# HG changeset patch # User charles-bernard # Date 1477557779 14400 # Node ID 1714165f5df026fddd65cf72da27f6aedc197d2c # Parent 728294cecd969dbfb6893e7f2902cb467d277965 Uploaded diff -r 728294cecd96 -r 1714165f5df0 ALFA/ALFA_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ALFA/ALFA_wrapper.py Thu Oct 27 04:42:59 2016 -0400 @@ -0,0 +1,194 @@ +#!/usr/bin/python + +import argparse +import logging +import os +import re +import shutil +import subprocess +import sys +import tempfile + +def exit_and_explain(msg): + logging.critical(msg) + sys.exit(msg) + +def cleanup_before_exit(tmp_dir): + if tmp_dir and os.path.exists(tmp_dir): + shutil.rmtree(tmp_dir) + +def get_arg(): + parser = argparse.ArgumentParser() + parser.add_argument('--project_name', dest='project_name', action='store', nargs=1, metavar='project_name', type=str) + #Input 1: Annotation File + parser.add_argument('--index', dest='indexes', action='store', nargs=2, metavar=('stranded_index_filename', 'unstranded_index_filename'), type=str) + parser.add_argument('--bi_index', dest='bi_indexes', action='store', nargs=1, metavar='built_in_indexes_dir_path', type=str ) + parser.add_argument('--annotation', dest='annotation_file', action='store', nargs=1, metavar='annotation_gtf_file', type=str ) + #Input 2: Mapped Reads + parser.add_argument('--reads_format', dest='reads_format', action='store', nargs=1, choices=['bam', 'bedgraph'], metavar='reads_format', type=str) + parser.add_argument('--reads', dest='reads', action='store', nargs='+', metavar=('bam_file1 label1',""), type=str) + parser.add_argument('--strandness', dest='strandness', action='store', nargs=1, default=['unstranded'], choices=['unstranded', 'forward', 'reverse'], metavar='strandness', type=str) + #Output files + parser.add_argument('--output_pdf', dest='output_pdf', action='store', nargs=1, metavar='output_pdf_filename', type=str) + parser.add_argument('--output_svg', dest='output_svg', action='store', nargs=2, metavar=('categories_svg_filename', 'biotypes_svg_filename'), type=str) + parser.add_argument('--output_png', dest='output_png', action='store', nargs=2, metavar=('categories_png_filename', 'biotypes_png_filename'), type=str) + parser.add_argument('--output_count', dest='output_count', action='store', nargs=1, metavar='output_count_filename', type=str) + parser.add_argument('--output_index', dest='output_indexes', action='store', nargs=2, metavar=('output_stranded_index_filename', 'output_unstranded_index_filename'), type=str) + #Output Options + parser.add_argument('--categories_depth', dest='categories_depth', action='store', nargs=1, default=[3], choices=range(1,5), metavar='categories_depth', type=int) + parser.add_argument('--plot_format', dest='plot_format', action='store', nargs=1, choices=['pdf', 'png', 'svg'], metavar='plot_format', type=str) + parser.add_argument('--threshold', dest='threshold', action='store', nargs=2, metavar=('yMin', 'yMax'), type=float) + #Internal variables + parser.add_argument('--log_report', dest='log_report', action='store', nargs=1, metavar='log_filename', type=str) + parser.add_argument('--galaxy_root', dest='GALAXY_ROOT_DIR', action='store', nargs=1, metavar='galaxy_root_path', type=str) + parser.add_argument('--tool_dir', dest='GALAXY_TOOL_DIR', action='store', nargs=1, metavar='galaxy_tool_dir_path', type=str) + args = parser.parse_args() + return args + +def make_tmp_dir(galaxy_root): + parent_dir = os.path.join(galaxy_root, 'database/tmp/') + if os.path.exists(parent_dir): + tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='', dir=parent_dir) + else: + tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='', dir='.') + return tmp_dir + +def mv_and_rename_user_indexes(stranded_index, unstranded_index): + index='index' + shutil.copy(stranded_index, index + '.stranded.index') + shutil.copy(unstranded_index, index + '.unstranded.index') + return index + +def get_input2_args(reads_list, format): + n = len(reads_list) + if n%2 != 0: + exit_and_explain('Problem with pairing reads filename and reads label') + input2_args='-i' + k = 0 + reads_filenames = [''] * (n/2) + reads_labels = [''] * (n/2) + for i in range(0, n, 2): + reads_filenames[k] = reads_list[i].split('__fname__')[1] + reads_labels[k] = reads_list[i+1].split('__label__')[1] + if not reads_labels[k]: + reads_labels[k] = 'sample_%s' % str(k+1) + input2_args='%s %s %s' % (input2_args, reads_filenames[k], reads_labels[k]) + k += 1 + if format == 'bedgraph': + input2_args = input2_args + ' --bedgraph' + return input2_args, reads_filenames, reads_labels + +def redirect_errors(alfa_out, alfa_err): + # When the option --n is enabled, alfa prints '### End of the program' in stderr even if the process worked- + # The following lines to avoid the tool from crashing in this case + if alfa_err and not re.search('### End of program', alfa_err): + # When alfa prints '### End of program' in stdout, all the messages in stderr are considered + # as warnings and not as errors. + if re.search('### End of program', alfa_out): + logging.warning("The script ALFA.py encountered the following warning:\n\n%s" % alfa_err) + logging.info("\n******************************************************************\n") + # True errors make the script exits + else: + exit_and_explain("The script ALFA.py encountered the following error:\n\n%s" % alfa_err) + +def merge_count_files(reads_labels): + merged_count_file = open('count_file.txt', 'wb') + for i in range(0, len(reads_labels)): + current_count_file = open(reads_labels[i] + '.categories_counts', 'r') + reads_label = reads_labels[i] + merged_count_file.write('##LABEL: %s\n\n' % reads_label) + merged_count_file.write(current_count_file.read()) + merged_count_file.write('__________________________________________________________________\n') + current_count_file.close() + merged_count_file.close() + return 'count_file.txt' + +def main(): + args = get_arg() + + if not (args.output_pdf or args.output_png or args.output_svg or args.output_indexes or args.output_count): + exit_and_explain('Error: no output to return\nProcess Aborted\n') + + tmp_dir = make_tmp_dir(args.GALAXY_TOOL_DIR[0]) + os.chdir(tmp_dir) + + logging.basicConfig(level=logging.INFO, filename=args.log_report[0], filemode="a+", format='%(message)s') + + alfa_path = os.path.join(args.GALAXY_TOOL_DIR[0], 'ALFA.py') + + #INPUT1: Annotation File + if args.indexes: + # The indexes submitted by the user must exhibit the suffix '.(un)stranded.index' and will be called by alfa by their prefix + index = mv_and_rename_user_indexes(args.indexes[0], args.indexes[1]) + input1_args = '-g %s' % index + elif args.bi_indexes: + input1_args = '-g %s' % args.bi_indexes[0] + elif args.annotation_file: + input1_args = '-a %s' % args.annotation_file[0] + else: + exit_and_explain('No annotation file submitted !') + + #INPUT 2: Mapped Reads + if args.reads: + input2_args, reads_filenames, reads_labels = get_input2_args(args.reads, args.reads_format[0]) + strandness = '-s %s' % args.strandness[0] + else: + exit_and_explain('No reads submitted !') + + ##Output options + categories_depth = '-d %s' % args.categories_depth[0] + if not (args.output_pdf or args.output_png or args.output_svg): + output_args = '--n' + else: + if args.output_pdf: + output_args = '--pdf plot.pdf' + if args.output_png: + output_args = '--png plot' + if args.output_svg: + output_args = '--svg plot' + if args.threshold: + output_args = '%s -t %.3f %.3f' % (output_args, args.threshold[0], args.threshold[1]) + + ##Run alfa + cmd = 'python %s %s %s %s %s %s' % (alfa_path, input1_args, input2_args, strandness, categories_depth, output_args) + logging.info("__________________________________________________________________\n") + logging.info("Alfa execution") + logging.info("__________________________________________________________________\n") + logging.info("Command Line:\n%s\n" % cmd) + logging.info("------------------------------------------------------------------\n") + alfa_result = subprocess.Popen(args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + alfa_out, alfa_err = alfa_result.communicate() + + ##Handle stdout, warning, errors... + redirect_errors(alfa_out, alfa_err) + + logging.info("Alfa prompt:\n%s" % alfa_out) + + ##Redirect outputs + if args.output_pdf: + shutil.move('plot.pdf', args.output_pdf[0]) + if args.output_png: + shutil.move('plot' + '.categories.png', args.output_png[0]) + shutil.move('plot' + '.biotypes.png', args.output_png[1]) + if args.output_svg: + shutil.move('plot' + '.categories.svg', args.output_svg[0]) + shutil.move('plot' + '.biotypes.svg', args.output_svg[1]) + if args.output_count: + count_filename = merge_count_files(reads_labels) + shutil.move(count_filename, args.output_count[0]) + if args.output_indexes: + if args.annotation_file: + indexes_regex = re.compile('.*\.index') + indexes = filter(indexes_regex.search, os.listdir('.')) + indexes.sort() + shutil.move(indexes[0], args.output_indexes[0]) + shutil.move(indexes[1], args.output_indexes[1]) + if args.indexes: + shutil.move(index + '.stranded.index', args.output_indexes[0]) + shutil.move(index + '.unstranded.index', args.output_indexes[1]) + if args.bi_indexes: + shutil.move(args.bi_indexes[0] + '.stranded.index', args.output_index[0]) + shutil.move(args.bi_indexes[1] + '.unstranded.index', args.output_index[1]) + + cleanup_before_exit(tmp_dir) +main() \ No newline at end of file diff -r 728294cecd96 -r 1714165f5df0 ALFA/alfa_wrapper.sh --- a/ALFA/alfa_wrapper.sh Tue Oct 11 11:10:18 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,235 +0,0 @@ -#!usr/bin/bash - -######################################################################################################### -# ARGUMENTS FROM alfa_wrapper.xml # -######################################################################################################### -galaxyRoot=$1; -toolDir=$2 -configFile=$3; -logReport=$4; -sed -i -e '/^$/d; s/\t//g;' $configFile; -printf "__________________________________________________________________\n\n" > $logReport -printf " ALFA CONFIG \n" >> $logReport -printf "__________________________________________________________________\n" >> $logReport -cat $configFile >> $logReport - -######################################################################################################### -# INITIALIZATION OF THE VARIABLES from $configFile # -######################################################################################################### -#_INPUT1 -annotationSource=`grep -P '^annotationSource ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; -if [ "$annotationSource" == "personal_gtf" ]; then - annotationFile=`grep -P '^annotationFile ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; -elif [ "$annotationSource" == "built_in_index" ]; then - built_in_index_prefix=`grep -P '^built_in_index_prefix ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; -else - strandedIndex=`grep -P '^strandedIndex ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; - unstrandedIndex=`grep -P '^unstrandedIndex ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; -fi - -#_INPUT2 -readsType=`grep -P '^readsType ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; -readsFileList=`grep -P '^readsFile\[[0-9]+\] ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; -readsLabelList=`grep -P '^readsLabel\[[0-9]+\] ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; - -#_OUTPUT CHOICES -plotChoice=`grep -P '^plotChoice ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; -countFileChoice=`grep -P '^countFileChoice ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; -indexChoice=`grep -P '^indexChoice ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; - -#_OUTPUT OPTIONS -strandness=`grep -P '^strandness ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; -categoriesDepth=`grep -P '^categoriesDepth ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; -plotFormat=`grep -P '^plotFormat ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; -plotThresholdChoice=`grep -P '^plotThresholdChoice ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; -if [ "$plotThresholdChoice" == "True" ]; then - yMin=`grep -P '^yMin ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; - yMax=`grep -P '^yMax ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; -fi - -#_OUTPUT FILES -if [ "$plotChoice" == "True" ]; then - if [ "$plotFormat" == "pdf" ]; then - outputPdf=`grep -P '^outputPdf ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; - elif [ "$plotFormat" == "svg" ]; then - outputCategoriesSvg=`grep -P '^outputCategoriesSvg ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; - outputBiotypesSvg=`grep -P '^outputBiotypesSvg ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; - else - outputCategoriesPng=`grep -P '^outputCategoriesPng ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; - outputBiotypesPng=`grep -P '^outputBiotypesPng ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; - fi -fi -if [ "$countFileChoice" == "True" ]; then - outputCountFile=`grep -P '^outputCountFile ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; -fi -if [ "$indexChoice" == "True" ]; then - outputStrandedIndex=`grep -P '^outputStrandedIndex ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; - outputUnstrandedIndex=`grep -P '^outputUnstrandedIndex ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`; -fi - -######################################################################################################### -# CREATION OF A TMP DIRECTORY FOR THE OUTPUT FILES OF ALFA AND cd # -######################################################################################################### -outputDirectory=`mktemp -d "$galaxyRoot"/database/tmp/tmpXXXXXX`; -if [ -d $outputDirectory ]; then - chmod -R ugo+wrx $outputDirectory; - rm -R $outputDirectory; -fi -mkdir $outputDirectory; -chmod -R ugo+wrx $outputDirectory; -cd $outputDirectory; - -######################################################################################################### -# TEST OF INPUT1 # -######################################################################################################### -if [ "$annotationSource" == "index" ]; then - #need to copy the files.dat to .*index because ALFA requires the extension ".(un)stranded.index" - index="index" - cp $strandedIndex $index".stranded.index" - cp $unstrandedIndex $index".unstranded.index" -fi - -######################################################################################################### -# TEST OF INPUT2 AND DETERMINATION OF PYTHON READS INPUT ARGUMENT # -######################################################################################################### -readsListLen=`echo "$readsFileList" | wc -l`; -readsInput=""; -for (( i = 1; i <= readsListLen; i++ )) do - readsFile[$i]=`echo "$readsFileList" | awk -v i=$i 'NR==i'`; - readsLabel[$i]=`echo "$readsLabelList" | awk -v i=$i 'NR==i' | sed -e 's/ /_/g'`; - if [ "$readsType" == "bam" ]; then - bamSorted=`samtools view -H "${readsFile[$i]}" | grep -c 'SO:unsorted'` - if [ "$bamSorted" != "0" ] ; then - samtools sort ${readsFile[$i]} ${readsFile[$i]} - fi - else - #need to copy the file.dat to tmp.bedgraph because ALFA requires the extension ".bedgraph" - bedgraphFile="tmpBedgraph_"$i - cp ${readsFile[$i]} $bedgraphFile".bedgraph" - readsFile[$i]=$bedgraphFile - fi - if [ "${readsLabel[$i]}" == "" ]; then - readsLabel[$i]="sample_""$i"; - fi - readsInput=$readsInput" "${readsFile[$i]}" "${readsLabel[$i]}; -done - -######################################################################################################### -# DETERMINATION OF THE APPROPRIATE SCRIPTS ARGUMENTS # -######################################################################################################### -scriptPath="$toolDir/"; -if [ "$annotationSource" == "index" ]; then - scriptInput="-g $index -i ""$readsInput"; -elif [ "$annotationSource" == "built_in_index" ]; then - scriptInput="-g $built_in_index_prefix -i ""$readsInput"; -else - scriptInput="-a $annotationFile -i ""$readsInput"; -fi -if [ "$readsType" = "bedgraph" ]; then - scriptInput=$scriptInput" --bedgraph"; -fi -scriptStrandness="-s "$strandness -scriptCategoriesDepth="-d "$categoriesDepth -if [ "$plotChoice" == "True" ]; then - if [ "$plotFormat" == "pdf" ]; then - scriptPlotOutput="--pdf plotFile.pdf"; - else - scriptPlotOutput="--"$plotFormat" plotFile"; - fi - if [ "$plotThresholdChoice" == "True" ]; then - scriptPlotOutput=$scriptPlotOutput" -t ""$yMin"" ""$yMax" - fi -else - scriptPlotOutput="--n"; -fi - -######################################################################################################### -# DISPLAY ALFA PROCESS # -######################################################################################################### -printf "__________________________________________________________________\n\n" >> $logReport -printf " ALFA PROCESS \n" >> $logReport -printf "__________________________________________________________________\n" >> $logReport - -if [ "$plotChoice" == "False" ] && [ "$countFileChoice" == "False" ] && [ "$indexChoice" == "False" ]; then -cat <&2 - -No output to return. -Process Aborted -error -exit 0 -fi - -printf "Command:\n" >> $logReport -echo "python ""$scriptPath"ALFA.py $scriptInput $scriptStrandness $scriptCategoriesDepth $scriptPlotOutput >> $logReport; -printf "\n******************************************************************\n" >> $logReport -printf "Temporary Output Directory:\n" >> $logReport -echo $outputDirectory >> $logReport -printf "\n******************************************************************\n" >> $logReport -printf "ALFA prompt:\n" >> $logReport -python "$scriptPath"ALFA.py $scriptInput $scriptStrandness $scriptCategoriesDepth $scriptPlotOutput >> $logReport 2>errorFile; -printf "\n******************************************************************\n" >> $logReport - -######################################################################################################### -# REDIRECTION OF ERRORS - TMP SOURCE ALFA.PY MUST BE CORRECTED SOON # -######################################################################################################### -if [[ -s errorFile ]]; then - #When the option --n is enabled, alfa prints '### End of the program' in stderr even if the process worked- - #The following lines to avoid the tool from crashing in this case - endProgram=`grep -c '### End of program' errorFile` - if [ "$endProgram" == "0" ]; then - #When alfa prints '### End of program' in stdout, all the messages in stderr are considered - #as warnings and not as errors. True errors make the script exits with code "2" - endProgram=`grep -c '### End of program' $logReport` - if [ "$endProgram" == "0" ]; then - >&2 printf "The script ALFA.py encountered the following error:\n\n" - >&2 cat errorFile - printf "ALFA error:\n" >> $logReport - cat errorFile >> $logReport - printf "\n******************************************************************\n" >> $logReport - exit 2 - else - >&2 printf "The script ALFA.py encountered the following warning:\n\n" - >&2 cat errorFile - printf "ALFA warning:\n" >> $logReport - cat errorFile >> $logReport - printf "\n******************************************************************\n" >> $logReport - fi - fi -fi - -######################################################################################################### -# OUTPUT REDIRECTIONS # -######################################################################################################### -if [ "$plotChoice" == "True" ]; then - if [ "$plotFormat" == "pdf" ]; then - mv "plotFile.pdf" $outputPdf; - elif [ "$plotFormat" == "png" ]; then - mv "plotFile.categories.png" $outputCategoriesPng; - mv "plotFile.biotypes.png" $outputBiotypesPng; - else - mv "plotFile.categories.svg" $outputCategoriesSvg; - mv "plotFile.biotypes.svg" $outputBiotypesSvg; - fi -fi -if [ "$countFileChoice" == "True" ]; then - > countFile; - for (( i = 1; i <= readsListLen; i++ )) do - printf "##LABEL: "${readsLabel[$i]}"\n\n" >> countFile; - cat ${readsLabel[$i]}".categories_counts" >> countFile; - printf "__________________________________________________________________\n" >> countFile; - done - mv countFile $outputCountFile; -fi -if [ "$indexChoice" == "True" ]; then - if [ "$annotationSource" == "index" ]; then - mv $strandedIndex $outputStrandedIndex - mv $unstrandedIndex $outputUnstrandedIndex - elif [ "$annotationSource" == "built_in_index" ]; then - cp $built_in_index_prefix".stranded.index" $outputStrandedIndex - cp $built_in_index_prefix".unstranded.index" $outputUnstrandedIndex - else - annotationFileName=`grep -P -o '[^/]*\.dat$' <<< $annotationFile` - mv $annotationFileName".stranded.index" $outputStrandedIndex - mv $annotationFileName".unstranded.index" $outputUnstrandedIndex - fi -fi \ No newline at end of file diff -r 728294cecd96 -r 1714165f5df0 ALFA/alfa_wrapper.xml --- a/ALFA/alfa_wrapper.xml Tue Oct 11 11:10:18 2016 -0400 +++ b/ALFA/alfa_wrapper.xml Thu Oct 27 04:42:59 2016 -0400 @@ -8,10 +8,61 @@ matplotlib - - alfa_wrapper.sh $__root_dir__ $__tool_directory__ $ALFA_config $logReport - - + + + @@ -29,7 +80,7 @@ - + @@ -74,7 +125,7 @@ -
+
@@ -92,6 +143,7 @@ +
@@ -124,61 +176,6 @@ - - - projectName=$projectName - - ##__INPUT 1__## - annotationSource=$annotation.annotationSource['annotationSourceSelection'] - #if str ( $annotation.annotationSource['annotationSourceSelection'] ) == "index" - annotationFile=None - strandedIndex=$annotation.annotationSource['strandedIndex'] - unstrandedIndex=$annotation.annotationSource['unstrandedIndex'] - #else if str ( $annotation.annotationSource['annotationSourceSelection'] ) == "built_in_index" - annotationFile=None - built_in_index_prefix=$annotation.annotationSource.built_in_index_prefix.fields.prefix - #else - annotationFile=$annotation.annotationSource['annotationFile'] - strandedIndex=None - unstrandedIndex=None - #end if - - ##__INPUT 2__## - readsType=$reads.readsType['readsTypeSelection'] - #for $i, $r in enumerate ( $reads.readsType['readsList'] ) - readsFile[$i]=$r.readsFile - readsLabel[$i]=$r.readsLabel - #end for - strandness=$reads['strandness'] - - ##__OUTPUT FILES__## - plotChoice=$outputFiles['plot'] - countFileChoice=$outputFiles['countFile'] - indexChoice=$outputFiles['index'] - - outputPdf=$outputPdf - outputCategoriesPng=$outputCategoriesPng - outputBiotypesPng=$outputBiotypesPng - outputCategoriesSvg=$outputCategoriesSvg - outputBiotypesSvg=$outputBiotypesSvg - outputCountFile=$outputCountFile - outputStrandedIndex=$outputStrandedIndex - outputUnstrandedIndex=$outputUnstrandedIndex - - ##__OUTPUT OPTIONS__## - categoriesDepth=$outputOptions['categoriesDepth'] - plotFormat=$outputOptions['plotFormat'] - plotThresholdChoice=$outputOptions.plotThreshold['plotThresholdChoice'] - #if str ( $outputOptions.plotThreshold['plotThresholdChoice'] ) == "True" - yMin=$outputOptions.plotThreshold.yMin - yMax=$outputOptions.plotThreshold.yMax - #else - yMin=None - yMax=None - #end if - - - @@ -221,13 +218,9 @@ -**ALFA acronym** - -- Annotation.Landscape.For.Aligned reads + + | Chromosome names in reads and in annotation file (gtf or indexes) must be the same for the intersection to occur + | -3. **Output files** +* **Output files** | The result of the intersection is a count file displaying the count of nucleotides in the reads for each genomic categories and biotypes. From this count file, plots of the raw and normalized distributions of the reads among these categories are generated. | In the output files section, the user can choose what kind of files he desires as ALFA output. Categories Count File and Plots are proposed by default. - -.. class:: infomark + | -The user can also select the 'indexes' option as output. This option is interesting if you plan to run ALFA again with the same submitted annotation file. *See Nota Bene/Input 1: Annotation File for more information.* + .. class:: infomark + | The user can also select the 'indexes' option as output. This option is interesting if you plan to run ALFA again with the same submitted annotation file. *See Nota Bene/Input 1: Annotation File for more information.* + | -- `How the plots look like`_ + - `How the plots look like`_ -.. _How the plots look like: https://github.com/biocompibens/ALFA#plots + .. _How the plots look like: https://github.com/biocompibens/ALFA#plots -- `How they are generated`_ + | -.. _How they are generated: https://github.com/biocompibens/ALFA#detailed-example + - `How they are generated`_ + + .. _How they are generated: https://github.com/biocompibens/ALFA#detailed-example ---- @@ -307,7 +313,7 @@ | Benoît Noël and Mathieu Bahin: *compbio team, Institut de Biologie de l'Ecole Normale Supérieure de Paris* - +]]> diff -r 728294cecd96 -r 1714165f5df0 ALFA/tool-data/alfa_genomes_indexes.loc.sample --- a/ALFA/tool-data/alfa_genomes_indexes.loc.sample Tue Oct 11 11:10:18 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -# -#Arabidopsis_thaliana TAIR10 30 Arabidopsis_t_TAIR10_30 Arabidopsis_t_TAIR10_30 Arabidopsis thaliana: TAIR10 /Arabidopsis_thaliana.TAIR10.30 -#Drosophila_melanogaster dm6 30 Drosophila_m_dm6_30 Drosophila_m_dm6_30 Drosophila melanogaster: dm6 /Drosophila_melanogaster.BDGP6.30 -#Homo_sapiens v38 82 Homo_s_v38_82 Homo_s_v38_82 Homo sapiens: v38 /Homo_sapiens.GRCh38.82 -#Mus_musculus v38 83 Mus_m_v38_83 Mus_m_v38_83 Mus musculus: v38 /Mus_musculus.GRCm38.83.chr diff -r 728294cecd96 -r 1714165f5df0 ALFA/tool-data/alfa_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ALFA/tool-data/alfa_indexes.loc.sample Thu Oct 27 04:42:59 2016 -0400 @@ -0,0 +1,2 @@ +# +#Dictyostelium_discoideum dicty_2 7 Dictyostelium_discoideum_dicty_2_7 Dictyostelium_discoideum_dicty_2_7 Dictyostelium_discoideum: dicty_2 (release 7) diff -r 728294cecd96 -r 1714165f5df0 ALFA/tool-data/alfa_indexes.loc.sample~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ALFA/tool-data/alfa_indexes.loc.sample~ Thu Oct 27 04:42:59 2016 -0400 @@ -0,0 +1,5 @@ +# +#Arabidopsis_thaliana TAIR10 30 Arabidopsis_t_TAIR10_30 Arabidopsis_t_TAIR10_30 Arabidopsis thaliana: TAIR10 /Arabidopsis_thaliana.TAIR10.30 +#Drosophila_melanogaster dm6 30 Drosophila_m_dm6_30 Drosophila_m_dm6_30 Drosophila melanogaster: dm6 /Drosophila_melanogaster.BDGP6.30 +#Homo_sapiens v38 82 Homo_s_v38_82 Homo_s_v38_82 Homo sapiens: v38 /Homo_sapiens.GRCh38.82 +#Mus_musculus v38 83 Mus_m_v38_83 Mus_m_v38_83 Mus musculus: v38 /Mus_musculus.GRCm38.83.chr diff -r 728294cecd96 -r 1714165f5df0 ALFA/tool_data_table_conf.xml.sample --- a/ALFA/tool_data_table_conf.xml.sample Tue Oct 11 11:10:18 2016 -0400 +++ b/ALFA/tool_data_table_conf.xml.sample Thu Oct 27 04:42:59 2016 -0400 @@ -2,6 +2,6 @@ species, version, release, value, dbkey, name, prefix - +
- \ No newline at end of file + diff -r 728294cecd96 -r 1714165f5df0 ALFA/tool_data_table_conf.xml.sample~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ALFA/tool_data_table_conf.xml.sample~ Thu Oct 27 04:42:59 2016 -0400 @@ -0,0 +1,7 @@ + + + + species, version, release, value, dbkey, name, prefix + +
+ \ No newline at end of file