgn0005673_1360|coord=2056|strand +|size=24|nreads=1 +TTTTCACAAAAGTCGAATTGCGAG +>FBgn0005673_1360|coord=2165|strand -|size=23|nreads=2 +TTTTGGAAAATGATACAGAGTAT +>FBgn0005673_1360|coord=2178|strand +|size=24|nreads=1 +TTTTCCAAATTCGTGCAAGACAAT +>FBgn0005673_1360|coord=3195|strand -|size=24|nreads=1 +TTTGCTAGAAGACGATTTTCGGGC +>FBgn0005673_1360|coord=3209|strand +|size=23|nreads=1 +TTCTAGCACAACACGCACACATA +>FBgn0005673_1360|coord=3209|strand +|size=26|nreads=1 +TTCTAGCACAACACGCACACATATAC +>FBgn0005673_1360|coord=3209|strand +|size=27|nreads=1 +TTCTAGCACAACACGCACACATATACG +>FBgn0005773_Bari1|coord=1617|strand -|size=24|nreads=1 +TTGCCTGAAATAGTTCTTATCGCT +>FBgn0005773_Bari1|coord=1631|strand +|size=24|nreads=1 +TTTCAGGCAAATCGGACAACAACA +>FBgn0010103_aurora-element|coord=1431|strand -|size=23|nreads=1 +TTGCTGGGAACGGCTGGCTGCCG +>FBgn0010103_aurora-element|coord=1444|strand +|size=27|nreads=1 +TTCCCAGCAACAGTCTGGAGAGAGGAG +>FBgn0010302_Burdock|coord=3125|strand -|size=26|nreads=1 +TTGAAGAAAAACGATTTCTCTTTAGA +>FBgn0010302_Burdock|coord=3127|strand -|size=24|nreads=1 +TTGAAGAAAAACGATTTCTCTTTA +>FBgn0010302_Burdock|coord=3141|strand +|size=23|nreads=1 +TTTTCTTCAAGGAAAGCGTCGAG +>FBgn0010302_Burdock|coord=3141|strand +|size=24|nreads=1 +TTTTCTTCAAGGAAAGCGTCGAGT +>FBgn0010302_Burdock|coord=3385|strand -|size=26|nreads=1 +TTTCATCGAAAGAAATTGGTATCTTT +>FBgn0010302_Burdock|coord=3401|strand +|size=25|nreads=2 +TTCGATGAAAGACAATGTTCTGCTT +>FBgn0014947_flea|coord=801|strand -|size=27|nreads=4 +TTCTCTAGAATTGCTTGTATTTGGTCG +>FBgn0014947_flea|coord=802|strand -|size=26|nreads=11 +TTCTCTAGAATTGCTTGTATTTGGTC +>FBgn0014947_flea|coord=803|strand -|size=25|nreads=12 +TTCTCTAGAATTGCTTGTATTTGGT +>FBgn0014947_flea|coord=804|strand -|size=24|nreads=2 +TTCTCTAGAATTGCTTGTATTTGG +>FBgn0014947_flea|coord=805|strand -|size=23|nreads=1 +TTCTCTAGAATTGCTTGTATTTG +>FBgn0014947_flea|coord=818|strand +|size=23|nreads=1 +TTCTAGAGAACGAAAGCGAGGAC +>FBgn0014947_flea|coord=1164|strand -|size=28|nreads=2 +TTCTAAGAAAAGTTCTGCTGATCCAATC +>FBgn0014947_flea|coord=1166|strand -|size=26|nreads=2 +TTCTAAGAAAAGTTCTGCTGATCCAA +>FBgn0014947_flea|coord=1167|strand -|size=25|nreads=1 +TTCTAAGAAAAGTTCTGCTGATCCA +>FBgn0014947_flea|coord=1168|strand -|size=24|nreads=1 +TTCTAAGAAAAGTTCTGCTGATCC +>FBgn0014947_flea|coord=1169|strand -|size=23|nreads=1 +TTCTAAGAAAAGTTCTGCTGATC +>FBgn0014947_flea|coord=1182|strand +|size=23|nreads=1 +TTTCTTAGAATCTGAATGTGTCA +>FBgn0014947_flea|coord=1182|strand +|size=25|nreads=2 +TTTCTTAGAATCTGAATGTGTCAGT +>FBgn0014947_flea|coord=2749|strand -|size=26|nreads=1 +TTTAGACCAAATTCTGCAGCTCTCTT +>FBgn0014947_flea|coord=2750|strand -|size=25|nreads=9 +TTTAGACCAAATTCTGCAGCTCTCT +>FBgn0014947_flea|coord=2751|strand -|size=24|nreads=1 +TTTAGACCAAATTCTGCAGCTCTC +>FBgn0014947_flea|coord=2752|strand -|size=23|nreads=2 +TTTAGACCAAATTCTGCAGCTCT +>FBgn0014947_flea|coord=2765|strand +|size=24|nreads=4 +TTGGTCTAAAAATAAAATGGAAGA +>FBgn0014947_flea|coord=2765|strand +|size=25|nreads=1 +TTGGTCTAAAAATAAAATGGAAGAA +>FBgn0014947_flea|coord=2765|strand +|size=26|nreads=1 +TTGGTCTAAAAATAAAATGGAAGAAG +>FBgn0014947_flea|coord=2765|strand +|size=28|nreads=1 +TTGGTCTAAAAATAAAATGGAAGAAGTG +>FBgn0015786_Porto1|coord=1003|strand -|size=25|nreads=1 +TTTCTTCCAATGAATTTAAAGCAGT +>FBgn0015786_Porto1|coord=1018|strand +|size=23|nreads=1 +TTGGAAGAAACACGATATGAACT +>FBgn0015786_Porto1|coord=4472|strand -|size=27|nreads=1 +TTTGTCTCAAGTTTGAGTTTTGGTGGC +>FBgn0015786_Porto1|coord=4473|strand -|size=26|nreads=1 +TTTGTCTCAAGTTTGAGTTTTGGTGG +>FBgn0015786_Porto1|coord=4489|strand +|size=25|nreads=1 +TTGAGACAAATACCGATGACAGAGT +>FBgn0015945_GATE|coord=3140|strand -|size=28|nreads=9 +TTGGAACGAAATTGGCCTGATTAGCGGA +>FBgn0015945_GATE|coord=3141|strand -|size=27|nreads=4 +TTGGAACGAAATTGGCCTGATTAGCGG +>FBgn0015945_GATE|coord=3142|strand -|size=26|nreads=17 +TTGGAACGAAATTGGCCTGATTAGCG +>FBgn0015945_GATE|coord=3143|strand -|size=25|nreads=86 +TTGGAACGAAATTGGCCTGATTAGC +>FBgn0015945_GATE|coord=3144|strand -|size=24|nreads=17 +TTGGAACGAAATTGGCCTGATTAG +>FBgn0015945_GATE|coord=3158|strand +|size=23|nreads=18 +TTCGTTCCAAATGAGCAAGCCGG +>FBgn0015945_GATE|coord=3158|strand +|size=24|nreads=10 +TTCGTTCCAAATGAGCAAGCCGGT +>FBgn0015945_GATE|coord=3158|strand +|size=25|nreads=10 +TTCGTTCCAAATGAGCAAGCCGGTG +>FBgn0015945_GATE|coord=3158|strand +|size=26|nreads=5 +TTCGTTCCAAATGAGCAAGCCGGTGT +>FBgn0015945_GATE|coord=3158|strand +|size=27|nreads=1 +TTCGTTCCAAATGAGCAAGCCGGTGTT +>FBgn0015945_GATE|coord=6230|strand -|size=26|nreads=1 +TTGAAGGAAATCGCGGGAAAGCAGGG +>FBgn0015945_GATE|coord=6231|strand -|size=25|nreads=1 +TTGAAGGAAATCGAGGGAAAGCAGG +>FBgn0015945_GATE|coord=6232|strand -|size=24|nreads=2 +TTGAAGGAAATCGCGGGAAAGCAG +>FBgn0015945_GATE|coord=6246|strand +|size=25|nreads=1 +TTTCCTTCAAGCCGTAAAAGAGTCG +>FBgn0015945_GATE|coord=6246|strand +|size=26|nreads=1 +TTTCCTTCAAGCCGTAAAAGAGTCGG +>FBgn0022937_Circe|coord=2068|strand -|size=28|nreads=1 +TTCGAAAGAAATCTTCGTGACGATGACA +>FBgn0022937_Circe|coord=2069|strand -|size=27|nreads=1 +TTCGAAAGAAATCTTCGTGACGATGAC +>FBgn0022937_Circe|coord=2070|strand -|size=26|nreads=1 +TTCGAAAGAAATCTTCGTGACGATGA +>FBgn0022937_Circe|coord=2071|strand -|size=25|nreads=5 +TTCGAAAGAAATCTTCGTGACGATG +>FBgn0022937_Circe|coord=2086|strand +|size=25|nreads=2 +TTCTTTCGAAGCACCCGGACAAAGC +>FBgn0022937_Circe|coord=2086|strand +|size=26|nreads=1 +TTCTTTCGAAGCACCCGGACAAAGCC +>FBgn0022937_Circe|coord=2086|strand +|size=28|nreads=1 +TTCTTTCGAAGCACCCGGACAAAGCCAA +>FBgn0022937_Circe|coord=3676|strand -|size=25|nreads=1 +TTCGGACAAATGCAAAAGATGGTCT +>FBgn0022937_Circe|coord=3691|strand +|size=26|nreads=1 +TTTGTCCGAAGTAGCCACCCAATTGC +>FBgn0022937_Circe|coord=5416|strand -|size=25|nreads=1 +TTCTTTGAAATTCGTCAGTTCTTGA +>FBgn0022937_Circe|coord=5418|strand -|size=23|nreads=1 +TTCTTTGAAATTCGTCAGTTCTT +>FBgn0022937_Circe|coord=5431|strand +|size=24|nreads=2 +TTTCAAAGAATTCGCTCCAACAGT +>FBgn0022937_Circe|coord=5431|strand +|size=25|nreads=1 +TTTCAAAGAATTCGCTCCAACAGTG +>FBgn0022937_Circe|coord=5431|strand +|size=25|nreads=1 +TTTCAAAGAATTCGCTCCAACATTG +>FBgn0042231_X-element|coord=269|strand -|size=26|nreads=2 +TTCTAGCCAAAACTTGAACCCTGGGA +>FBgn0042231_X-element|coord=285|strand +|size=25|nreads=1 +TTGGCTAGAACCCTGGTGATTTGGT +>FBgn0042231_X-element|coord=3939|strand -|size=26|nreads=2 +TTGATGCCAATATTCCAACGTCTTGC +>FBgn0042231_X-element|coord=3955|strand +|size=24|nreads=2 +TTGGCATCAATAGCAGTAAATCCA +>FBgn0042682_Rt1b|coord=1070|strand -|size=26|nreads=2 +TTCTTGGCGACAGATGCGTAGCTGCC +>FBgn0042682_Rt1b|coord=1071|strand -|size=25|nreads=1 +TTCTTGGAGACAGATGCGTAGCTGC +>FBgn0042682_Rt1b|coord=1071|strand -|size=25|nreads=3 +TTCTTGGCGACAGATGCGTAGCTGC +>FBgn0042682_Rt1b|coord=1072|strand -|size=24|nreads=3 +TTCTTGGCGACAGATGCGTAGCTG +>FBgn0042682_Rt1b|coord=1073|strand -|size=23|nreads=1 +TTCTTGGCGACAGATGCGTAGCT +>FBgn0042682_Rt1b|coord=1086|strand +|size=23|nreads=1 +TTGCCAAGAATGCTAGCACGGGT +>FBgn0042682_Rt1b|coord=2902|strand -|size=28|nreads=1 +TTGGTAACAAGCTTGTAGGCGAGGCCCC +>FBgn0042682_Rt1b|coord=2903|strand -|size=27|nreads=1 +TTGGTAACAAGCTTGTAGGCGAGGCCC +>FBgn0042682_Rt1b|coord=2904|strand -|size=26|nreads=1 +TTGGTAACAAGCTTGTAGGCGAGTCC +>FBgn0042682_Rt1b|coord=2904|strand -|size=26|nreads=2 +TTGGTAACAAGCTTGTAGGCGAGGCC +>FBgn0042682_Rt1b|coord=2905|strand -|size=25|nreads=1 +TTGGTAACAAGCTTGTAGGCGAGGT +>FBgn0042682_Rt1b|coord=2905|strand -|size=25|nreads=2 +TTGGTAACAAGCTTGTAGGCGAGGC +>FBgn0042682_Rt1b|coord=2906|strand -|size=24|nreads=25 +TTGGTAACAAGCTTGTAGGCGAGG +>FBgn0042682_Rt1b|coord=2907|strand -|size=23|nreads=1 +TTGGTAACAAGCTTGGAGGCGAG +>FBgn0042682_Rt1b|coord=2907|strand -|size=23|nreads=15 +TTGGTAACAAGCTTGTAGGCGAG +>FBgn0042682_Rt1b|coord=2920|strand +|size=23|nreads=1 +TTGTTACCAAAAAGCTAAGGAGG +>FBgn0042682_Rt1b|coord=2920|strand +|size=23|nreads=1 +TTGTTACCAACAAGCTAAGGAGG +>FBgn0042682_Rt1b|coord=2920|strand +|size=24|nreads=2 +TTGTTACCAACAAGCTAAGGAGGA +>FBgn0042682_Rt1b|coord=2920|strand +|size=25|nreads=1 +TTGTTACCAAAAAGCTAAGGAGGAG +>FBgn0042682_Rt1b|coord=2920|strand +|size=26|nreads=1 +TTGTTACCAAAAAGCTAAGGAGGAGA +>FBgn0042682_Rt1b|coord=2920|strand +|size=27|nreads=1 +TTGTTACCAAAAAGCTAAGGAGGAGAG +>FBgn0042682_Rt1b|coord=4357|strand -|size=29|nreads=2 +TTGCCTGGAAGCGCCACTCCGCATTAGGC +>FBgn0042682_Rt1b|coord=4359|strand -|size=27|nreads=1 +TTGCCTGGAAGCGCCACTCCGCATTAG +>FBgn0042682_Rt1b|coord=4360|strand -|size=26|nreads=5 +TTGCCTGGAAGCGCCACTCCGCATTA +>FBgn0042682_Rt1b|coord=4361|strand -|size=25|nreads=4 +TTGCCTGGAAGCGCCACTCCGCATA +>FBgn0042682_Rt1b|coord=4361|strand -|size=25|nreads=6 +TTGCCTGGAAGCGCCACTCCGCATT +>FBgn0042682_Rt1b|coord=4362|strand -|size=24|nreads=6 +TTGCCTGGAAGCGCCACTCCGCAT +>FBgn0042682_Rt1b|coord=4363|strand -|size=23|nreads=2 +TTGCCTGGAAGCGCCACTCCGCA +>FBgn0042682_Rt1b|coord=4376|strand +|size=24|nreads=1 +TTCCAGGCAAGAGGCACACGAGTG +>FBgn0042682_Rt1b|coord=4376|strand +|size=26|nreads=1 +TTCCAGGCAAGAGGCACACGAGTGGC +>FBgn0044355_Quasimodo|coord=1370|strand -|size=26|nreads=1 +TTCTTAGCAACTCTTCGTATGGGATT +>FBgn0044355_Quasimodo|coord=1372|strand -|size=24|nreads=1 +TTCTTAGCAACTCTTCGTATGGGA +>FBgn0044355_Quasimodo|coord=1386|strand +|size=24|nreads=1 +TTGCTAAGAAGACTTTACAACACC +>FBgn0063427_invader4|coord=691|strand -|size=26|nreads=15 +TTCCTACGAATCGCTGTATGAACAGT +>FBgn0063427_invader4|coord=707|strand +|size=23|nreads=3 +TTCGTAGGAATTGAGACGTCGGC +>FBgn0063428_invader3|coord=425|strand -|size=25|nreads=1 +TTCTGGGGAAATGGCCTGCAGACGC +>FBgn0063428_invader3|coord=427|strand -|size=23|nreads=1 +TTCTGGGGAAATGGCCTGCAGAC +>FBgn0063428_invader3|coord=440|strand +|size=23|nreads=1 +TTCCCCAGAAACGCGTGGAGATT +>FBgn0063428_invader3|coord=440|strand +|size=27|nreads=1 +TTCCCCAGAAACGCGTGGCGATTCACC +>FBgn0063428_invader3|coord=440|strand +|size=29|nreads=1 +TTCCCCAGAAACGCGTGGAGATTCACCGC +>FBgn0063428_invader3|coord=1923|strand -|size=26|nreads=2 +TTTCGTCCAAGAACTACATTATGACT +>FBgn0063428_invader3|coord=1939|strand +|size=25|nreads=1 +TTGGACGAAATTTCATGGAAGCGTG +>FBgn0063429_invader2|coord=1460|strand -|size=24|nreads=1 +TTTGCTGCAAAGTGCCCCATCTCA +>FBgn0063429_invader2|coord=1474|strand +|size=25|nreads=1 +TTGCAGCAAAGTGCCTAAAAAACAA +>FBgn0063430_invader1|coord=621|strand -|size=26|nreads=1 +TTTCGGACAAGATGTAGTCCACCGTT +>FBgn0063430_invader1|coord=637|strand +|size=27|nreads=4 +TTGTCCGAAAACCAACTGGAAGGCAGC +>FBgn0063430_invader1|coord=1750|strand -|size=26|nreads=3 +TTCTTGACAATTTTTGGAACCGGATT +>FBgn0063430_invader1|coord=1751|strand -|size=25|nreads=2 +TTCTTGACAATTTTTGGAACCGGAT +>FBgn0063430_invader1|coord=1752|strand -|size=24|nreads=3 +TTCTTGACAATTTTTGGAACCGGA +>FBgn0063430_invader1|coord=1766|strand +|size=25|nreads=1 +TTGTCAAGAATTCCATAGGCGTAGT +>FBgn0063430_invader1|coord=1766|strand +|size=27|nreads=1 +TTGTCAAGAATTCCATAGGCGTAGTCG +>FBgn0063430_invader1|coord=2077|strand -|size=25|nreads=3 +TTTTATCGAACCAATAGAACTCGTA +>FBgn0063430_invader1|coord=2079|strand -|size=23|nreads=1 +TTTTATCGAACCAATAGAACTCG +>FBgn0063430_invader1|coord=2092|strand +|size=24|nreads=1 +TTCGATAAAATGTCTAAGTATGTT +>FBgn0063430_invader1|coord=2092|strand +|size=26|nreads=1 +TTCGATAAAATGTCTAAGTATGTTCG +>FBgn0063431_gypsy6|coord=3031|strand -|size=29|nreads=1 +TTTCTAAGAACGCGTTTCTGACTAAGGGT +>FBgn0063431_gypsy6|coord=3050|strand +|size=25|nreads=1 +TTCTTAGAAATGCTGAAGACTAGGA +>FBgn0063433_gypsy4|coord=2735|strand -|size=28|nreads=1 +TTGAGGTCAAGAGTAGTAAAGTACTGTG +>FBgn0063433_gypsy4|coord=2736|strand -|size=27|nreads=5 +TTGAGGTCAAGAGTAGTAAAGTACTGT +>FBgn0063433_gypsy4|coord=2737|strand -|size=26|nreads=11 +TTGAGGTCAAGAGTAGTAAAGTACTG +>FBgn0063433_gypsy4|coord=2738|strand -|size=25|nreads=1 +TTGAGGTCAAGGGTAGTAAAGTACT +>FBgn0063433_gypsy4|coord=2738|strand -|size=25|nreads=5 +TTGAGGTCAAGAGTAGTAAAGTACT +>FBgn0063433_gypsy4|coord=2739|strand -|size=24|nreads=2 +TTGAGGTCAAGGGTAGTAAAGTAC +>FBgn0063433_gypsy4|coord=2739|strand -|size=24|nreads=25 +TTGAGGTCAAGAGTAGTAAAGTAC +>FBgn0063433_gypsy4|coord=2740|strand -|size=23|nreads=1 +TTGAGGTCAAGAGTAGTAAAGTA +>FBgn0063433_gypsy4|coord=2753|strand +|size=24|nreads=2 +TTGACCTCAAATCGGGATTTCATC +>FBgn0063433_gypsy4|coord=2753|strand -|size=27|nreads=1 +TTTGATGAAATCCCGATTTGAGGTCAA +>FBgn0063433_gypsy4|coord=2754|strand -|size=26|nreads=1 +TTTGATGAAATCCCGATTTGAGGTCA +>FBgn0063433_gypsy4|coord=2770|strand +|size=23|nreads=1 +TTTCATCAAATCGAATTAGCGGA +>FBgn0063433_gypsy4|coord=3040|strand -|size=28|nreads=1 +TTTTGAAGAACTTGGATTTTTCTTGAGA +>FBgn0063433_gypsy4|coord=3044|strand -|size=24|nreads=1 +TTTTGAAGAACTTGGATTTTTCTT +>FBgn0063433_gypsy4|coord=3058|strand +|size=24|nreads=1 +TTCTTCAAAAAGAGCGTGGAATAT +>FBgn0063436_gtwin|coord=5250|strand -|size=24|nreads=1 +TTTTAACGAAAACCTCGTCTCCTA +>FBgn0063436_gtwin|coord=5264|strand +|size=27|nreads=1 +TTCGTTAAAAACAACAGAAGGTTAGGA +>FBgn0063440_baggins|coord=3296|strand -|size=26|nreads=3 +TTTTAGCAAAAACGATGTCAAGCTGA +>FBgn0063440_baggins|coord=3298|strand -|size=24|nreads=1 +TTTTAGCAAAAACGATGTCAAGCT +>FBgn0063440_baggins|coord=3312|strand +|size=24|nreads=1 +TTTGCTAAAAACGTTCGAAAAGCT +>FBgn0063507_G2|coord=1906|strand -|size=27|nreads=1 +TTCCGTGGGATCGCCTGAAGCCAAACT +>FBgn0063507_G2|coord=1906|strand -|size=27|nreads=1 +TTTCGTGGGATCGCCTGAAGCCAAACT +>FBgn0063507_G2|coord=1908|strand -|size=25|nreads=3 +TTCCGTGGGATCGCCTGAAGCCAAA +>FBgn0063507_G2|coord=1923|strand +|size=29|nreads=1 +TTCCACGGAACACCCGAGCAATGCCACCG +>FBgn0063534_Doc2-element|coord=327|strand -|size=25|nreads=1 +TTCGTTGCAATGAGAGCCGGCGATC +>FBgn0063534_Doc2-element|coord=342|strand +|size=25|nreads=1 +TTGCAACGAAACAACGCGTACTTCT +>FBgn0063534_Doc2-element|coord=3605|strand -|size=28|nreads=1 +TTTTTGCGAAAGCCAAACTGATGCGATG +>FBgn0063534_Doc2-element|coord=3606|strand -|size=27|nreads=2 +TTTTTGCGAAAGCCAAACTGATGCGAT +>FBgn0063534_Doc2-element|coord=3607|strand -|size=26|nreads=4 +TTTTTGCGAAAGCCAAACTGATGCGA +>FBgn0063534_Doc2-element|coord=3608|strand -|size=25|nreads=7 +TTTTTGCGAAAGCCAAACTGATGCG +>FBgn0063534_Doc2-element|coord=3609|strand -|size=24|nreads=1 +TTTTTGCGAAAGCCAAACTGATGC +>FBgn0063534_Doc2-element|coord=3610|strand -|size=23|nreads=3 +TTTTTGCGAAAGCCAAACTGATG +>FBgn0063534_Doc2-element|coord=3623|strand +|size=23|nreads=1 +TTCGCAAAAATCACGGAACGATC +>FBgn0063534_Doc2-element|coord=3623|strand +|size=26|nreads=1 +TTCGCAAAAATCACGGAACGATCGAA +>FBgn0063594_Cr1a|coord=2037|strand -|size=27|nreads=1 +TTGTTACAAGACATAGATCCAACAGTC +>FBgn0063594_Cr1a|coord=2039|strand -|size=25|nreads=1 +TTGTTACAAAACATAGATCCAACAG +>FBgn0063594_Cr1a|coord=2054|strand +|size=24|nreads=2 +TTTGTAACAAGTCCTGAAAGTGTG +>FBgn0063919_Max-element|coord=3879|strand -|size=29|nreads=1 +TTGCTGAGAAGCGTGTTGAGCGAATCAGG +>FBgn0063919_Max-element|coord=3880|strand -|size=28|nreads=1 +TTGCTGAGAAGCGTGTCGAGCGAATCAG +>FBgn0063919_Max-element|coord=3880|strand -|size=28|nreads=1 +TTGCTGAGAAGCGTGTTGAGCGAATCAG +>FBgn0063919_Max-element|coord=3882|strand -|size=26|nreads=1 +TTGCTGAGAAGCGTGTCGAGCGAATC +>FBgn0063919_Max-element|coord=3883|strand -|size=25|nreads=1 +TTGCTGAGAAGCGTGTCGAGCGAAT +>FBgn0063919_Max-element|coord=3884|strand -|size=24|nreads=1 +TTGCTGAGAAGCGTGTTGAGCGAA +>FBgn0063919_Max-element|coord=3898|strand +|size=23|nreads=1 +TTCTCAGCAAGTTCTGGGAGGTG +>FBgn0063919_Max-element|coord=3898|strand +|size=24|nreads=1 +TTCTCAGCAAGTTCTGGGAGGTGT +>FBgn0063919_Max-element|coord=3898|strand +|size=24|nreads=2 +TTCTCAGCAAGTTCTGGGAGGTGG +>FBgn0063919_Max-element|coord=3898|strand +|size=25|nreads=1 +TTCTCAGCAAGTTCTGGGAGGTGGA +>FBgn0067385_invader6|coord=3007|strand -|size=27|nreads=4 +TTCTAGTCAAAGTCGAAGGACTGCATA +>FBgn0067385_invader6|coord=3008|strand -|size=26|nreads=3 +TTCTAGTCAAAGTCGAAGGACTGCAT +>FBgn0067385_invader6|coord=3009|strand -|size=25|nreads=5 +TTCTAGTCAAAGTCGAAGGACTGCA +>FBgn0067385_invader6|coord=3010|strand -|size=24|nreads=4 +TTCTAGTCAAAGTCGAAGGACTGC +>FBgn0067385_invader6|coord=3011|strand -|size=23|nreads=1 +TTCTAGTCAAAGTCGAAGGACTG +>FBgn0067385_invader6|coord=3024|strand +|size=26|nreads=1 +TTGACTAGAATGACTTAGACTTAGAA +>FBgn0067624_BS3|coord=1011|strand -|size=25|nreads=3 +TTGATGCCAATGTTCCAGCGTTTTG +>FBgn0067624_BS3|coord=1013|strand -|size=23|nreads=3 +TTGATGCCAATGTTCCAACGTCT +>FBgn0067624_BS3|coord=1026|strand +|size=24|nreads=1 +TTGGCATCAATGGTGACAAATCTG +>FBgn0067624_BS3|coord=1026|strand +|size=25|nreads=1 +TTGGCATCAATGGTGACAAATCTGC +>FBgn0067624_BS3|coord=1026|strand +|size=26|nreads=1 +TTGGCATCAATGGTGACAAATCAGCG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_2.fa Tue Jan 07 11:59:34 2020 +0000 @@ -0,0 +1,416 @@ +>FBgn0000004_17.6|coord=5844|strand -|size=21|nreads=1 +TTTTCGTCAAGTGTGCTAAAT +>FBgn0000004_17.6|coord=5855|strand +|size=23|nreads=1 +TTGACGAAAATGATCGAGTGGAT +>FBgn0000005_297|coord=1334|strand -|size=23|nreads=1 +TTTTGCGCAATGGTAATTAAGGA +>FBgn0000005_297|coord=1347|strand +|size=21|nreads=1 +TTGCACAAAATGAGGGAATTT +>FBgn0000007_1731|coord=4545|strand -|size=20|nreads=1 +TTGAGAGCAAAGGCCGAATG +>FBgn0000007_1731|coord=4555|strand +|size=24|nreads=1 +TTGCTCTCAATGCGCTGAGTTTGG +>FBgn0000155_roo|coord=2682|strand -|size=20|nreads=2 +TTTTTACCAAACGGATGCCT +>FBgn0000155_roo|coord=2692|strand +|size=24|nreads=1 +TTGGTAAAAAATGTATAAGTGAGC +>FBgn0000155_roo|coord=2692|strand +|size=27|nreads=1 +TTGGTAAAAAATGTATAAGTGAGCAGC +>FBgn0000155_roo|coord=3225|strand -|size=26|nreads=1 +TTTTGCCCAAGGAGACCGTCTATTTT +>FBgn0000155_roo|coord=3226|strand -|size=25|nreads=1 +TTTTGCCCAAGGAGACCGTCTATTT +>FBgn0000155_roo|coord=3227|strand -|size=24|nreads=2 +TTTTGCCCAAGGAGACCGTCTATT +>FBgn0000155_roo|coord=3228|strand -|size=23|nreads=1 +TTTTGCCCAAGGAGACCGTCTAT +>FBgn0000155_roo|coord=3229|strand -|size=22|nreads=2 +TTTTGCCCAAGGAGACCGTCTA +>FBgn0000155_roo|coord=3230|strand -|size=21|nreads=1 +TTTTGCCCAAGGAGACCGTCT +>FBgn0000155_roo|coord=3231|strand -|size=20|nreads=2 +TTTTGCCCAAGGAGACCGTC +>FBgn0000155_roo|coord=3241|strand +|size=20|nreads=1 +TTGGGCAAAAAACTGATTTC +>FBgn0000155_roo|coord=3241|strand +|size=24|nreads=1 +TTGGGCAAAAAACTGATTTCGGGT +>FBgn0000155_roo|coord=3241|strand +|size=27|nreads=1 +TTGGGCAAAAAACTGATTTCGGGTGGA +>FBgn0000155_roo|coord=3241|strand +|size=28|nreads=1 +TTGGGCAAAAAACTGATTTCGGGTGGAT +>FBgn0000155_roo|coord=8644|strand -|size=21|nreads=1 +TTCTGCCAAAGGGCCAGCAAG +>FBgn0000155_roo|coord=8645|strand -|size=20|nreads=1 +TTCTGCCAAAGGGCCAGCAA +>FBgn0000155_roo|coord=8655|strand +|size=25|nreads=1 +TTTGGCAGAATGTTCACACATGAAA +>FBgn0000349_copia|coord=658|strand -|size=22|nreads=1 +TTCTCAAGAATCTGACGCGCCG +>FBgn0000349_copia|coord=670|strand +|size=25|nreads=1 +TTCTTGAGAATTTGGACGCCGTTTA +>FBgn0000349_copia|coord=4614|strand -|size=24|nreads=1 +TTGCAGCAAACCCAATTTGTCTCG +>FBgn0000349_copia|coord=4628|strand +|size=20|nreads=1 +TTTGCTGCAAGACGACCAAT +>FBgn0000652_F-element|coord=1546|strand -|size=28|nreads=1 +TTCGAGAAAATTACTTCAGGATTTGTCT +>FBgn0000652_F-element|coord=1546|strand -|size=28|nreads=1 +TTCGGGAAAATTACTTCAGGATTTGTCT +>FBgn0000652_F-element|coord=1547|strand -|size=27|nreads=1 +TTCGGGAAAATTACTTCAGGATTTGTC +>FBgn0000652_F-element|coord=1547|strand -|size=27|nreads=1 +TTTGAGAAAATTACTTCAGGATTTGTC +>FBgn0000652_F-element|coord=1547|strand -|size=27|nreads=74 +TTCGAGAAAATTACTTCAGGATTTGTC +>FBgn0000652_F-element|coord=1548|strand -|size=26|nreads=3 +TTCGAGAAAATTACTTCAGGATTTGT +>FBgn0000652_F-element|coord=1549|strand -|size=25|nreads=1 +TTCGGGAAAATTACTTCAGGATTTG +>FBgn0000652_F-element|coord=1549|strand -|size=25|nreads=22 +TTCGAGAAAATTACTTCAGGATTTG +>FBgn0000652_F-element|coord=1550|strand -|size=24|nreads=2 +TTCGAGAAAATTACTTCAGGATTT +>FBgn0000652_F-element|coord=1551|strand -|size=23|nreads=7 +TTCGAGAAAATTACTTCAGGATT +>FBgn0000652_F-element|coord=1554|strand -|size=20|nreads=1 +TTCGAGAAAATTACTTCAGG +>FBgn0000652_F-element|coord=1564|strand +|size=20|nreads=1 +TTTTCTCGAAAGCAGCTAGT +>FBgn0000652_F-element|coord=1564|strand +|size=20|nreads=2 +TTTTCTCGAAAGCAGCAAGT +>FBgn0000652_F-element|coord=1564|strand +|size=23|nreads=2 +TTTTCTCGAAAGCAGCAAGTTTC +>FBgn0000652_F-element|coord=1564|strand +|size=23|nreads=2 +TTTTCTCGAAAGCAGCTAGTTTC +>FBgn0000652_F-element|coord=1564|strand +|size=24|nreads=2 +TTTTCTCGAAAGCAGCAAGTTTCG +>FBgn0000652_F-element|coord=1564|strand +|size=24|nreads=5 +TTTTCTCGAAAGCAGCTAGTTTCG +>FBgn0000652_F-element|coord=1564|strand +|size=25|nreads=1 +TTTTCTCGAAAGCAGCTAGTTTCGC +>FBgn0000652_F-element|coord=2231|strand -|size=27|nreads=1 +TTGGAAGAAATCCAGGAATTGAGCTTC +>FBgn0000652_F-element|coord=2233|strand -|size=25|nreads=5 +TTGGAAGAAATCCAGGAATTGAGCT +>FBgn0000652_F-element|coord=2248|strand +|size=20|nreads=1 +TTTCTTCCAAGCACTAGGGC +>FBgn0000652_F-element|coord=2248|strand +|size=21|nreads=1 +TTTCTTCCAAGCACTAGGGCC +>FBgn0000652_F-element|coord=2471|strand -|size=21|nreads=2 +TTTAACCAAACTGCGGGAAAT +>FBgn0000652_F-element|coord=2472|strand -|size=20|nreads=1 +TTTAACCAAACTGCGGGAAA +>FBgn0000652_F-element|coord=2482|strand +|size=23|nreads=2 +TTTGGTTAAAGCTGAATGTCTGC +>FBgn0000652_F-element|coord=2482|strand +|size=24|nreads=2 +TTTGGTTAAAGCTGAATGTCTGCC +>FBgn0000652_F-element|coord=2482|strand +|size=26|nreads=3 +TTTGGTTAAAGCTGAATGTCTGCCGG +>FBgn0000652_F-element|coord=2482|strand +|size=27|nreads=1 +TTTGGTTAAAGCTGAATGTCTGCCGGA +>FBgn0000652_F-element|coord=3507|strand -|size=27|nreads=1 +TTTCGCGAAATCCAAATTGGTGGGCTG +>FBgn0000652_F-element|coord=3509|strand -|size=25|nreads=6 +TTTCGCGAAATCCAAATTGGTGGGC +>FBgn0000652_F-element|coord=3510|strand -|size=24|nreads=1 +TTTCGCGAAATCCAAATTGGTGGG +>FBgn0000652_F-element|coord=3513|strand -|size=21|nreads=3 +TTTCGCGAAATCCAAATTGGT +>FBgn0000652_F-element|coord=3524|strand +|size=20|nreads=2 +TTTCGCGAAAGCCATGGAAC +>FBgn0000652_F-element|coord=3524|strand +|size=21|nreads=2 +TTTCGCGAAAGCCACGGAACC +>FBgn0000652_F-element|coord=3524|strand +|size=22|nreads=1 +TTTCGCGAAAGCCACGGAACCA +>FBgn0000652_F-element|coord=3524|strand +|size=23|nreads=1 +TTTCGCGAAAGCCACGGAACCAT +>FBgn0000652_F-element|coord=3524|strand +|size=24|nreads=1 +TTTCGCGAAAGCCATGGAACCATT +>FBgn0000652_F-element|coord=3524|strand +|size=26|nreads=1 +TTTCGCGAAAGCCATGGAACCATTGA +>FBgn0000652_F-element|coord=3524|strand +|size=27|nreads=1 +TTTCGCGAAAGCCACGGAACCATTGAA +>FBgn0002697_mdg1|coord=4301|strand -|size=22|nreads=1 +TTCTTTGGAAAGAATTTGGGGC +>FBgn0002697_mdg1|coord=4302|strand -|size=21|nreads=1 +TTCTTTGGAAAGAATTTGGGG +>FBgn0002697_mdg1|coord=4303|strand -|size=20|nreads=1 +TTCTTTGGAAAGAATTTGGG +>FBgn0002697_mdg1|coord=4313|strand +|size=25|nreads=1 +TTCCAAAGAATGATGACCCTTGCAT +>FBgn0003007_opus|coord=5540|strand -|size=28|nreads=1 +TTTCTAGGAACGTAGAATGGAATCTCTC +>FBgn0003007_opus|coord=5540|strand -|size=28|nreads=1 +TTTCTAGGAACGTAGAGTGGAATCTCTC +>FBgn0003007_opus|coord=5542|strand -|size=26|nreads=1 +TTTCTAGGAACGTAGAATGGAATCTC +>FBgn0003007_opus|coord=5542|strand -|size=26|nreads=2 +TTTCTAGGAACGTAGAGTGGAATCTC +>FBgn0003007_opus|coord=5543|strand -|size=25|nreads=1 +TTTCTAGGAACGTAGAGTGGAATCT +>FBgn0003007_opus|coord=5544|strand -|size=24|nreads=7 +TTTCTAGGAACGTAGAGTGGAATC +>FBgn0003007_opus|coord=5558|strand +|size=21|nreads=1 +TTCCTAGAAATTTATCGTTGC +>FBgn0003122_pogo|coord=1804|strand -|size=25|nreads=1 +TTCCATAGAATTCAAGTTTTGCAAA +>FBgn0003122_pogo|coord=1806|strand -|size=23|nreads=1 +TTCCATAGAATTCAAGTTTTGCA +>FBgn0003122_pogo|coord=1819|strand +|size=22|nreads=1 +TTCTATGGAAGACAAGCTGTTT +>FBgn0003908_R1A1-element|coord=4671|strand -|size=29|nreads=1 +TTTTCGCCAAGGCGCTGCACTCCAAGTCC +>FBgn0003908_R1A1-element|coord=4672|strand -|size=28|nreads=8 +TTTTCGCCAAGGCGCTGCACTCCAAGTC +>FBgn0003908_R1A1-element|coord=4673|strand -|size=27|nreads=1 +TTTTCGCCAAGGCGCTGCACCCCAAGT +>FBgn0003908_R1A1-element|coord=4673|strand -|size=27|nreads=4 +TTTTCGCCAAGGCGCTGCACTCCAAGT +>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=1 +TTTTCGCCAAGGCGCTGCACCCCAAG +>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=1 +TTTTCGTCAAGGCGCTGCACTCCAAG +>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=2 +TTTTCGCCAAGGCGCTGCACTTCAAG +>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=29 +TTTTCGCCAAGGCGCTGCACTCCAAG +>FBgn0003908_R1A1-element|coord=4675|strand -|size=25|nreads=1 +TTTTCGCCAAGGCGCTGCACCCCAA +>FBgn0003908_R1A1-element|coord=4675|strand -|size=25|nreads=1 +TTTTCGCCAAGGCGCTGCACTTCAA +>FBgn0003908_R1A1-element|coord=4675|strand -|size=25|nreads=10 +TTTTCGCCAAGGCGCTGCACTCCAA +>FBgn0003908_R1A1-element|coord=4676|strand -|size=24|nreads=2 +TTTTCGCCAAGGCGCTGCACTTCA +>FBgn0003908_R1A1-element|coord=4676|strand -|size=24|nreads=21 +TTTTCGCCAAGGCGCTGCACTCCA +>FBgn0003908_R1A1-element|coord=4677|strand -|size=23|nreads=12 +TTTTCGCCAAGGCGCTGCACTCC +>FBgn0003908_R1A1-element|coord=4678|strand -|size=22|nreads=1 +TTTTCGCCAAGGCGCTGCACTT +>FBgn0003908_R1A1-element|coord=4678|strand -|size=22|nreads=18 +TTTTCGCCAAGGCGCTGCACTC +>FBgn0003908_R1A1-element|coord=4679|strand -|size=21|nreads=1 +TTTTCGCCAAGGCGCTGCACC +>FBgn0003908_R1A1-element|coord=4679|strand -|size=21|nreads=6 +TTTTCGCCAAGGCGCTGCACT +>FBgn0003908_R1A1-element|coord=4680|strand -|size=20|nreads=4 +TTTTCGCCAAGGCGCTGCAC +>FBgn0003908_R1A1-element|coord=4690|strand +|size=20|nreads=2 +TTGGCGAAAACTGGATCTTC +>FBgn0003908_R1A1-element|coord=4690|strand +|size=21|nreads=6 +TTGGCGAAAACTGGATCTTCG +>FBgn0003908_R1A1-element|coord=4690|strand +|size=22|nreads=1 +TTGGCGAAAACTAGATCTTCGA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=22|nreads=8 +TTGGCGAAAACTGGATCTTCGA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=23|nreads=8 +TTGGCGAAAACTGGATCTTCGAG +>FBgn0003908_R1A1-element|coord=4690|strand +|size=24|nreads=7 +TTGGCGAAAACTGGATCTTCGAGG +>FBgn0003908_R1A1-element|coord=4690|strand +|size=24|nreads=9 +TTGGCGAAAACTGGATCTTCGAGA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=25|nreads=11 +TTGGCGAAAACTGGATCTTCGAGAG +>FBgn0003908_R1A1-element|coord=4690|strand +|size=25|nreads=12 +TTGGCGAAAACTGGATCTTCGAGGG +>FBgn0003908_R1A1-element|coord=4690|strand +|size=26|nreads=2 +TTGGCGAAAACTGGATCTTCGAGGGA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=26|nreads=6 +TTGGCGAAAACTGGATCTTCGAGAGA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=27|nreads=20 +TTGGCGAAAACTGGATCTTCGAGAGAA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=27|nreads=9 +TTGGCGAAAACTGGATCTTCGAGGGAA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=28|nreads=1 +TTGGCGAAAACTGGATCTTCGAGGGAAT +>FBgn0003908_R1A1-element|coord=4690|strand +|size=28|nreads=4 +TTGGCGAAAACTGGATCTTCGAGAGAAT +>FBgn0005673_1360|coord=773|strand -|size=22|nreads=1 +TTTTCGCAATCATTCCATCCTG +>FBgn0005673_1360|coord=785|strand +|size=26|nreads=6 +TTTGCGAAAAATTGTTTGCTCAGAGC +>FBgn0005673_1360|coord=3197|strand -|size=22|nreads=1 +TTTGCTAGAAGACGATTTTCGG +>FBgn0005673_1360|coord=3209|strand +|size=23|nreads=1 +TTCTAGCACAACACGCACACATA +>FBgn0005673_1360|coord=3209|strand +|size=26|nreads=1 +TTCTAGCACAACACGCACACATATAC +>FBgn0005673_1360|coord=3209|strand +|size=27|nreads=1 +TTCTAGCACAACACGCACACATATACG +>FBgn0010302_Burdock|coord=3390|strand -|size=21|nreads=1 +TTTCATCGAAAGAAATTGGTA +>FBgn0010302_Burdock|coord=3401|strand +|size=25|nreads=2 +TTCGATGAAAGACAATGTTCTGCTT +>FBgn0014947_flea|coord=801|strand -|size=27|nreads=4 +TTCTCTAGAATTGCTTGTATTTGGTCG +>FBgn0014947_flea|coord=802|strand -|size=26|nreads=11 +TTCTCTAGAATTGCTTGTATTTGGTC +>FBgn0014947_flea|coord=803|strand -|size=25|nreads=12 +TTCTCTAGAATTGCTTGTATTTGGT +>FBgn0014947_flea|coord=804|strand -|size=24|nreads=2 +TTCTCTAGAATTGCTTGTATTTGG +>FBgn0014947_flea|coord=805|strand -|size=23|nreads=1 +TTCTCTAGAATTGCTTGTATTTG +>FBgn0014947_flea|coord=818|strand +|size=22|nreads=1 +TTCTAGAGAACGAAAGCGAGGA +>FBgn0014947_flea|coord=1164|strand -|size=28|nreads=2 +TTCTAAGAAAAGTTCTGCTGATCCAATC +>FBgn0014947_flea|coord=1166|strand -|size=26|nreads=2 +TTCTAAGAAAAGTTCTGCTGATCCAA +>FBgn0014947_flea|coord=1167|strand -|size=25|nreads=1 +TTCTAAGAAAAGTTCTGCTGATCCA +>FBgn0014947_flea|coord=1168|strand -|size=24|nreads=1 +TTCTAAGAAAAGTTCTGCTGATCC +>FBgn0014947_flea|coord=1169|strand -|size=23|nreads=1 +TTCTAAGAAAAGTTCTGCTGATC +>FBgn0014947_flea|coord=1182|strand +|size=22|nreads=1 +TTTCTTAGAATCTGAATGTGTC +>FBgn0014947_flea|coord=2754|strand -|size=21|nreads=1 +TTTAGACCAAATTCTGCAGCT +>FBgn0014947_flea|coord=2765|strand +|size=24|nreads=4 +TTGGTCTAAAAATAAAATGGAAGA +>FBgn0014947_flea|coord=2765|strand +|size=25|nreads=1 +TTGGTCTAAAAATAAAATGGAAGAA +>FBgn0014947_flea|coord=2765|strand +|size=26|nreads=1 +TTGGTCTAAAAATAAAATGGAAGAAG +>FBgn0014947_flea|coord=2765|strand +|size=28|nreads=1 +TTGGTCTAAAAATAAAATGGAAGAAGTG +>FBgn0015945_GATE|coord=3140|strand -|size=28|nreads=9 +TTGGAACGAAATTGGCCTGATTAGCGGA +>FBgn0015945_GATE|coord=3141|strand -|size=27|nreads=4 +TTGGAACGAAATTGGCCTGATTAGCGG +>FBgn0015945_GATE|coord=3142|strand -|size=26|nreads=17 +TTGGAACGAAATTGGCCTGATTAGCG +>FBgn0015945_GATE|coord=3143|strand -|size=25|nreads=86 +TTGGAACGAAATTGGCCTGATTAGC +>FBgn0015945_GATE|coord=3144|strand -|size=24|nreads=17 +TTGGAACGAAATTGGCCTGATTAG +>FBgn0015945_GATE|coord=3158|strand +|size=20|nreads=3 +TTCGTTCCAAATGAGCAAGC +>FBgn0015945_GATE|coord=3158|strand +|size=21|nreads=1 +TTCGTTCCAAATGAGCAAGCC +>FBgn0015945_GATE|coord=3158|strand +|size=22|nreads=2 +TTCGTTCCAAATGAGCAAGCCG +>FBgn0015945_GATE|coord=6234|strand -|size=22|nreads=1 +TTGAAGGAAATCGCGGGAAAGC +>FBgn0015945_GATE|coord=6246|strand +|size=25|nreads=1 +TTTCCTTCAAGCCGTAAAAGAGTCG +>FBgn0015945_GATE|coord=6246|strand +|size=26|nreads=1 +TTTCCTTCAAGCCGTAAAAGAGTCGG +>FBgn0042682_Rt1b|coord=1075|strand -|size=21|nreads=1 +TTCTTGGCGACAGATGCGTAG +>FBgn0042682_Rt1b|coord=1076|strand -|size=20|nreads=1 +TTCTTGGCGACAGATGCGTA +>FBgn0042682_Rt1b|coord=1086|strand +|size=23|nreads=1 +TTGCCAAGAATGCTAGCACGGGT +>FBgn0042682_Rt1b|coord=2902|strand -|size=28|nreads=1 +TTGGTAACAAGCTTGTAGGCGAGGCCCC +>FBgn0042682_Rt1b|coord=2903|strand -|size=27|nreads=1 +TTGGTAACAAGCTTGTAGGCGAGGCCC +>FBgn0042682_Rt1b|coord=2904|strand -|size=26|nreads=1 +TTGGTAACAAGCTTGTAGGCGAGTCC +>FBgn0042682_Rt1b|coord=2904|strand -|size=26|nreads=2 +TTGGTAACAAGCTTGTAGGCGAGGCC +>FBgn0042682_Rt1b|coord=2905|strand -|size=25|nreads=1 +TTGGTAACAAGCTTGTAGGCGAGGT +>FBgn0042682_Rt1b|coord=2905|strand -|size=25|nreads=2 +TTGGTAACAAGCTTGTAGGCGAGGC +>FBgn0042682_Rt1b|coord=2906|strand -|size=24|nreads=25 +TTGGTAACAAGCTTGTAGGCGAGG +>FBgn0042682_Rt1b|coord=2907|strand -|size=23|nreads=1 +TTGGTAACAAGCTTGGAGGCGAG +>FBgn0042682_Rt1b|coord=2907|strand -|size=23|nreads=15 +TTGGTAACAAGCTTGTAGGCGAG +>FBgn0042682_Rt1b|coord=2908|strand -|size=22|nreads=1 +TTGGTAACAAGCTTGTAGGCGA +>FBgn0042682_Rt1b|coord=2909|strand -|size=21|nreads=6 +TTGGTAACAAGCTTGTAGGCG +>FBgn0042682_Rt1b|coord=2920|strand +|size=22|nreads=1 +TTGTTACCAAAAAGCTAAGGAG +>FBgn0042682_Rt1b|coord=2920|strand +|size=23|nreads=1 +TTGTTACCAAAAAGCTAAGGAGG +>FBgn0042682_Rt1b|coord=2920|strand +|size=23|nreads=1 +TTGTTACCAACAAGCTAAGGAGG +>FBgn0042682_Rt1b|coord=2920|strand +|size=24|nreads=2 +TTGTTACCAACAAGCTAAGGAGGA +>FBgn0042682_Rt1b|coord=2920|strand +|size=25|nreads=1 +TTGTTACCAAAAAGCTAAGGAGGAG +>FBgn0042682_Rt1b|coord=2920|strand +|size=26|nreads=1 +TTGTTACCAAAAAGCTAAGGAGGAGA +>FBgn0042682_Rt1b|coord=2920|strand +|size=27|nreads=1 +TTGTTACCAAAAAGCTAAGGAGGAGAG +>FBgn0042682_Rt1b|coord=4364|strand -|size=22|nreads=1 +TTGCCTGGAAGCGCCACTCCGC +>FBgn0042682_Rt1b|coord=4365|strand -|size=21|nreads=1 +TTGCCTGGAAGCGCCACTCCG +>FBgn0042682_Rt1b|coord=4366|strand -|size=20|nreads=4 +TTGCCTGGAAGCGCCACTCC +>FBgn0042682_Rt1b|coord=4376|strand +|size=24|nreads=1 +TTCCAGGCAAGAGGCACACGAGTG +>FBgn0042682_Rt1b|coord=4376|strand +|size=26|nreads=1 +TTCCAGGCAAGAGGCACACGAGTGGC +>FBgn0062343_Dm88|coord=4210|strand -|size=21|nreads=1 +TTGGTTAGAACATCTGCCATC +>FBgn0062343_Dm88|coord=4221|strand +|size=24|nreads=1 +TTCTAACCAAGAATTTGAATAGAT +>FBgn0063427_invader4|coord=691|strand -|size=26|nreads=15 +TTCCTACGAATCGCTGTATGAACAGT +>FBgn0063427_invader4|coord=707|strand +|size=22|nreads=2 +TTCGTAGGAATGGAGACGTCGG +>FBgn0063428_invader3|coord=425|strand -|size=25|nreads=1 +TTCTGGGGAAATGGCCTGCAGACGC +>FBgn0063428_invader3|coord=427|strand -|size=23|nreads=1 +TTCTGGGGAAATGGCCTGCAGAC +>FBgn0063428_invader3|coord=440|strand +|size=22|nreads=2 +TTCCCCAGAAACGCGTGGCGAT +>FBgn0063430_invader1|coord=2082|strand -|size=20|nreads=1 +TTTTATCGAACCAATAGAAC +>FBgn0063430_invader1|coord=2092|strand +|size=24|nreads=1 +TTCGATAAAATGTCTAAGTATGTT +>FBgn0063430_invader1|coord=2092|strand +|size=26|nreads=1 +TTCGATAAAATGTCTAAGTATGTTCG +>FBgn0063433_gypsy4|coord=3040|strand -|size=28|nreads=1 +TTTTGAAGAACTTGGATTTTTCTTGAGA +>FBgn0063433_gypsy4|coord=3044|strand -|size=24|nreads=1 +TTTTGAAGAACTTGGATTTTTCTT +>FBgn0063433_gypsy4|coord=3058|strand +|size=22|nreads=1 +TTCTTCAAAAAGAGCGTGGAAT +>FBgn0063440_baggins|coord=5154|strand -|size=26|nreads=1 +TTTTGTGCAAATGGCTGTGAAGTCGG +>FBgn0063440_baggins|coord=5170|strand +|size=21|nreads=1 +TTGCACAAAATTGGCATTGCA +>FBgn0063919_Max-element|coord=3887|strand -|size=21|nreads=2 +TTGCTGAGAAGCGTGTTGAGC +>FBgn0063919_Max-element|coord=3898|strand +|size=23|nreads=1 +TTCTCAGCAAGTTCTGGGAGGTG +>FBgn0063919_Max-element|coord=3898|strand +|size=24|nreads=1 +TTCTCAGCAAGTTCTGGGAGGTGT +>FBgn0063919_Max-element|coord=3898|strand +|size=24|nreads=2 +TTCTCAGCAAGTTCTGGGAGGTGG +>FBgn0063919_Max-element|coord=3898|strand +|size=25|nreads=1 +TTCTCAGCAAGTTCTGGGAGGTGGA +>FBgn0067385_invader6|coord=3007|strand -|size=27|nreads=4 +TTCTAGTCAAAGTCGAAGGACTGCATA +>FBgn0067385_invader6|coord=3008|strand -|size=26|nreads=3 +TTCTAGTCAAAGTCGAAGGACTGCAT +>FBgn0067385_invader6|coord=3009|strand -|size=25|nreads=5 +TTCTAGTCAAAGTCGAAGGACTGCA +>FBgn0067385_invader6|coord=3010|strand -|size=24|nreads=4 +TTCTAGTCAAAGTCGAAGGACTGC +>FBgn0067385_invader6|coord=3011|strand -|size=23|nreads=1 +TTCTAGTCAAAGTCGAAGGACTG +>FBgn0067385_invader6|coord=3014|strand -|size=20|nreads=1 +TTCTAGTCAAAGTCGAAGGA +>FBgn0067385_invader6|coord=3024|strand +|size=21|nreads=1 +TTGACTAGAATGACTTAGACT +>FBgn0067385_invader6|coord=3024|strand +|size=26|nreads=1 +TTGACTAGAATGACTTAGACTTAGAA +>FBgn0067624_BS3|coord=1016|strand -|size=20|nreads=1 +TTGATGCCAATGTTCCAACG +>FBgn0067624_BS3|coord=1026|strand +|size=24|nreads=1 +TTGGCATCAATGGTGACAAATCTG +>FBgn0067624_BS3|coord=1026|strand +|size=25|nreads=1 +TTGGCATCAATGGTGACAAATCTGC +>FBgn0067624_BS3|coord=1026|strand +|size=26|nreads=1 +TTGGCATCAATGGTGACAAATCAGCG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_3.fa Tue Jan 07 11:59:34 2020 +0000 @@ -0,0 +1,416 @@ +>FBgn0000004_17.6|coord=5844|strand -|size=21|nreads=1 +TTTTCGTCAAGTGTGCTAAAT +>FBgn0000004_17.6|coord=5855|strand +|size=23|nreads=1 +TTGACGAAAATGATCGAGTGGAT +>FBgn0000005_297|coord=1334|strand -|size=23|nreads=1 +TTTTGCGCAATGGTAATTAAGGA +>FBgn0000005_297|coord=1347|strand +|size=21|nreads=1 +TTGCACAAAATGAGGGAATTT +>FBgn0000007_1731|coord=4545|strand -|size=20|nreads=1 +TTGAGAGCAAAGGCCGAATG +>FBgn0000007_1731|coord=4555|strand +|size=24|nreads=1 +TTGCTCTCAATGCGCTGAGTTTGG +>FBgn0000155_roo|coord=2682|strand -|size=20|nreads=2 +TTTTTACCAAACGGATGCCT +>FBgn0000155_roo|coord=2692|strand +|size=24|nreads=1 +TTGGTAAAAAATGTATAAGTGAGC +>FBgn0000155_roo|coord=2692|strand +|size=27|nreads=1 +TTGGTAAAAAATGTATAAGTGAGCAGC +>FBgn0000155_roo|coord=3225|strand -|size=26|nreads=1 +TTTTGCCCAAGGAGACCGTCTATTTT +>FBgn0000155_roo|coord=3226|strand -|size=25|nreads=1 +TTTTGCCCAAGGAGACCGTCTATTT +>FBgn0000155_roo|coord=3227|strand -|size=24|nreads=2 +TTTTGCCCAAGGAGACCGTCTATT +>FBgn0000155_roo|coord=3228|strand -|size=23|nreads=1 +TTTTGCCCAAGGAGACCGTCTAT +>FBgn0000155_roo|coord=3229|strand -|size=22|nreads=2 +TTTTGCCCAAGGAGACCGTCTA +>FBgn0000155_roo|coord=3230|strand -|size=21|nreads=1 +TTTTGCCCAAGGAGACCGTCT +>FBgn0000155_roo|coord=3231|strand -|size=20|nreads=2 +TTTTGCCCAAGGAGACCGTC +>FBgn0000155_roo|coord=3241|strand +|size=20|nreads=1 +TTGGGCAAAAAACTGATTTC +>FBgn0000155_roo|coord=3241|strand +|size=24|nreads=1 +TTGGGCAAAAAACTGATTTCGGGT +>FBgn0000155_roo|coord=3241|strand +|size=27|nreads=1 +TTGGGCAAAAAACTGATTTCGGGTGGA +>FBgn0000155_roo|coord=3241|strand +|size=28|nreads=1 +TTGGGCAAAAAACTGATTTCGGGTGGAT +>FBgn0000155_roo|coord=8644|strand -|size=21|nreads=1 +TTCTGCCAAAGGGCCAGCAAG +>FBgn0000155_roo|coord=8645|strand -|size=20|nreads=1 +TTCTGCCAAAGGGCCAGCAA +>FBgn0000155_roo|coord=8655|strand +|size=25|nreads=1 +TTTGGCAGAATGTTCACACATGAAA +>FBgn0000349_copia|coord=658|strand -|size=22|nreads=1 +TTCTCAAGAATCTGACGCGCCG +>FBgn0000349_copia|coord=670|strand +|size=25|nreads=1 +TTCTTGAGAATTTGGACGCCGTTTA +>FBgn0000349_copia|coord=4614|strand -|size=24|nreads=1 +TTGCAGCAAACCCAATTTGTCTCG +>FBgn0000349_copia|coord=4628|strand +|size=20|nreads=1 +TTTGCTGCAAGACGACCAAT +>FBgn0000652_F-element|coord=1546|strand -|size=28|nreads=1 +TTCGAGAAAATTACTTCAGGATTTGTCT +>FBgn0000652_F-element|coord=1546|strand -|size=28|nreads=1 +TTCGGGAAAATTACTTCAGGATTTGTCT +>FBgn0000652_F-element|coord=1547|strand -|size=27|nreads=1 +TTCGGGAAAATTACTTCAGGATTTGTC +>FBgn0000652_F-element|coord=1547|strand -|size=27|nreads=1 +TTTGAGAAAATTACTTCAGGATTTGTC +>FBgn0000652_F-element|coord=1547|strand -|size=27|nreads=74 +TTCGAGAAAATTACTTCAGGATTTGTC +>FBgn0000652_F-element|coord=1548|strand -|size=26|nreads=3 +TTCGAGAAAATTACTTCAGGATTTGT +>FBgn0000652_F-element|coord=1549|strand -|size=25|nreads=1 +TTCGGGAAAATTACTTCAGGATTTG +>FBgn0000652_F-element|coord=1549|strand -|size=25|nreads=22 +TTCGAGAAAATTACTTCAGGATTTG +>FBgn0000652_F-element|coord=1550|strand -|size=24|nreads=2 +TTCGAGAAAATTACTTCAGGATTT +>FBgn0000652_F-element|coord=1551|strand -|size=23|nreads=7 +TTCGAGAAAATTACTTCAGGATT +>FBgn0000652_F-element|coord=1554|strand -|size=20|nreads=1 +TTCGAGAAAATTACTTCAGG +>FBgn0000652_F-element|coord=1564|strand +|size=20|nreads=1 +TTTTCTCGAAAGCAGCTAGT +>FBgn0000652_F-element|coord=1564|strand +|size=20|nreads=2 +TTTTCTCGAAAGCAGCAAGT +>FBgn0000652_F-element|coord=1564|strand +|size=23|nreads=2 +TTTTCTCGAAAGCAGCAAGTTTC +>FBgn0000652_F-element|coord=1564|strand +|size=23|nreads=2 +TTTTCTCGAAAGCAGCTAGTTTC +>FBgn0000652_F-element|coord=1564|strand +|size=24|nreads=2 +TTTTCTCGAAAGCAGCAAGTTTCG +>FBgn0000652_F-element|coord=1564|strand +|size=24|nreads=5 +TTTTCTCGAAAGCAGCTAGTTTCG +>FBgn0000652_F-element|coord=1564|strand +|size=25|nreads=1 +TTTTCTCGAAAGCAGCTAGTTTCGC +>FBgn0000652_F-element|coord=2231|strand -|size=27|nreads=1 +TTGGAAGAAATCCAGGAATTGAGCTTC +>FBgn0000652_F-element|coord=2233|strand -|size=25|nreads=5 +TTGGAAGAAATCCAGGAATTGAGCT +>FBgn0000652_F-element|coord=2248|strand +|size=20|nreads=1 +TTTCTTCCAAGCACTAGGGC +>FBgn0000652_F-element|coord=2248|strand +|size=21|nreads=1 +TTTCTTCCAAGCACTAGGGCC +>FBgn0000652_F-element|coord=2471|strand -|size=21|nreads=2 +TTTAACCAAACTGCGGGAAAT +>FBgn0000652_F-element|coord=2472|strand -|size=20|nreads=1 +TTTAACCAAACTGCGGGAAA +>FBgn0000652_F-element|coord=2482|strand +|size=23|nreads=2 +TTTGGTTAAAGCTGAATGTCTGC +>FBgn0000652_F-element|coord=2482|strand +|size=24|nreads=2 +TTTGGTTAAAGCTGAATGTCTGCC +>FBgn0000652_F-element|coord=2482|strand +|size=26|nreads=3 +TTTGGTTAAAGCTGAATGTCTGCCGG +>FBgn0000652_F-element|coord=2482|strand +|size=27|nreads=1 +TTTGGTTAAAGCTGAATGTCTGCCGGA +>FBgn0000652_F-element|coord=3507|strand -|size=27|nreads=1 +TTTCGCGAAATCCAAATTGGTGGGCTG +>FBgn0000652_F-element|coord=3509|strand -|size=25|nreads=6 +TTTCGCGAAATCCAAATTGGTGGGC +>FBgn0000652_F-element|coord=3510|strand -|size=24|nreads=1 +TTTCGCGAAATCCAAATTGGTGGG +>FBgn0000652_F-element|coord=3513|strand -|size=21|nreads=3 +TTTCGCGAAATCCAAATTGGT +>FBgn0000652_F-element|coord=3524|strand +|size=20|nreads=2 +TTTCGCGAAAGCCATGGAAC +>FBgn0000652_F-element|coord=3524|strand +|size=21|nreads=2 +TTTCGCGAAAGCCACGGAACC +>FBgn0000652_F-element|coord=3524|strand +|size=22|nreads=1 +TTTCGCGAAAGCCACGGAACCA +>FBgn0000652_F-element|coord=3524|strand +|size=23|nreads=1 +TTTCGCGAAAGCCACGGAACCAT +>FBgn0000652_F-element|coord=3524|strand +|size=24|nreads=1 +TTTCGCGAAAGCCATGGAACCATT +>FBgn0000652_F-element|coord=3524|strand +|size=26|nreads=1 +TTTCGCGAAAGCCATGGAACCATTGA +>FBgn0000652_F-element|coord=3524|strand +|size=27|nreads=1 +TTTCGCGAAAGCCACGGAACCATTGAA +>FBgn0002697_mdg1|coord=4301|strand -|size=22|nreads=1 +TTCTTTGGAAAGAATTTGGGGC +>FBgn0002697_mdg1|coord=4302|strand -|size=21|nreads=1 +TTCTTTGGAAAGAATTTGGGG +>FBgn0002697_mdg1|coord=4303|strand -|size=20|nreads=1 +TTCTTTGGAAAGAATTTGGG +>FBgn0002697_mdg1|coord=4313|strand +|size=25|nreads=1 +TTCCAAAGAATGATGACCCTTGCAT +>FBgn0003007_opus|coord=5540|strand -|size=28|nreads=1 +TTTCTAGGAACGTAGAATGGAATCTCTC +>FBgn0003007_opus|coord=5540|strand -|size=28|nreads=1 +TTTCTAGGAACGTAGAGTGGAATCTCTC +>FBgn0003007_opus|coord=5542|strand -|size=26|nreads=1 +TTTCTAGGAACGTAGAATGGAATCTC +>FBgn0003007_opus|coord=5542|strand -|size=26|nreads=2 +TTTCTAGGAACGTAGAGTGGAATCTC +>FBgn0003007_opus|coord=5543|strand -|size=25|nreads=1 +TTTCTAGGAACGTAGAGTGGAATCT +>FBgn0003007_opus|coord=5544|strand -|size=24|nreads=7 +TTTCTAGGAACGTAGAGTGGAATC +>FBgn0003007_opus|coord=5558|strand +|size=21|nreads=1 +TTCCTAGAAATTTATCGTTGC +>FBgn0003122_pogo|coord=1804|strand -|size=25|nreads=1 +TTCCATAGAATTCAAGTTTTGCAAA +>FBgn0003122_pogo|coord=1806|strand -|size=23|nreads=1 +TTCCATAGAATTCAAGTTTTGCA +>FBgn0003122_pogo|coord=1819|strand +|size=22|nreads=1 +TTCTATGGAAGACAAGCTGTTT +>FBgn0003908_R1A1-element|coord=4671|strand -|size=29|nreads=1 +TTTTCGCCAAGGCGCTGCACTCCAAGTCC +>FBgn0003908_R1A1-element|coord=4672|strand -|size=28|nreads=8 +TTTTCGCCAAGGCGCTGCACTCCAAGTC +>FBgn0003908_R1A1-element|coord=4673|strand -|size=27|nreads=1 +TTTTCGCCAAGGCGCTGCACCCCAAGT +>FBgn0003908_R1A1-element|coord=4673|strand -|size=27|nreads=4 +TTTTCGCCAAGGCGCTGCACTCCAAGT +>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=1 +TTTTCGCCAAGGCGCTGCACCCCAAG +>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=1 +TTTTCGTCAAGGCGCTGCACTCCAAG +>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=2 +TTTTCGCCAAGGCGCTGCACTTCAAG +>FBgn0003908_R1A1-element|coord=4674|strand -|size=26|nreads=29 +TTTTCGCCAAGGCGCTGCACTCCAAG +>FBgn0003908_R1A1-element|coord=4675|strand -|size=25|nreads=1 +TTTTCGCCAAGGCGCTGCACCCCAA +>FBgn0003908_R1A1-element|coord=4675|strand -|size=25|nreads=1 +TTTTCGCCAAGGCGCTGCACTTCAA +>FBgn0003908_R1A1-element|coord=4675|strand -|size=25|nreads=10 +TTTTCGCCAAGGCGCTGCACTCCAA +>FBgn0003908_R1A1-element|coord=4676|strand -|size=24|nreads=2 +TTTTCGCCAAGGCGCTGCACTTCA +>FBgn0003908_R1A1-element|coord=4676|strand -|size=24|nreads=21 +TTTTCGCCAAGGCGCTGCACTCCA +>FBgn0003908_R1A1-element|coord=4677|strand -|size=23|nreads=12 +TTTTCGCCAAGGCGCTGCACTCC +>FBgn0003908_R1A1-element|coord=4678|strand -|size=22|nreads=1 +TTTTCGCCAAGGCGCTGCACTT +>FBgn0003908_R1A1-element|coord=4678|strand -|size=22|nreads=18 +TTTTCGCCAAGGCGCTGCACTC +>FBgn0003908_R1A1-element|coord=4679|strand -|size=21|nreads=1 +TTTTCGCCAAGGCGCTGCACC +>FBgn0003908_R1A1-element|coord=4679|strand -|size=21|nreads=6 +TTTTCGCCAAGGCGCTGCACT +>FBgn0003908_R1A1-element|coord=4680|strand -|size=20|nreads=4 +TTTTCGCCAAGGCGCTGCAC +>FBgn0003908_R1A1-element|coord=4690|strand +|size=20|nreads=2 +TTGGCGAAAACTGGATCTTC +>FBgn0003908_R1A1-element|coord=4690|strand +|size=21|nreads=6 +TTGGCGAAAACTGGATCTTCG +>FBgn0003908_R1A1-element|coord=4690|strand +|size=22|nreads=1 +TTGGCGAAAACTAGATCTTCGA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=22|nreads=8 +TTGGCGAAAACTGGATCTTCGA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=23|nreads=8 +TTGGCGAAAACTGGATCTTCGAG +>FBgn0003908_R1A1-element|coord=4690|strand +|size=24|nreads=7 +TTGGCGAAAACTGGATCTTCGAGG +>FBgn0003908_R1A1-element|coord=4690|strand +|size=24|nreads=9 +TTGGCGAAAACTGGATCTTCGAGA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=25|nreads=11 +TTGGCGAAAACTGGATCTTCGAGAG +>FBgn0003908_R1A1-element|coord=4690|strand +|size=25|nreads=12 +TTGGCGAAAACTGGATCTTCGAGGG +>FBgn0003908_R1A1-element|coord=4690|strand +|size=26|nreads=2 +TTGGCGAAAACTGGATCTTCGAGGGA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=26|nreads=6 +TTGGCGAAAACTGGATCTTCGAGAGA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=27|nreads=20 +TTGGCGAAAACTGGATCTTCGAGAGAA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=27|nreads=9 +TTGGCGAAAACTGGATCTTCGAGGGAA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=28|nreads=1 +TTGGCGAAAACTGGATCTTCGAGGGAAT +>FBgn0003908_R1A1-element|coord=4690|strand +|size=28|nreads=4 +TTGGCGAAAACTGGATCTTCGAGAGAAT +>FBgn0005673_1360|coord=773|strand -|size=22|nreads=1 +TTTTCGCAATCATTCCATCCTG +>FBgn0005673_1360|coord=785|strand +|size=26|nreads=6 +TTTGCGAAAAATTGTTTGCTCAGAGC +>FBgn0005673_1360|coord=3197|strand -|size=22|nreads=1 +TTTGCTAGAAGACGATTTTCGG +>FBgn0005673_1360|coord=3209|strand +|size=23|nreads=1 +TTCTAGCACAACACGCACACATA +>FBgn0005673_1360|coord=3209|strand +|size=26|nreads=1 +TTCTAGCACAACACGCACACATATAC +>FBgn0005673_1360|coord=3209|strand +|size=27|nreads=1 +TTCTAGCACAACACGCACACATATACG +>FBgn0010302_Burdock|coord=3390|strand -|size=21|nreads=1 +TTTCATCGAAAGAAATTGGTA +>FBgn0010302_Burdock|coord=3401|strand +|size=25|nreads=2 +TTCGATGAAAGACAATGTTCTGCTT +>FBgn0014947_flea|coord=801|strand -|size=27|nreads=4 +TTCTCTAGAATTGCTTGTATTTGGTCG +>FBgn0014947_flea|coord=802|strand -|size=26|nreads=11 +TTCTCTAGAATTGCTTGTATTTGGTC +>FBgn0014947_flea|coord=803|strand -|size=25|nreads=12 +TTCTCTAGAATTGCTTGTATTTGGT +>FBgn0014947_flea|coord=804|strand -|size=24|nreads=2 +TTCTCTAGAATTGCTTGTATTTGG +>FBgn0014947_flea|coord=805|strand -|size=23|nreads=1 +TTCTCTAGAATTGCTTGTATTTG +>FBgn0014947_flea|coord=818|strand +|size=22|nreads=1 +TTCTAGAGAACGAAAGCGAGGA +>FBgn0014947_flea|coord=1164|strand -|size=28|nreads=2 +TTCTAAGAAAAGTTCTGCTGATCCAATC +>FBgn0014947_flea|coord=1166|strand -|size=26|nreads=2 +TTCTAAGAAAAGTTCTGCTGATCCAA +>FBgn0014947_flea|coord=1167|strand -|size=25|nreads=1 +TTCTAAGAAAAGTTCTGCTGATCCA +>FBgn0014947_flea|coord=1168|strand -|size=24|nreads=1 +TTCTAAGAAAAGTTCTGCTGATCC +>FBgn0014947_flea|coord=1169|strand -|size=23|nreads=1 +TTCTAAGAAAAGTTCTGCTGATC +>FBgn0014947_flea|coord=1182|strand +|size=22|nreads=1 +TTTCTTAGAATCTGAATGTGTC +>FBgn0014947_flea|coord=2754|strand -|size=21|nreads=1 +TTTAGACCAAATTCTGCAGCT +>FBgn0014947_flea|coord=2765|strand +|size=24|nreads=4 +TTGGTCTAAAAATAAAATGGAAGA +>FBgn0014947_flea|coord=2765|strand +|size=25|nreads=1 +TTGGTCTAAAAATAAAATGGAAGAA +>FBgn0014947_flea|coord=2765|strand +|size=26|nreads=1 +TTGGTCTAAAAATAAAATGGAAGAAG +>FBgn0014947_flea|coord=2765|strand +|size=28|nreads=1 +TTGGTCTAAAAATAAAATGGAAGAAGTG +>FBgn0015945_GATE|coord=3140|strand -|size=28|nreads=9 +TTGGAACGAAATTGGCCTGATTAGCGGA +>FBgn0015945_GATE|coord=3141|strand -|size=27|nreads=4 +TTGGAACGAAATTGGCCTGATTAGCGG +>FBgn0015945_GATE|coord=3142|strand -|size=26|nreads=17 +TTGGAACGAAATTGGCCTGATTAGCG +>FBgn0015945_GATE|coord=3143|strand -|size=25|nreads=86 +TTGGAACGAAATTGGCCTGATTAGC +>FBgn0015945_GATE|coord=3144|strand -|size=24|nreads=17 +TTGGAACGAAATTGGCCTGATTAG +>FBgn0015945_GATE|coord=3158|strand +|size=20|nreads=3 +TTCGTTCCAAATGAGCAAGC +>FBgn0015945_GATE|coord=3158|strand +|size=21|nreads=1 +TTCGTTCCAAATGAGCAAGCC +>FBgn0015945_GATE|coord=3158|strand +|size=22|nreads=2 +TTCGTTCCAAATGAGCAAGCCG +>FBgn0015945_GATE|coord=6234|strand -|size=22|nreads=1 +TTGAAGGAAATCGCGGGAAAGC +>FBgn0015945_GATE|coord=6246|strand +|size=25|nreads=1 +TTTCCTTCAAGCCGTAAAAGAGTCG +>FBgn0015945_GATE|coord=6246|strand +|size=26|nreads=1 +TTTCCTTCAAGCCGTAAAAGAGTCGG +>FBgn0042682_Rt1b|coord=1075|strand -|size=21|nreads=1 +TTCTTGGCGACAGATGCGTAG +>FBgn0042682_Rt1b|coord=1076|strand -|size=20|nreads=1 +TTCTTGGCGACAGATGCGTA +>FBgn0042682_Rt1b|coord=1086|strand +|size=23|nreads=1 +TTGCCAAGAATGCTAGCACGGGT +>FBgn0042682_Rt1b|coord=2902|strand -|size=28|nreads=1 +TTGGTAACAAGCTTGTAGGCGAGGCCCC +>FBgn0042682_Rt1b|coord=2903|strand -|size=27|nreads=1 +TTGGTAACAAGCTTGTAGGCGAGGCCC +>FBgn0042682_Rt1b|coord=2904|strand -|size=26|nreads=1 +TTGGTAACAAGCTTGTAGGCGAGTCC +>FBgn0042682_Rt1b|coord=2904|strand -|size=26|nreads=2 +TTGGTAACAAGCTTGTAGGCGAGGCC +>FBgn0042682_Rt1b|coord=2905|strand -|size=25|nreads=1 +TTGGTAACAAGCTTGTAGGCGAGGT +>FBgn0042682_Rt1b|coord=2905|strand -|size=25|nreads=2 +TTGGTAACAAGCTTGTAGGCGAGGC +>FBgn0042682_Rt1b|coord=2906|strand -|size=24|nreads=25 +TTGGTAACAAGCTTGTAGGCGAGG +>FBgn0042682_Rt1b|coord=2907|strand -|size=23|nreads=1 +TTGGTAACAAGCTTGGAGGCGAG +>FBgn0042682_Rt1b|coord=2907|strand -|size=23|nreads=15 +TTGGTAACAAGCTTGTAGGCGAG +>FBgn0042682_Rt1b|coord=2908|strand -|size=22|nreads=1 +TTGGTAACAAGCTTGTAGGCGA +>FBgn0042682_Rt1b|coord=2909|strand -|size=21|nreads=6 +TTGGTAACAAGCTTGTAGGCG +>FBgn0042682_Rt1b|coord=2920|strand +|size=22|nreads=1 +TTGTTACCAAAAAGCTAAGGAG +>FBgn0042682_Rt1b|coord=2920|strand +|size=23|nreads=1 +TTGTTACCAAAAAGCTAAGGAGG +>FBgn0042682_Rt1b|coord=2920|strand +|size=23|nreads=1 +TTGTTACCAACAAGCTAAGGAGG +>FBgn0042682_Rt1b|coord=2920|strand +|size=24|nreads=2 +TTGTTACCAACAAGCTAAGGAGGA +>FBgn0042682_Rt1b|coord=2920|strand +|size=25|nreads=1 +TTGTTACCAAAAAGCTAAGGAGGAG +>FBgn0042682_Rt1b|coord=2920|strand +|size=26|nreads=1 +TTGTTACCAAAAAGCTAAGGAGGAGA +>FBgn0042682_Rt1b|coord=2920|strand +|size=27|nreads=1 +TTGTTACCAAAAAGCTAAGGAGGAGAG +>FBgn0042682_Rt1b|coord=4364|strand -|size=22|nreads=1 +TTGCCTGGAAGCGCCACTCCGC +>FBgn0042682_Rt1b|coord=4365|strand -|size=21|nreads=1 +TTGCCTGGAAGCGCCACTCCG +>FBgn0042682_Rt1b|coord=4366|strand -|size=20|nreads=4 +TTGCCTGGAAGCGCCACTCC +>FBgn0042682_Rt1b|coord=4376|strand +|size=24|nreads=1 +TTCCAGGCAAGAGGCACACGAGTG +>FBgn0042682_Rt1b|coord=4376|strand +|size=26|nreads=1 +TTCCAGGCAAGAGGCACACGAGTGGC +>FBgn0062343_Dm88|coord=4210|strand -|size=21|nreads=1 +TTGGTTAGAACATCTGCCATC +>FBgn0062343_Dm88|coord=4221|strand +|size=24|nreads=1 +TTCTAACCAAGAATTTGAATAGAT +>FBgn0063427_invader4|coord=691|strand -|size=26|nreads=15 +TTCCTACGAATCGCTGTATGAACAGT +>FBgn0063427_invader4|coord=707|strand +|size=22|nreads=2 +TTCGTAGGAATGGAGACGTCGG +>FBgn0063428_invader3|coord=425|strand -|size=25|nreads=1 +TTCTGGGGAAATGGCCTGCAGACGC +>FBgn0063428_invader3|coord=427|strand -|size=23|nreads=1 +TTCTGGGGAAATGGCCTGCAGAC +>FBgn0063428_invader3|coord=440|strand +|size=22|nreads=2 +TTCCCCAGAAACGCGTGGCGAT +>FBgn0063430_invader1|coord=2082|strand -|size=20|nreads=1 +TTTTATCGAACCAATAGAAC +>FBgn0063430_invader1|coord=2092|strand +|size=24|nreads=1 +TTCGATAAAATGTCTAAGTATGTT +>FBgn0063430_invader1|coord=2092|strand +|size=26|nreads=1 +TTCGATAAAATGTCTAAGTATGTTCG +>FBgn0063433_gypsy4|coord=3040|strand -|size=28|nreads=1 +TTTTGAAGAACTTGGATTTTTCTTGAGA +>FBgn0063433_gypsy4|coord=3044|strand -|size=24|nreads=1 +TTTTGAAGAACTTGGATTTTTCTT +>FBgn0063433_gypsy4|coord=3058|strand +|size=22|nreads=1 +TTCTTCAAAAAGAGCGTGGAAT +>FBgn0063440_baggins|coord=5154|strand -|size=26|nreads=1 +TTTTGTGCAAATGGCTGTGAAGTCGG +>FBgn0063440_baggins|coord=5170|strand +|size=21|nreads=1 +TTGCACAAAATTGGCATTGCA +>FBgn0063919_Max-element|coord=3887|strand -|size=21|nreads=2 +TTGCTGAGAAGCGTGTTGAGC +>FBgn0063919_Max-element|coord=3898|strand +|size=23|nreads=1 +TTCTCAGCAAGTTCTGGGAGGTG +>FBgn0063919_Max-element|coord=3898|strand +|size=24|nreads=1 +TTCTCAGCAAGTTCTGGGAGGTGT +>FBgn0063919_Max-element|coord=3898|strand +|size=24|nreads=2 +TTCTCAGCAAGTTCTGGGAGGTGG +>FBgn0063919_Max-element|coord=3898|strand +|size=25|nreads=1 +TTCTCAGCAAGTTCTGGGAGGTGGA +>FBgn0067385_invader6|coord=3007|strand -|size=27|nreads=4 +TTCTAGTCAAAGTCGAAGGACTGCATA +>FBgn0067385_invader6|coord=3008|strand -|size=26|nreads=3 +TTCTAGTCAAAGTCGAAGGACTGCAT +>FBgn0067385_invader6|coord=3009|strand -|size=25|nreads=5 +TTCTAGTCAAAGTCGAAGGACTGCA +>FBgn0067385_invader6|coord=3010|strand -|size=24|nreads=4 +TTCTAGTCAAAGTCGAAGGACTGC +>FBgn0067385_invader6|coord=3011|strand -|size=23|nreads=1 +TTCTAGTCAAAGTCGAAGGACTG +>FBgn0067385_invader6|coord=3014|strand -|size=20|nreads=1 +TTCTAGTCAAAGTCGAAGGA +>FBgn0067385_invader6|coord=3024|strand +|size=21|nreads=1 +TTGACTAGAATGACTTAGACT +>FBgn0067385_invader6|coord=3024|strand +|size=26|nreads=1 +TTGACTAGAATGACTTAGACTTAGAA +>FBgn0067624_BS3|coord=1016|strand -|size=20|nreads=1 +TTGATGCCAATGTTCCAACG +>FBgn0067624_BS3|coord=1026|strand +|size=24|nreads=1 +TTGGCATCAATGGTGACAAATCTG +>FBgn0067624_BS3|coord=1026|strand +|size=25|nreads=1 +TTGGCATCAATGGTGACAAATCTGC +>FBgn0067624_BS3|coord=1026|strand +|size=26|nreads=1 +TTGGCATCAATGGTGACAAATCAGCG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_4.fa Tue Jan 07 11:59:34 2020 +0000 @@ -0,0 +1,70 @@ +>FBgn0000155_roo|coord=3229|strand -|size=22|nreads=2 +TTTTGCCCAAGGAGACCGTCTA +>FBgn0000155_roo|coord=3230|strand -|size=21|nreads=1 +TTTTGCCCAAGGAGACCGTCT +>FBgn0000155_roo|coord=3231|strand -|size=20|nreads=2 +TTTTGCCCAAGGAGACCGTC +>FBgn0000155_roo|coord=3241|strand +|size=20|nreads=1 +TTGGGCAAAAAACTGATTTC +>FBgn0000652_F-element|coord=1554|strand -|size=20|nreads=1 +TTCGAGAAAATTACTTCAGG +>FBgn0000652_F-element|coord=1564|strand +|size=20|nreads=1 +TTTTCTCGAAAGCAGCTAGT +>FBgn0000652_F-element|coord=1564|strand +|size=20|nreads=2 +TTTTCTCGAAAGCAGCAAGT +>FBgn0000652_F-element|coord=2471|strand -|size=21|nreads=2 +TTTAACCAAACTGCGGGAAAT +>FBgn0000652_F-element|coord=2472|strand -|size=20|nreads=1 +TTTAACCAAACTGCGGGAAA +>FBgn0000652_F-element|coord=2482|strand +|size=21|nreads=1 +TTTGGTTAAAGCTGAATGTCT +>FBgn0000652_F-element|coord=2482|strand +|size=22|nreads=2 +TTTGGTTAAAGCTGAATGTCTG +>FBgn0000652_F-element|coord=3513|strand -|size=21|nreads=3 +TTTCGCGAAATCCAAATTGGT +>FBgn0000652_F-element|coord=3524|strand +|size=20|nreads=2 +TTTCGCGAAAGCCATGGAAC +>FBgn0000652_F-element|coord=3524|strand +|size=21|nreads=2 +TTTCGCGAAAGCCACGGAACC +>FBgn0000652_F-element|coord=3524|strand +|size=22|nreads=1 +TTTCGCGAAAGCCACGGAACCA +>FBgn0002697_mdg1|coord=4646|strand -|size=21|nreads=1 +TTTCTCAGAAAAGTTCTTAAT +>FBgn0002697_mdg1|coord=4657|strand +|size=22|nreads=1 +TTCTGAGAAATCACGCCACTTA +>FBgn0002697_mdg1|coord=5354|strand -|size=21|nreads=2 +TTTCAACAAACACTTATGCTT +>FBgn0002697_mdg1|coord=5365|strand +|size=21|nreads=2 +TTTGTTGAAAAGAGGAAAACA +>FBgn0003519_Stalker|coord=6708|strand -|size=21|nreads=1 +TTTGTCTCAAAGCATTTTTGT +>FBgn0003519_Stalker|coord=6719|strand +|size=21|nreads=1 +TTGAGACAAAACATTGCTAAT +>FBgn0003908_R1A1-element|coord=4678|strand -|size=22|nreads=1 +TTTTCGCCAAGGCGCTGCACTT +>FBgn0003908_R1A1-element|coord=4678|strand -|size=22|nreads=18 +TTTTCGCCAAGGCGCTGCACTC +>FBgn0003908_R1A1-element|coord=4679|strand -|size=21|nreads=1 +TTTTCGCCAAGGCGCTGCACC +>FBgn0003908_R1A1-element|coord=4679|strand -|size=21|nreads=6 +TTTTCGCCAAGGCGCTGCACT +>FBgn0003908_R1A1-element|coord=4680|strand -|size=20|nreads=4 +TTTTCGCCAAGGCGCTGCAC +>FBgn0003908_R1A1-element|coord=4690|strand +|size=20|nreads=2 +TTGGCGAAAACTGGATCTTC +>FBgn0003908_R1A1-element|coord=4690|strand +|size=21|nreads=6 +TTGGCGAAAACTGGATCTTCG +>FBgn0003908_R1A1-element|coord=4690|strand +|size=22|nreads=1 +TTGGCGAAAACTAGATCTTCGA +>FBgn0003908_R1A1-element|coord=4690|strand +|size=22|nreads=8 +TTGGCGAAAACTGGATCTTCGA +>FBgn0042682_Rt1b|coord=2908|strand -|size=22|nreads=1 +TTGGTAACAAGCTTGTAGGCGA +>FBgn0042682_Rt1b|coord=2909|strand -|size=21|nreads=6 +TTGGTAACAAGCTTGTAGGCG +>FBgn0042682_Rt1b|coord=2920|strand +|size=22|nreads=1 +TTGTTACCAAAAAGCTAAGGAG +>FBgn0067385_invader6|coord=3014|strand -|size=20|nreads=1 +TTCTAGTCAAAGTCGAAGGA +>FBgn0067385_invader6|coord=3024|strand +|size=21|nreads=1 +TTGACTAGAATGACTTAGACT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/z.tab Tue Jan 07 11:59:34 2020 +0000 @@ -0,0 +1,1331 @@ +FBgn0000004_17.6 5 0 -0.612372435696 +FBgn0000004_17.6 6 0 -0.612372435696 +FBgn0000004_17.6 7 1 1.63299316186 +FBgn0000004_17.6 8 0 -0.612372435696 +FBgn0000004_17.6 9 0 -0.612372435696 +FBgn0000004_17.6 10 1 1.63299316186 +FBgn0000004_17.6 11 0 -0.612372435696 +FBgn0000004_17.6 12 0 -0.612372435696 +FBgn0000004_17.6 13 0 -0.612372435696 +FBgn0000004_17.6 14 0 -0.612372435696 +FBgn0000004_17.6 15 1 1.63299316186 +FBgn0000005_297 5 0 0 +FBgn0000005_297 6 0 0 +FBgn0000005_297 7 0 0 +FBgn0000005_297 8 0 0 +FBgn0000005_297 9 0 0 +FBgn0000005_297 10 0 0 +FBgn0000005_297 11 0 0 +FBgn0000005_297 12 0 0 +FBgn0000005_297 13 0 0 +FBgn0000005_297 14 0 0 +FBgn0000005_297 15 0 0 +FBgn0000006_412 5 0 -0.733235575107 +FBgn0000006_412 6 2 0.0733235575107 +FBgn0000006_412 7 1 -0.329956008798 +FBgn0000006_412 8 0 -0.733235575107 +FBgn0000006_412 9 5 1.28316225644 +FBgn0000006_412 10 8 2.49300095536 +FBgn0000006_412 11 3 0.476603123819 +FBgn0000006_412 12 0 -0.733235575107 +FBgn0000006_412 13 1 -0.329956008798 +FBgn0000006_412 14 0 -0.733235575107 +FBgn0000006_412 15 0 -0.733235575107 +FBgn0000007_1731 5 0 -0.565685424949 +FBgn0000007_1731 6 0 -0.565685424949 +FBgn0000007_1731 7 0 -0.565685424949 +FBgn0000007_1731 8 0 -0.565685424949 +FBgn0000007_1731 9 0 -0.565685424949 +FBgn0000007_1731 10 1 0.989949493661 +FBgn0000007_1731 11 2 2.54558441227 +FBgn0000007_1731 12 0 -0.565685424949 +FBgn0000007_1731 13 0 -0.565685424949 +FBgn0000007_1731 14 1 0.989949493661 +FBgn0000007_1731 15 0 -0.565685424949 +FBgn0000155_roo 5 0 -1.25325662732 +FBgn0000155_roo 6 2 -0.442325868465 +FBgn0000155_roo 7 1 -0.847791247891 +FBgn0000155_roo 8 3 -0.0368604890387 +FBgn0000155_roo 9 2 -0.442325868465 +FBgn0000155_roo 10 8 1.99046640809 +FBgn0000155_roo 11 7 1.58500102867 +FBgn0000155_roo 12 3 -0.0368604890387 +FBgn0000155_roo 13 0 -1.25325662732 +FBgn0000155_roo 14 4 0.368604890387 +FBgn0000155_roo 15 4 0.368604890387 +FBgn0000199_blood 5 0 -0.886405260428 +FBgn0000199_blood 6 0 -0.886405260428 +FBgn0000199_blood 7 1 0.0 +FBgn0000199_blood 8 0 -0.886405260428 +FBgn0000199_blood 9 0 -0.886405260428 +FBgn0000199_blood 10 0 -0.886405260428 +FBgn0000199_blood 11 1 0.0 +FBgn0000199_blood 12 2 0.886405260428 +FBgn0000199_blood 13 3 1.77281052086 +FBgn0000199_blood 14 1 0.0 +FBgn0000199_blood 15 3 1.77281052086 +FBgn0000224_BS 5 0 -0.316227766017 +FBgn0000224_BS 6 0 -0.316227766017 +FBgn0000224_BS 7 0 -0.316227766017 +FBgn0000224_BS 8 0 -0.316227766017 +FBgn0000224_BS 9 0 -0.316227766017 +FBgn0000224_BS 10 0 -0.316227766017 +FBgn0000224_BS 11 0 -0.316227766017 +FBgn0000224_BS 12 0 -0.316227766017 +FBgn0000224_BS 13 1 3.16227766017 +FBgn0000224_BS 14 0 -0.316227766017 +FBgn0000224_BS 15 0 -0.316227766017 +FBgn0000349_copia 5 0 -0.697485832463 +FBgn0000349_copia 6 0 -0.697485832463 +FBgn0000349_copia 7 0 -0.697485832463 +FBgn0000349_copia 8 0 -0.697485832463 +FBgn0000349_copia 9 1 0.581238193719 +FBgn0000349_copia 10 2 1.8599622199 +FBgn0000349_copia 11 1 0.581238193719 +FBgn0000349_copia 12 0 -0.697485832463 +FBgn0000349_copia 13 0 -0.697485832463 +FBgn0000349_copia 14 0 -0.697485832463 +FBgn0000349_copia 15 2 1.8599622199 +FBgn0000481_Doc 5 0 -0.732519874033 +FBgn0000481_Doc 6 0 -0.732519874033 +FBgn0000481_Doc 7 0 -0.732519874033 +FBgn0000481_Doc 8 1 -0.366259937017 +FBgn0000481_Doc 9 0 -0.732519874033 +FBgn0000481_Doc 10 3 0.366259937017 +FBgn0000481_Doc 11 3 0.366259937017 +FBgn0000481_Doc 12 5 1.09877981105 +FBgn0000481_Doc 13 9 2.56381955912 +FBgn0000481_Doc 14 0 -0.732519874033 +FBgn0000481_Doc 15 1 -0.366259937017 +FBgn0000638_FB 5 0 0 +FBgn0000638_FB 6 0 0 +FBgn0000638_FB 7 0 0 +FBgn0000638_FB 8 0 0 +FBgn0000638_FB 9 0 0 +FBgn0000638_FB 10 0 0 +FBgn0000638_FB 11 0 0 +FBgn0000638_FB 12 0 0 +FBgn0000638_FB 13 0 0 +FBgn0000638_FB 14 0 0 +FBgn0000638_FB 15 0 0 +FBgn0000652_F-element 5 0 -1.07547773595 +FBgn0000652_F-element 6 1 -0.921838059382 +FBgn0000652_F-element 7 2 -0.768198382818 +FBgn0000652_F-element 8 11 0.614558706255 +FBgn0000652_F-element 9 17 1.53639676564 +FBgn0000652_F-element 10 16 1.38275708907 +FBgn0000652_F-element 11 5 -0.307279353127 +FBgn0000652_F-element 12 0 -1.07547773595 +FBgn0000652_F-element 13 2 -0.768198382818 +FBgn0000652_F-element 14 7 0.0 +FBgn0000652_F-element 15 16 1.38275708907 +FBgn0001100_G-element 5 0 -0.553398590529 +FBgn0001100_G-element 6 4 2.92510683566 +FBgn0001100_G-element 7 0 -0.553398590529 +FBgn0001100_G-element 8 0 -0.553398590529 +FBgn0001100_G-element 9 1 0.316227766017 +FBgn0001100_G-element 10 0 -0.553398590529 +FBgn0001100_G-element 11 0 -0.553398590529 +FBgn0001100_G-element 12 0 -0.553398590529 +FBgn0001100_G-element 13 0 -0.553398590529 +FBgn0001100_G-element 14 1 0.316227766017 +FBgn0001100_G-element 15 1 0.316227766017 +FBgn0001167_gypsy 5 0 -0.316227766017 +FBgn0001167_gypsy 6 0 -0.316227766017 +FBgn0001167_gypsy 7 0 -0.316227766017 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