# HG changeset patch # User nikos # Date 1410272881 14400 # Node ID a47f03c50780abbd70f63e5ff8569d7a91a2704c # Parent 0847315fa035c7ef942aea68e491a9bd9bd00c1b Uploaded diff -r 0847315fa035 -r a47f03c50780 bedClip.sh --- a/bedClip.sh Tue Sep 09 10:22:40 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -#!/bin/bash - -bedClip $1 <(fetchChromSizes $2 2> /dev/null) $3 diff -r 0847315fa035 -r a47f03c50780 bedClip.xml --- a/bedClip.xml Tue Sep 09 10:22:40 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ - - Remove lines from bed file that refer to off-chromosome places. - - fetchChromSizes - bedClip - - - ## Set genome assembly - - #set $Genome = str( $genome_cond.genome ) - #if str( $genome_cond ) == 'OTHER': - #set $Genome = str( $genome_cond.genome_other ) - #end if - - bedClip.sh $input $Genome $output - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**What it does** -bedClip - Remove lines from bed file that refer to off-chromosome places. - -**Usage** - - bedClip input.bed chrom.sizes output.bed - - - diff -r 0847315fa035 -r a47f03c50780 bedExtendRanges.xml --- a/bedExtendRanges.xml Tue Sep 09 10:22:40 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ - - Extend length of entries in bed 6+. - - bedExtendRanges - - - ## Set genome assembly - - #set $Genome = str( $genome_cond.genome ) - #if str( $genome_cond ) == 'OTHER': - #set $Genome = str( $genome_cond.genome_other ) - #end if - - bedExtendRanges -user=genome -host=genome-mysql.cse.ucsc.edu $Genome $length $input 2> /dev/null > $output - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**What it does** - -bedExtendRanges_ - extend length of entries in bed 6+ data to be at least the given length, -taking strand directionality into account. - -.. _bedExtendRanges: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedExtendRanges - -**Usage** - - bedExtendRanges database length files(s) - -**Example** - - * bedExtendRanges -user=genome -host=genome-mysql.cse.ucsc.edu hg18 250 stdin - - will transform: - chr1 500 525 . 100 + - chr1 1000 1025 . 100 - - to: - chr1 500 750 . 100 + - chr1 775 1025 . 100 - - - - diff -r 0847315fa035 -r a47f03c50780 bigWigSummary.xml --- a/bigWigSummary.xml Tue Sep 09 10:22:40 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,43 +0,0 @@ - - Extract summary information from a bigWig file. - - bigWigSummary $input $chrom $start $end $dataPoints -type=$type> $output - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**Usage** - * bigWigSummary file.bigWig chrom start end dataPoints - * Get summary data from bigWig for indicated region, broken into dataPoints equal parts. (Use dataPoints=1 for simple summary.) - - - diff -r 0847315fa035 -r a47f03c50780 bigwig2summary.sh --- a/bigwig2summary.sh Tue Sep 09 10:22:40 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,131 +0,0 @@ -#!/bin/bash -# $Id: bigwig2summary_stdout 34 2014-02-20 08:31:20Z jens $ - -#USE IN GALAXY -#This script extract summary values (mean, min, max, std or coverage) from a bigwig file for a number of equal sized bins across genomic regions given in bed file. -#If the bed file contains 6 columns (or more), column 6 is expected to contain strand information. Summary values from a negative strand will be reversed. - -######################################## -#bigwigSummary has 3 non-standard outputs: -#1) n/a #(no data in bin) -#2) no data #(no data in entire region) -#3) is not a valid option (typically if negative coordinate) - -#Default settings & input parsing. "" indicates required user input. -nbins=1 -rm_header_line=0 -summary_type=mean - -#parse input -while getopts hef:b:o:n:t: myarg -do case "$myarg" in - h) echo "Usage: bigwig2summary_stdout -f -b -o -n -t

-e" - echo "Corrects for strand if bed-file has 6 columns or more. Col 6 assumed to contain strand infomation" - exit ;; - f) bigwig_file="$OPTARG" ;; - b) bed_file="$OPTARG" ;; #must be tab separated without header - o) org_assembly="$OPTARG" ;; - n) nbins="$OPTARG" ;; - t) summary_type="$OPTARG" ;; - e) rm_header_line=2 ;; #flag. if -e then first line is removed - [?]) echo "Usage: bigwig2summary_stdout -f -b -o -n -t

-e" - echo "Corrects for strand if bed-file has 6 columns or more. Col 6 assumed to contain strand infomation" - exit 1 ;; - esac -done - -################################################### -###VALIDATE INPUT -################################################### - -#get chromosome sizes from bigwig file. bigwig file does not contain name of genome assembly. -org_assembly_file=`mktemp -u` -fetchChromSizes $org_assembly 2>/dev/null > $org_assembly_file -if [ $? -ne 0 ]; then - echo "ERROR: Organism genome assembly does not exist" - rm $org_assembly_file - exit -fi - -#check input bed_file. bedClip only checks first 3 columns! -if [ `bedClip -verbose=2 <(tail -n +${rm_header_line} $bed_file) $org_assembly_file /dev/null 2>&1 | wc -l` -gt 0 ]; then - echo -e "ERROR: Input bed file is not in proper format!\nTry 'bedClip' to find lines causing error" - echo "Make sure that bigwig and bed files are using the same genome assembly" - exit 1 -fi - -#make string of "nbins" 0's to insert in regions, where no reads are found -if [ $nbins -gt 1 ]; then - seq_string=`seq 1 $nbins` - zero_string=`printf "0\t%.s" {$seq_string} | perl -pe "s/\t$//"` -fi - -#make sure the given summary type exists -if [ `echo $summary_type | egrep "(mean|max|min|std|coverage)" | wc -l` -ne 1 ]; then - echo "ERROR: Summary type must be: mean, max, min, std or coverage. Default is 'mean'" - exit 1 -fi - -#determine number of fields in bed_file -if [ `tail -n +${rm_header_line} $bed_file | awk '{print NF}' | uniq | wc -l` -eq 1 ]; then - nfields_bed=`tail -n +${rm_header_line} $bed_file | awk '{print NF}' | uniq` -else - echo "ERROR: Bed file does not have constant number of line columns" - exit 1 -fi - -if [[ $nbins -gt 1 && $nfields_bed -ge 6 ]]; then - strand_uniq_chars=`tail -n +${rm_header_line} $bed_file | cut -f6 | sort -u | perl -pe "s/\n//"` - if [[ $strand_uniq_chars != "+-" && $strand_uniq_chars != "-+" ]] ; then - echo "ERROR: Column 6 in bed file must only contain '+' or '-' characters" - exit 1 - fi -fi - -################################################### -###EXTRACT DENSITIES FROM NORMALIZED BIGWIG FILE -################################################### - - -#if more than 1 bin AND >= 6 fields (i.e. has strand column) -if [[ $nbins -gt 1 && $nfields_bed -ge 6 ]]; then - - #cut columns 1-3+6 | rm header if flag set - cut -f1-3,6 $bed_file | tail -n +${rm_header_line} | while read -r line; do - - #read 4 fields into variables - read -r cur_chr cur_start cur_end cur_strand <<<"$line" - #run bigWigSummary. Combine stdout and stderr | treat exceptions and errors after 'done' - bigWigSummary $bigwig_file $cur_chr $cur_start $cur_end $nbins -type=${summary_type} 2>&1 | perl -pe "s/no data.+$/${zero_string}/" | awk 'BEGIN{OFS="\t"}{ if("'"$cur_strand"'"=="-") { for (i=NF; i>0; i--) { printf("%s\t",$i) } printf("\n") } else { print $0 } }' - done | perl -pe "s/n\/a/0/g" | perl -pe "s/^\t?0\t?$/${zero_string}/" | perl -pe "s/ +/\t/g" | perl -pe "s/\t$//" | sed '/^$/d' - -#if more than 1 bin AND less than 6 fields (i.e. no strand column) -elif [[ $nbins -gt 1 && $nfields_bed -lt 6 ]]; then - - #cut columns 1-3 | rm header if flag set - cut -f1-3 $bed_file | tail -n +${rm_header_line} | while read -r line; do - - #read 3 fields into variables - read -r cur_chr cur_start cur_end <<<"$line" - #run bigWigSummary. Combine stdout and stderr | treat exceptions and errors after 'done' - bigWigSummary $bigwig_file $cur_chr $cur_start $cur_end $nbins -type=${summary_type} 2>&1 - - done | perl -pe "s/n\/a/0/g" | perl -pe "s/no data.+$/${zero_string}/" | perl -pe "s/^\t?0\t?$/${zero_string}/" | perl -pe "s/ +/\t/g" | sed '/^$/d' - - -#if 1 bin. Strand column irrelevant -else - - cut -f1-3 $bed_file | tail -n +${rm_header_line} | while read -r line; do - - read -r cur_chr cur_start cur_end <<<"$line" - bigWigSummary $bigwig_file $cur_chr $cur_start $cur_end 1 -type=${summary_type} 2>&1 - - done | perl -pe "s/no data.+$/0/" | perl -pe "s/n\/a/0/g" | sed '/^$/d' - -fi - - - - - diff -r 0847315fa035 -r a47f03c50780 bigwig2summary.xml --- a/bigwig2summary.xml Tue Sep 09 10:22:40 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,106 +0,0 @@ - - Extract summary information from a bigWig file across multiple genomic regions specified by the user. - - bigWigSummary - fetchChromSizes - bedClip - - - bigwig2summary.sh -f $input_bw -b $input_bed -n $bins -o $assembly -t $type $header > $output - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -This tool extracts summary values (mean, min, max, std or coverage) from a **bigWig** file for a number of equal sized bins across genomic regions given in an a "BED-like" file. - -The script this tool is based on is written by Jens Vilstrup Johansen and uses bigWigSummary_, bedClip_ and fetchChromSizes_. - -.. _bigWigSummary: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigSummary - -.. _bedClip: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip - --- _fetchChromSizes: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes - ------ - -.. class:: infomark - -The file contaning the genomic region must be TAB-delimited with at list 3 columns representing Chromosome, ChrStart and ChrEnd. If the file contains 6 columns (or more), column 6 is expected to contain strand information. Summary values from a negative strand will be reversed. - ------ - -**Example 1** - -Input BED file:: - - chr19 50178708 50180708 - chr6 90348174 90350174 - chr16 58495848 58497848 - chr5 180580242 180582242 - chr9 120177017 120179017 - -Extract summary (*#* of bins = 3):: - - 0 0 0 - 0.144886 0 0 - 0.507327 1.14649 1.38456 - 0.221471 0.144886 0.309857 - 0.348944 0.426638 0.244495 - -**Example 2** - -Input BED file (with strand information):: - - chr19 50178708 50180708 NM_198318 0 + PRMT1 - chr6 90348174 90350174 NM_020466 0 - LYRM2 - chr16 58495848 58497848 NM_020465 0 + NDRG4 - chr5 180580242 180582242 NM_206880 0 + OR2V2 - chr9 120177017 120179017 NM_014010 0 - ASTN2 - -Extract summary (*#* of bins = 3):: - - 0 0 0 - 0 0 0.144886 - 0.507327 1.14649 1.38456 - 0.221471 0.144886 0.309857 - 0.244495 0.426638 0.348944 - - - diff -r 0847315fa035 -r a47f03c50780 faCount.xml --- a/faCount.xml Tue Sep 09 10:22:40 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,78 +0,0 @@ - - Count base statistics and CpGs in FASTA files. - - faCount - - - faCount $summary $dinuc $strands $input > $output - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**What it does** - -faCount_ - Count base statistics and CpGs in FA files. - -.. _faCount: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faCount - -**Usage** - -faCount file(s).fa -summary -dinuc -strands - -**Examples** - -Example 1:: - - faCount 1.fasta - - #seq len A C G T N cpg - HSFAU1 515 125 138 146 106 0 23 - HSFAU2 514 124 138 146 106 0 25 - HSFAU3 518 125 139 149 105 0 25 - HSFAU4 524 128 142 148 106 0 26 - HSFAU5 518 124 138 147 109 0 25 - total 2589 626 695 736 532 0 124 - -Example 2:: - - faCount 1.fasta -summary - - #seq len A C G T N cpg - total 2589 626 695 736 532 0 124 - prcnt 1.0 0.2418 0.2684 0.2843 0.2055 0.0000 0.0479 - -Example 3:: - - faCount 1.fasta -summary -strands - - #seq len A C G T N cpg - total 5178 1158 1431 1431 1158 0 248 - prcnt 1.0 0.2236 0.2764 0.2764 0.2236 0.0000 0.0479 - - - - diff -r 0847315fa035 -r a47f03c50780 test-data/.DS_Store Binary file test-data/.DS_Store has changed diff -r 0847315fa035 -r a47f03c50780 test-data/._.DS_Store Binary file test-data/._.DS_Store has changed diff -r 0847315fa035 -r a47f03c50780 test-data/1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.bed Tue Sep 09 10:28:01 2014 -0400 @@ -0,0 +1,5 @@ +chr19 50178708 50180708 +chr6 90348174 90350174 +chr16 58495848 58497848 +chr5 180580242 180582242 +chr9 120177017 120179017 diff -r 0847315fa035 -r a47f03c50780 test-data/1.bigwig Binary file test-data/1.bigwig has changed diff -r 0847315fa035 -r a47f03c50780 test-data/1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.fasta Tue Sep 09 10:28:01 2014 -0400 @@ -0,0 +1,50 @@ +>HSFAU1 +ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc +agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg +cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc +tcctggcaggccccctggaggatgaggccactctgggccagtgcggggtggaggccc +tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc +gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga +agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca +cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc +tctaataaaaaagccacttagttcagtcaaaaaaaaaa +>HSFAU2 +ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc +agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg +cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc +tcctggcaggcgcgcccctggaggatgcactctgggccagtgcggggtggaggccc +tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc +gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga +agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca +cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc +tctaataaaaaagccacttagttcagtcaaaaaaaaaa +>HSFAU3 +ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc +agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg +cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc +tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc +tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc +gtgctggaaaagtgagaggtcagactcctaagggggccaaacaggagaagaagaagaaga +agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca +cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc +tctaataaaaaagccacttagttcagtcaaaaaaaaaa +>HSFAU4 +ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc +agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg +cccagatcaaggctcatgaaatagcctcactggagggcattgccccggaagatcaagtcgtgc +tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc +tgactaccctggaagtagcaggccgcatgcttgcccgaggtaaagttcatggttccctggccc +gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga +agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca +cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc +tctaataaaaaagccacttagttcagtcaaaaaaaaaa +>HSFAU5 +ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc +agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg +cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc +tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc +tgactaccctggaagtaggccgcatgctttttggaggtaaagttcatggttccctggccc +gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga +agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca +cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc +tctaataaaaaagccacttagttcagtcaaaaaaaaaa \ No newline at end of file diff -r 0847315fa035 -r a47f03c50780 test-data/1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.tabular Tue Sep 09 10:28:01 2014 -0400 @@ -0,0 +1,4 @@ +0.144886 0 0 +0.507327 1.14649 1.38456 +0.221471 0.144886 0.309857 +0.348944 0.426638 0.244495 diff -r 0847315fa035 -r a47f03c50780 test-data/1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.txt Tue Sep 09 10:28:01 2014 -0400 @@ -0,0 +1,1 @@ +0.796113 0.273952 0.437672 diff -r 0847315fa035 -r a47f03c50780 test-data/2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.bed Tue Sep 09 10:28:01 2014 -0400 @@ -0,0 +1,5 @@ +chr19 50178708 50180708 NM_198318 0 + PRMT1 +chr6 90348174 90350174 NM_020466 0 - LYRM2 +chr16 58495848 58497848 NM_020465 0 + NDRG4 +chr5 180580242 180582242 NM_206880 0 + OR2V2 +chr9 120177017 120179017 NM_014010 0 - ASTN2 diff -r 0847315fa035 -r a47f03c50780 test-data/2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.tabular Tue Sep 09 10:28:01 2014 -0400 @@ -0,0 +1,4 @@ +0 0 0 0.144886 0 +0.396878 0.970009 1.1091 1.17538 1.40612 +0.203829 0.21262 0.144886 0.409996 0.274558 +0.180424 0.430989 0.458898 0.35171 0.307157 diff -r 0847315fa035 -r a47f03c50780 test-data/3.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3.bed Tue Sep 09 10:28:01 2014 -0400 @@ -0,0 +1,7 @@ +chr19 50178708 50180708 +chr21 48119895 48139895 +chr6 90348174 90350174 +chr16 58495848 58497848 +chr5 180580242 180582242 +chr17 81194210 81196210 +chr9 120177017 120179017 diff -r 0847315fa035 -r a47f03c50780 test-data/3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3.tabular Tue Sep 09 10:28:01 2014 -0400 @@ -0,0 +1,7 @@ +#seq len A C G T N cpg +HSFAU1 515 125 138 146 106 0 23 +HSFAU2 514 124 138 146 106 0 25 +HSFAU3 518 125 139 149 105 0 25 +HSFAU4 524 128 142 148 106 0 26 +HSFAU5 518 124 138 147 109 0 25 +total 2589 626 695 736 532 0 124 diff -r 0847315fa035 -r a47f03c50780 test-data/4.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4.bed Tue Sep 09 10:28:01 2014 -0400 @@ -0,0 +1,5 @@ +chr19 50178708 50183708 NM_198318 0 + PRMT1 +chr6 90345174 90350174 NM_020466 0 - LYRM2 +chr16 58495848 58500848 NM_020465 0 + NDRG4 +chr5 180580242 180585242 NM_206880 0 + OR2V2 +chr9 120174017 120179017 NM_014010 0 - ASTN2 diff -r 0847315fa035 -r a47f03c50780 test-data/4.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4.tabular Tue Sep 09 10:28:01 2014 -0400 @@ -0,0 +1,3 @@ +#seq len A C G T N cpg AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT +total 5178 1158 1431 1431 1158 0 248 360 238 408 142 328 447 248 408 320 426 447 238 150 320 328 360 +prcnt 1.0 0.2236 0.2764 0.2764 0.2236 0.0000 0.0479 0.0695 0.0460 0.0788 0.0274 0.0633 0.0863 0.0479 0.0788 0.0618 0.0823 0.0863 0.0460 0.0290 0.0618 0.0633 0.0695 diff -r 0847315fa035 -r a47f03c50780 test-data/test-data/1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-data/1.fasta Tue Sep 09 10:28:01 2014 -0400 @@ -0,0 +1,50 @@ +>HSFAU1 +ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc +agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg +cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc +tcctggcaggccccctggaggatgaggccactctgggccagtgcggggtggaggccc +tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc +gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga +agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca +cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc +tctaataaaaaagccacttagttcagtcaaaaaaaaaa +>HSFAU2 +ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc +agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg +cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc +tcctggcaggcgcgcccctggaggatgcactctgggccagtgcggggtggaggccc +tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc +gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga +agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca +cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc +tctaataaaaaagccacttagttcagtcaaaaaaaaaa +>HSFAU3 +ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc +agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg +cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc +tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc +tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc +gtgctggaaaagtgagaggtcagactcctaagggggccaaacaggagaagaagaagaaga +agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca +cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc +tctaataaaaaagccacttagttcagtcaaaaaaaaaa +>HSFAU4 +ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc +agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg +cccagatcaaggctcatgaaatagcctcactggagggcattgccccggaagatcaagtcgtgc +tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc +tgactaccctggaagtagcaggccgcatgcttgcccgaggtaaagttcatggttccctggccc +gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga +agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca +cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc +tctaataaaaaagccacttagttcagtcaaaaaaaaaa +>HSFAU5 +ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc +agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg +cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc +tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc +tgactaccctggaagtaggccgcatgctttttggaggtaaagttcatggttccctggccc +gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga +agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca +cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc +tctaataaaaaagccacttagttcagtcaaaaaaaaaa \ No newline at end of file diff -r 0847315fa035 -r a47f03c50780 test-data/test-data/3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-data/3.tabular Tue Sep 09 10:28:01 2014 -0400 @@ -0,0 +1,7 @@ +#seq len A C G T N cpg +HSFAU1 515 125 138 146 106 0 23 +HSFAU2 514 124 138 146 106 0 25 +HSFAU3 518 125 139 149 105 0 25 +HSFAU4 524 128 142 148 106 0 26 +HSFAU5 518 124 138 147 109 0 25 +total 2589 626 695 736 532 0 124 diff -r 0847315fa035 -r a47f03c50780 test-data/test-data/4.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-data/4.tabular Tue Sep 09 10:28:01 2014 -0400 @@ -0,0 +1,3 @@ +#seq len A C G T N cpg AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT +total 5178 1158 1431 1431 1158 0 248 360 238 408 142 328 447 248 408 320 426 447 238 150 320 328 360 +prcnt 1.0 0.2236 0.2764 0.2764 0.2236 0.0000 0.0479 0.0695 0.0460 0.0788 0.0274 0.0633 0.0863 0.0479 0.0788 0.0618 0.0823 0.0863 0.0460 0.0290 0.0618 0.0633 0.0695 diff -r 0847315fa035 -r a47f03c50780 tool_dependencies.xml --- a/tool_dependencies.xml Tue Sep 09 10:22:40 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,88 +0,0 @@ - - - - - - http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigSummary - - . - $INSTALL_DIR - - $INSTALL_DIR/bigWigSummary - - $INSTALL_DIR - - - - - - - - - - http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedClip - - . - $INSTALL_DIR - - $INSTALL_DIR/bedClip - - $INSTALL_DIR - - - - - - - - - - http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedExtendRanges - - . - $INSTALL_DIR - - $INSTALL_DIR/bedExtendRanges - - $INSTALL_DIR - - - - - - - - - - http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faCount - - . - $INSTALL_DIR - - $INSTALL_DIR/faCount - - $INSTALL_DIR - - - - - - - - - - http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes - - . - $INSTALL_DIR - - $INSTALL_DIR/fetchChromSizes - - $INSTALL_DIR - - - - - - -