# HG changeset patch # User ryo_tas # Date 1419932734 -32400 # Node ID 97bd5bb4204c5220ee4507e30cac26598936489b commit diff -r 000000000000 -r 97bd5bb4204c ceas.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ceas.xml Tue Dec 30 18:45:34 2014 +0900 @@ -0,0 +1,400 @@ + + Annotate the given intervals and scores with genome features such as gene body + /bin/bash $shscript + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +#!/bin/bash +#import os + +#set $dollar = chr(36) +#set $gt = chr(62) +#set $lt = chr(60) +#set $ad = chr(38) + +if [ $bfile == "None" ];then + if [ $wfile == "None" ];then + echo "Either wig or bed file is required!" ${gt}${ad}2 + exit; + fi +fi + + +#if $bfile != None + dbkey=$bfile.metadata.dbkey +#elif $wfile != None + dbkey=$wfile.metadata.dbkey +#end if + + +##REMOVING WIG VALIDATORS +##if [ $wfile != "None" ];then +## wigsize=`du -b $wfile | awk '{print ${dollar}1}'` +## +## if [[ ${dollar}wigsize -gt 2097152000 ]];then +## echo "wig file is too big! 2G is the maximum!" ${gt}${ad}2 +## exit; +## fi +##fi + + +#if $genegroup.enable == "yes" +#set $gngroups = str($genegroup.genelist) +#set $gnlabels = str($genegroup.label) +lines=`wc -l $gngroups | tail -1 | awk '{print ${dollar}1}'` +if [[ ${dollar}lines -gt 100000 ]];then + echo "Total lines of the gene list has to between 100 and 100000!" ${gt}${ad}2; + exit; +fi +if [[ ${dollar}lines -lt 100 ]];then + echo "Total lines of the gene list has to between 100 and 100000!" ${gt}${ad}2; + exit; +fi +genelength=`echo $gnlabels |awk '{print length($0)}'` +if [[ ${dollar}genelength -gt 255 ]];then + echo "Gene List Label exceed the limit of 255 characters!" ${gt}${ad}2; + exit; +fi +#end if +#if $genegroup.enable == "yes" +#set $gngroups = str($genegroup.genelist) +#set $gnlabels = str($genegroup.label) +#for $m in $genegroup.more +#set $gngroups = $gngroups+","+str($m.genelist) +#set $gnlabels = $gnlabels+","+str($m.label) +#end for +#set $gngroupspara = "--gn-groups="+$gngroups +#set $gnlabelspara = "--gn-group-names='"+$gnlabels+"'"+str($genegroup.idtype.value) +#else +#set $gngroupspara = "" +#set $gnlabelspara = "" +#end if + +#set $path = $os.path.abspath($__app__.config.tool_path) + +WIG="" +if [ $wfile != "None" ]; then #were we sent in a value for the wig file? + WIG="-w $wfile" +fi + +BED="" +if [ $bfile != "None" ]; then #were we sent in a value for the wig file? + BED="-b $bfile" + lines=`wc -l $bfile | tail -1 | awk '{print ${dollar}1}'` + format=`$path/validation/fcfunc.py $bfile` + + if [[ ${dollar}lines -gt 500000 ]];then + echo "BED file is too big! 100K lines are the maximum!" ${gt}${ad}2 + exit; + fi + if [[ ${dollar}format != "passed" ]]; then + echo ${dollar}format ${gt}${ad}2 + exit; + fi +fi + +#set $sizes = str($lowersize) + "," + str($middlesize) + "," + str($uppersize) +#set $bisizes = str($lowerbisize) + "," + str($upperbisize) + +#set $gtpath = os.path.join( os.path.abspath($__app__.config.cistrome_static_library_path), "ceaslib", "GeneTable", $dbkey ) +#set $length_file = os.path.join( os.path.abspath($__app__.config.cistrome_static_library_path), "chromLen", $dbkey+".len" ) + + +#if str($wfile) != "None" +#if $wfile.extension == "wig" +ceas ${dollar}WIG ${dollar}BED --span=$span --pf-res=$pfres --sizes=$sizes --bisizes=$bisizes \ + --rel-dist=$reldist -g $gtpath $gngroupspara $gnlabelspara --name=ceas_out ${ad}${gt} $log +#elif $wfile.extension == "bigwig" +ceasBW ${dollar}WIG ${dollar}BED --span=$span --pf-res=$pfres --sizes=$sizes --bisizes=$bisizes -l $length_file\ + --rel-dist=$reldist -g $gtpath $gngroupspara $gnlabelspara --name=ceas_out ${ad}${gt} $log +#end if +#else +ceas ${dollar}WIG ${dollar}BED --span=$span --pf-res=$pfres --sizes=$sizes --bisizes=$bisizes \ + --rel-dist=$reldist -g $gtpath $gngroupspara $gnlabelspara --name=ceas_out ${ad}${gt} $log +#end if + + +R --vanilla ${lt} ceas_out.R ${ad}${gt}/dev/null +if [ $imagetype == "PNG" ]; then +convert ceas_out.pdf ceas_out.png +convert ceas_out-*.png -append ceas_out_joint.png +mv ceas_out_joint.png $output +else +mv ceas_out.pdf $output +fi + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +This tool annotates the given intervals and scores with genome +features such as gene body. It's the major module in CEAS package +which is written by Hyunjin Gene Shin, published in Bioinformatics +(pubmed id:19689956). + +.. class:: warningmark + +**NEED IMPROVEMENT** + +----- + +**Parameters** + +- **WIGGLE file** contains the scores for the experiment in a wiggle + format file. Normally, it's produced by the peak calling tool. It's + optional. +- **BED file** contains the peak locations for the experiment in a BED + format file. +- **Span** from TSS and TTS in the gene-centered annotation. ChIP + regions within this range from TSS and TTS are considered when + calculating the coverage rates in promoter and downstream. +- **Profiling resolution** is the WIGGLE profiling resolution. +- **Promoter/downstream intervals** for ChIP region annotation are + comma-separated three values or a single value can be given. If a + single value is given, it will be segmented into three equal + fractions (ie, 3000 is equivalent to 1000,2000,3000) +- **BiPromoter ranges** is for ChIP region annotation. It's + comma-separated two values or a single value can be given. If a + single value is given, it will be segmented into two equal fractions + (ie, 5000 is equivalent to 2500,5000) +- **Relative distance** is the relative distance to TSS/TTS in WIGGLE file + profiling +- **Genome Annotation Version** to specify the annotations according to + the data set. The annotations are downloaded from UCSC genome site. +- **Image type** specify the output image format, either in PNG or in + PDF format. +- If **Specify gene list in the signal profiling** is set, you can specify + different gene groups for CEAS to put them together in the profile + figure. You need to select several **Gene List** files from history which + contains the RefSeq ids or Gene Symbols for each row, and + **Gene List Label** for each gene list file. + +----- + +**Outputs** + +- **PNG/PDF file** is the result for CEAS analysis, containing 5 pages. +- **LOG file** for job log. If you see errors, please attached this in + the bug report + +----- + +**script parameter list of CEAS 0.9.8** + +Options: + --version show program's version number and exit + -h, --help Show this help message and exit. + -b BED, --bed=BED BED file of ChIP regions. + -w WIG, --wig=WIG WIG file for either wig profiling or genome background + annotation. WARNING: --bg flag must be set for genome + background re-annotation. + -e EBED, --ebed=EBED BED file of extra regions of interest (eg, non-coding + regions) + -g GDB, --gt=GDB Gene annotation table (eg, a refGene table in sqlite3 + db format provided through the CEAS web, + http://liulab.dfci.harvard.edu/CEAS/download.html). + --name=NAME Experiment name. This will be used to name the output + files. If an experiment name is not given, the stem of + the input BED file name will be used instead (eg, if + 'peaks.bed', 'peaks' will be used as a name.) + --sizes=SIZES Promoter (also dowsntream) sizes for ChIP region + annotation. Comma-separated three values or a single + value can be given. If a single value is given, it + will be segmented into three equal fractions (ie, 3000 + is equivalent to 1000,2000,3000), DEFAULT: + 1000,2000,3000. WARNING: Values > 10000bp are + automatically set to 10000bp. + --bisizes=BISIZES Bidirectional-promoter sizes for ChIP region + annotation Comma-separated two values or a single + value can be given. If a single value is given, it + will be segmented into two equal fractions (ie, 5000 + is equivalent to 2500,5000) DEFAULT: 2500,5000bp. + WARNING: Values > 20000bp are automatically set to + 20000bp. + --bg Run genome BG annotation again. WARNING: This flag is + effective only if a WIG file is given through -w + (--wig). Otherwise, ignored. + --span=SPAN Span from TSS and TTS in the gene-centered annotation. + ChIP regions within this range from TSS and TTS are + considered when calculating the coverage rates in + promoter and downstream, DEFAULT=3000bp + --pf-res=PF_RES Wig profiling resolution, DEFAULT: 50bp. WARNING: + Value smaller than the wig interval (resolution) may + cause aliasing error. + --rel-dist=REL_DIST Relative distance to TSS/TTS in wig profiling, + DEFAULT: 3000bp + --gn-groups=GN_GROUPS + Gene-groups of particular interest in wig profiling. + Each gene group file must have gene names in the 1st + column. The file names are separated by commas w/ no + space (eg, --gn-groups=top10.txt,bottom10.txt) + --gn-group-names=GN_NAMES + The names of the gene groups in --gn-groups. The gene + group names are separated by commas. (eg, --gn-group- + names='top 10%,bottom 10%'). These group names appear + in the legends of the wig profiling plots. If no group + names given, the groups are represented as 'Group 1, + Group2,...Group n'. + --gname2 Whether or not use the 'name2' column of the gene + annotation table when reading the gene IDs in the + files given through --gn-groups. This flag is + meaningful only with --gn-groups. + + + + diff -r 000000000000 -r 97bd5bb4204c fcfunc.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fcfunc.py Tue Dec 30 18:45:34 2014 +0900 @@ -0,0 +1,92 @@ +#!/usr/bin/env python + +import sys + +def checkFormat(file): + f = open(file) + n = 0 #line count + oldlen=0 #length of previous line + + for line in f: + line=line.rstrip('\n\t ') + n=n+1 + if line.find('track') == -1 and line.find('browse') == -1 and line and n<20: + row=line.split(); + rowlen=len(row) + + #check for 3 fields + if rowlen < 3: + sys.stdout.write('Error with BED file format: need atleast 3 fields per line\n') + sys.exit() + + #check is field 3 is greater thant field 2 + if int(row[2]) < int(row[1]): + sys.stdout.write('Error with BED file format: field 3 needs to be greater than row 2\n') + sys.exit() + + #check each field + m=0 #field number + while m < len(row): + #check if length of lines are consistent + if rowlen != oldlen and oldlen != 0: + sys.stdout.write('Error with BED file format: number of fields do not match\n') + sys.exit() + #column 1 & 4 + #if (m==0 or m==3) and row[m].isdigit() == 1: + # pass + + #column 2 + elif m==1: + if row[m].isdigit() == 0: + sys.stdout.write('Error with BED file format: line%d,field%d need a number\n' %(n,m+1)) + sys.exit() + elif row[m] < 0: + sys.stdout.write('Error with BED file format: line%d,field%d can not be negative\n' %(n.m)) + sys.exit() + #column 3, 7, 8, 10 + elif (m==2 or m==6 or m==7 or m==9): + if row[m].isdigit() == 0: + sys.stdout.write('Error with BED file format: line%d,field%d need a number\n' %(n,m+1)) + sys.exit() + elif m==9: + blockCount=int(row[9]) + #column 5 + #elif m==4: + # try: + # float(row[4]) + # except ValueError: + # sys.stdout.write('Error with BED file format: line%d,field%d needs to be a number\n' %(n,m+1)) + # sys.exit() + # else: + # pass + + #column 6 + elif m==5 and (row[5] != '-' and row[5] != '+'): + sys.stdout.write('Error with BED file format: need +/- in line%d,field%d\n' %(n,m+1)) + sys.exit() + #column 9 + elif m==8 and row[8] != '0': + sys.stdout.write('Error with BED file format: line%d,field%d is always 0\n' %(n,m+1)) + sys.exit() + #column 11 & 12 + elif m==10 or m==11: + if row[m].find(',')==-1: + sys.stdout.write('Error with BED file format: need comma separated list at line%d,field%d\n' %(n,m+1)) + sys.exit() + else: + col=row[m].strip(',').split(',') + if len(col) != blockCount: + sys.stdout.write('Error with BED file format: block count does not match list length at line%d,field%d\n' %(n,m+1)) + sys.exit() + else: + for l in col: + if l.isdigit() == 0: + sys.stdout.write('Error with BED file format: need list of numbers at line%d,field%d\n' %(n,m+1)) + sys.exit() + m=m+1 + oldlen=rowlen + #elif n>=20: + # break +if __name__ == '__main__': + checkFormat(sys.argv[1]) + sys.stdout.write('passed') diff -r 000000000000 -r 97bd5bb4204c macs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs.xml Tue Dec 30 18:45:34 2014 +0900 @@ -0,0 +1,785 @@ + + Model-based Analysis for ChIP-Seq + /bin/bash $shscript + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +#!/bin/bash +#set $dollar = chr(36) +#set $gt = chr(62) +#set $lt = chr(60) +#set $ad = chr(38) + +tfilesize=`du -b $tfile | awk '{print ${dollar}1}'` + +if [[ ${dollar}tfilesize -gt 10000000000 ]];then + echo "Treatment file is too big! 10G is the maximum!" ${gt}${ad}2 + exit; +fi + +if [ $cfile != "None" ];then + cfilesize=`du -b $cfile | awk '{print ${dollar}1}'` + + if [[ ${dollar}cfilesize -gt 10000000000 ]];then + echo "Control file is too big! 10G is the maximum!" ${gt}${ad}2 + exit; + fi +fi + +#if $model.use_model == "" +#if $model.sfold.value > $model.lfold.value + echo "Large Fold has to be greater than Small Fold" ${gt}${ad}2 + exit; +#end if +#end if + +#if $diag_report.diag_report_select == "yes" +#if $diag_report.femin.value > $diag_report.femax.value + echo "Maximum Fold Enrichment has to be greater than Minimum Fold Enrichment" ${gt}${ad}2 + exit; +#end if +#end if + +#if $advopt.advopt_select == "yes" +#if $advopt.lambda_small.value > $advopt.lambda_large.value + echo "Large lambda has to be greater than Small lambda" ${gt}${ad}2 + exit; +#end if +#end if + +#NOTE: IF --nomodel is used, then we feed in the shiftsize param, ELSE feed in mfold param. +#if $model.use_model == "nomodel" +#set $m="--nomodel --shiftsize "+str($model.shift_size) +#else +#set $m="--mfold "+str($model.sfold)+","+str($model.lfold) +#end if + +#NOTE: the control file is optional, if it is unspecified it is sent as 'None' +#if str($cfile) != "None" +#set $c = " -c "+ str($cfile) +#else +#set $c = "" +#end if + +##set $extracommand = "touch "+str($wigoutput) + +#if $advopt.advopt_select == "yes" +#if str($advopt.lambda) == "nolambda" +#set $lamb="--"+str($advopt.lambda) +#else +#set $lamb="" +#end if +#if str($advopt.make_wig) == "wig" +#set $mkwig="--"+str($advopt.make_wig) +#else +#set $mkwig="" +#end if +#set $advparam = "--bw="+str($advopt.bandwidth)+" "+str($lamb)+" --slocal="+str($advopt.lambda_small)+" --llocal="+str($advopt.lambda_large)+" "+str($mkwig) +#if $advopt.make_wig.value != "" +#set $extracommand = "zcat macs_output_MACS_wiggle/treat/*.gz > "+str($wigoutput) +#end if +#else +#set $advparam = "--bw=300 --wig" +#set $extracommand = "zcat macs_output_MACS_wiggle/treat/*.gz > "+str($wigoutput) +#end if + +#if $diag_report.diag_report_select == "yes" +#set $diagparam = "--diag --fe-min=0 --fe-step=20" +#if $diag_report.femin.value != "" +#set $diagparam = $diagparam.replace("--fe-min=0", "--fe-min="+str($diag_report.femin.value)) +#end if +#if $diag_report.festep.value != "" +#set $diagparam = $diagparam.replace("--fe-step=20", "--fe-step="+str($diag_report.festep.value)) +#end if +#if str($diag_report.femax.value) != "" +#set $diagparam = $diagparam+" --fe-max="+str($diag_report.femax.value) +#end if +#else +#set $diagparam = " " +#end if + +#set genomeSize = $genome_size_cond.genome_size +#if $genome_size_cond.genome_size == "OTHER" +#set $genomeSize = $genome_size_cond.genome_size_other +#end if + +#set $keepdup = "--keep-dup "+ str($keep_dup) + +macs14 -t $tfile $c --format=$format --gsize=$genomeSize --tsize=$tag_size $m $advparam --pvalue=$pvalue --name=macs_output $diagparam --single-profile $keepdup ${ad}${gt} $log +cp macs_output_peaks.bed $bedoutput +cp macs_output_summits.bed $summitsoutput +cp macs_output_peaks.xls $xlsoutput +#if $diag_report.diag_report_select == "yes" +cp macs_output_diag.xls $xlsdiagreport +#end if + +#if $advopt.advopt_select == "yes" +#if $advopt.make_wig.value != "" +$extracommand +#end if +#else +$extracommand +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +This tool performs peak calling for ChIP-Seq data. MACS is developped +in Xiaole Shirley Liu's lab, by Tao Liu and Yong Zhang, and published +on Genome Biology (pubmed: 18798982). The version deployed here is +1.4.0rc2. + +.. class:: infomark + +**TIP:** Please first upload your treatment and control files using the **Upload File from your computer tool**. + +.. class:: infomark + +**TIP:** If you choose to generate a wiggle file, it will take longer +time. + +----- + +**Parameters** + +- **Treatment file** The input file for ChIP/treatment channel chosen from the + history. Approporiate format is BED, ELAND, and ELAND_MULTI. SAM and BAM are + also supported. MACS can accept pair-end sequencing data in SAM/BAM format. +- **Control file** The input file for input/control channel chosen + from the history. +- **Format** The format of input files. Choices are AUTO (Auto detect format) + BED ( >= 6 columns), ELAND ( eland_result), ELAND_MULTI ( eland_multi), + ELANDMULTIPET, ELANDEXPORT, SAM (SAM format), BAM ( binary BAM format) + and BOWTIE ( bowtie .map output) +- **Effective genome size** Select the desired genome assembly and the correct + size will be selected. The choices are hg18(2.77e9), hg19(2.79e9), mm8(1.87e9), + mm9(1.91e9), ce4(9.03e7), ce6(9.03e7), dm2(1.19e8), and dm3(1.52e8). +- **Tag size** is the size of reads. +- **P-Value** is the pvalue cutoff. Default is 0.00001, for looser + results, try 0.001 instead. +- **Use Model** is whether or not to use Macs paired peaks model. +- **Model fold** is available when **Use Model** is true, which is the + foldchange to chose paired peaks to build paired peaks model. Users + need to set a lower(smaller) and upper(larger) number for fold change + so that MACS will only use the peaks within these foldchange range to + build model. +- **Shift size** is available when **Use Model** is false, which will + represent the *HALF* of the fragment size of your sample. If your + sonication and size selection size is 300 bps, after you trim out + nearly 100 bps adapters, the fragment size is about 200 bps, so you + can specify 100 here. +- **Keep Duplicate Tags** It controls the MACS behavior towards + duplicate tags at the exact same location -- the same coordination and + the same strand. The default 'auto' option makes MACS calculate the + maximum tags at the exact same location based on binomal distribution + using 1e-5 as pvalue cutoff; and the 'all' option keeps every tags. + If an integer is given, at most this number of tags will be kept at + the same location. Default: 1 +- **Advanced Options** to turn on advanced settings. You will lose + advanced settings and go back to default parameters when you choose + 'No'. +- **Bandwidth (Advanced)** is the bandwidth to scan for paired peaks when **Use + Model** is on, and is the *HALF* of the window size to detect actual + peaks when **Use Model** is off. +- **Use Lambda (Advanced)** to turn on or off local lambda model which + can use the local bias at peak regions to throw out false positives. +- **Small Lambda (Advanced)** The small nearby region in basepairs to calculate + dynamic lambda. This is used to capture the bias near the peak summit region. + Invalid if there is no control data. DEFAULT: 1000 +- **Large Lambda (Advanced)** The large nearby region in basepairs to calculate + dynamic lambda. This is used to capture the surround bias. DEFAULT: 10000. +- **Generate a wig file (Advanced)** to turn on or off the wiggle file + generation for ChIP channel. The wiggle file is the fragment pileup + accumulations at every 10 bps. +- **Diagnostic Report** whether or not to produce a diagnosis report. +- **Minimum Fold Enrichment (Diagnosis)** Minimum fold enrichment to consider. +- **Maximum Fold Enrichment (Diagnosis)** Maximum fold enrchment to consider. + Leave blank for default max value. +- **Fold Enrichment Step (Diagnosis)** Interval of fold enrichment. + +----- + +**Outputs** + +- **BED file** for peak locations in BED format. Typically used in gene association study like CEAS, or correlation calculation. +- **BED file** for peak summits locations in BED format. Typically used in DNA motif analysis or conservation check. +- **XLS file** for detail informations in a tab-delimited file. +- **WIGGLE file** for fragments pileup at every 10 bps of chIP channel + in WIGGLE format. +- **LOG file** for job log. If you see errors, please attach this in + the bug report +- **Diagnosis Report** empty unless diagnosis report is set to yes + + + + diff -r 000000000000 -r 97bd5bb4204c peak2gene.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/peak2gene.xml Tue Dec 30 18:45:34 2014 +0900 @@ -0,0 +1,89 @@ + + + This tool is abolished, please use BETA-minus instead. + /bin/bash $shscript + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +#!/bin/bash + +#import os + +#set $dollar = chr(36) +#set $gt = chr(62) +#set $lt = chr(60) +#set $ad = chr(38) + +#set $path = $os.path.abspath($__app__.config.tool_path) + +lines=`wc -l $bfile | tail -1 | awk '{print ${dollar}1}'` +format=`$path/cistrome/fcfunc.py $bfile` + +if [[ ${dollar}lines -gt 500000 ]];then + echo "BED file is too big! 100K lines are the maximum!" ${gt}${ad}2 + exit; +fi +if [[ ${dollar}format != "passed" ]]; then + echo ${dollar}format ${gt}${ad}2 + exit; +fi + +#set $advparam = "" +#if $dist +#set $advparam = $advparam+"-d "+str($dist) +#end if + +#set $gtpath = os.path.join( os.path.abspath("tool-data"), "ceaslib", "GeneTable", $bfile.metadata.dbkey ) + +PCGA.py -t $bfile --name=output -g $gtpath --op=$op $genetype $advparam ${ad}${gt} $log +mv output_peaks_annotation.txt $output_peak_annotation +mv output_gene_annotation.txt $output_gene_annotation + + + + + + + + + + + + + + +This tool is abolished, please use BETA-minus instead. + + +