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Commit message:
Deleted selected files |
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removed:
aggregate.py aggregate.xml |
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| diff -r b24ed1fb8fde -r 6587180179b6 aggregate.py --- a/aggregate.py Mon Feb 13 22:05:15 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,297 +0,0 @@\n-# A translation of aggregate.pl into python! For analysis of Tn-Seq.\n-# This script requires BioPython just like calc_fitness.py, so you need it installed along with its dependencies if you want to run these scripts on your own.\n-# How to install BioPython and a list of its dependencies can be found here: http://biopython.org/DIST/docs/install/Installation.html\n-# K. McCoy\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-##### ARGUMENTS #####\n-\n-def print_usage():\n-\tprint "Aggregate.py\'s usage is as follows:" + "\\n\\n"\n-\tprint "\\033[1m" + "Required" + "\\033[0m" + "\\n"\n-\tprint "-o" + "\\t\\t" + "Output file for aggregated data." + "\\n"\n-\tprint "\\n"\n-\tprint "\\033[1m" + "Optional" + "\\033[0m" + "\\n"\n-\tprint "-c" + "\\t\\t" + "Check for missing genes in the data set - provide a reference genome in genbank format. Missing genes will be sent to stdout." + "\\n"\n-\tprint "-m" + "\\t\\t" + "Place a mark in an extra column for this set of genes. Provide a file with a list of genes seperated by newlines." + "\\n"\n-\tprint "-x" + "\\t\\t" + "Cutoff: Don\'t include fitness scores with average counts (c1+c2)/2 < x (default: 0)" + "\\n"\n-\tprint "-b" + "\\t\\t" + "Bottleneck value: The percentage of insertions randomly lost, which will be discounted for all genes (for example, 20% would be entered as 0.20; default 0.0)" + "\\n"\n-\tprint "-f" + "\\t\\t" + "An in-between file carrying information on the blank count found from calc_fitness or consol_fitness; one of two ways to pass a blank count to this script" + "\\n"\n-\tprint "-w" + "\\t\\t" + "Use weighted algorithm to calculate averages, variance, sd, se" + "\\n"\n-\tprint "-l" + "\\t\\t" + "Weight ceiling: maximum value to use as a weight (default: 999,999)" + "\\n"\n-\tprint "\\n"\n-\tprint "All remainder arguements will be treated as fitness files (those files created by calc_fitness.py)" + "\\n"\n-\tprint "\\n"\n-\t\n-import argparse \n-parser = argparse.ArgumentParser()\n-parser.add_argument("-o", action="store", dest="summary")\n-parser.add_argument("-c", action="store", dest="find_missing")\n-parser.add_argument("-m", action="store", dest="marked")\n-parser.add_argument("-x", action="store", dest="cutoff")\n-parser.add_argument("-b", action="store", dest="blank_pc")\n-parser.add_argument("-f", action="store", dest="blank_file")\n-parser.add_argument("-w", action="store", dest="weighted")\n-parser.add_argument("-l", action="store", dest="weight_ceiling")\n-parser.add_argument("fitnessfiles", nargs=argparse.REMAINDER)\n-\n-arguments = parser.parse_args()\n-\n-if not arguments.summary:\n-\tprint "\\n" + "You are missing a value for the -o flag. "\n-\tprint_usage() \n-\tquit()\n-\n-if not arguments.fitnessfiles:\n-\tprint "\\n" + "You are missing fitness file(s); these should be entered immediately after all the flags. "\n-\tprint_usage() \n-\tquit()\n-\t\n-# 999,999 is a trivial placeholder number\n-\t\n-if (not arguments.weight_ceiling):\n-\targuments.weight_ceiling = 999999\n-\t\n-# Cutoff exists to discard positions with a low number of counted transcripts, because their fitness may not be as accurate - for the same reasoning that studies with low sample sizes can be innacurate. \n-\t\n-if (not arguments.cutoff):\n-\targuments.cutoff = 0\n-\n-# Gets information from the txt output file of calc_fit / consol, if inputted\n-\n-if arguments.blank_file:\n-\twith open(arguments.blank_file) as file:\n-\t\tblank_pc = file.read().splitlines()\n-\t\targuments.blank_pc = float(blank_pc[0].split()[1])\n-\n-if (not arguments.blank_pc):\n-\targuments.blank_pc = 0\n-\n-\n-\n-\n-\n-##### SUBROUTINES #####\n-\n-# A subroutine that calculates the average, variance, standard deviation (sd), and standard error (se) of a group of scores; for use when aggregating scores by gene later on\n-\n-import math\n-def unweighted_average(scores):\n-\tsum = 0\n-\tnum = 0\n-\ti = 0\n-\twhile i < len(scores):\n-\t\tif not scores[i]:\n-\t\t\tscores[i] = 0.0\n-\t\tsum += float(scores[i])\n-\t\tnum += 1\n-\t\ti += 1\n-\taverage = sum/num\n-\txminusxbars = 0\n-\twhile i < len(scores):\n-\t\txminusxbars += (float(scores[i]) - average)**2\n-\tif num <= 1:\n-\t\tvariance = 0\n-\telse:\n-\t'..b'"]]\n-\thandle = open(arguments.find_missing, "rU")\n-\tfor record in SeqIO.parse(handle, "genbank"):\n-\t\trefname = record.id\n-\t\tfeatures = record.features\n-\thandle.close()\n-\t\n-#Goes through the features to find which are genes\n-\t\n-\tfor feature in features:\n-\t\tgene = ""\n-\t\tif feature.type == "gene":\n-\t\t\tlocus = "".join(feature.qualifiers["locus_tag"])\n-\t\t\tif "gene" in feature.qualifiers:\n-\t\t\t\tgene = "".join(feature.qualifiers["gene"])\n-\t\telse:\n-\t\t\tcontinue\n-\t\t\t\n-#Goes through the fitness scores of insertions within each gene, and removes whatever % of blank fitness scores were requested along with their corresponding weights\n-\n-\t\tsum = 0\n-\t\tnum = 0\n-\t\tavgsum = 0\n-\t\tblank_ws = 0\n-\t\ti = 0\n-\t\tif locus in gene_summary.keys():\n-\t\t\tfor w in gene_summary[locus]["w"]:\n-\t\t\t\tif float(w) == 0:\n-\t\t\t\t\tblank_ws += 1\n-\t\t\t\telse:\n-\t\t\t\t\tsum += float(w)\n-\t\t\t\t\tnum += 1\n-\t\t\tcount = num + blank_ws\t\t\n-\t\t\tremoved = 0\n-\t\t\tto_remove = int(float(arguments.blank_pc)*count)\n-\t\t\tif blank_ws > 0:\n-\t\t\t\ti = 0\n-\t\t\t\twhile i < len(gene_summary[locus]["w"]):\n-\t\t\t\t\tw = gene_summary[locus]["w"][i] \n-\t\t\t\t\tif removed == to_remove:\n-\t\t\t\t\t\tbreak\n-\t\t\t\t\tif float(w) == 0:\n-\t\t\t\t\t\tdel gene_summary[locus]["w"][i]\n-\t\t\t\t\t\tdel gene_summary[locus]["s"][i]\n-\t\t\t\t\t\tremoved += 1\n-\t\t\t\t\t\ti -= 1\n-\t\t\t\t\ti += 1\n-\t\t\t\n-#If all the fitness values within a gene are empty, sets mean/var to 0.10 and Xs out sd/se; marks the gene if that\'s requested\n-\n-\t\t\tif num == 0:\t\n-\t\t\t\tif (arguments.marked and locus in marked_set):\n-\t\t\t\t\toutput.append([locus, "0.10", "0.10", "X", "X", gene, count, blank_ws, num, removed, "M", "\\n"])\n-\t\t\t\telse:\n-\t\t\t\t\toutput.append([locus, "0.10", "0.10", "X", "X", gene, count, blank_ws, num, removed, "\\n"])\n-\n-#Otherwise calls average() or weighted_average() to find the aggregate w / count / standard deviation / standard error of the insertions within each gene; marks the gene if that\'s requested\n-\n-\t\t\telse:\n-\t\t\t\tif not arguments.weighted:\n-\t\t\t\t\t(average, variance, stdev, stderr) = unweighted_average(gene_summary[locus]["w"])\n-\t\t\t\telse:\n-\t\t\t\t\t(average, variance, stdev, stderr) = weighted_average(gene_summary[locus]["w"],gene_summary[locus]["s"])\n-\t\t\t\tif (arguments.marked and locus in marked_set):\n-\t\t\t\t\toutput.append([locus, average, variance, stdev, stderr, gene, count, blank_ws, num, removed, "M", "\\n"])\n-\t\t\t\telse:\n-\t\t\t\t\toutput.append([locus, average, variance, stdev, stderr, gene, count, blank_ws, num, removed, "\\n"])\n-\t\t\n-#If a gene doesn\'t have any insertions, sets mean/var to 0.10 and Xs out sd/se, plus leaves count through removed blank because there were no reads.\n-\n-\t\telse:\n-\t\t\tif (arguments.marked and locus in marked_set):\n-\t\t\t\toutput.append([locus, "0.10", "0.10", "X", "X", gene, "", "", "", "", "M", "\\n"])\n-\t\t\telse:\n-\t\t\t\toutput.append([locus, "0.10", "0.10", "X", "X", gene, "", "", "", "", "\\n"])\n-\n-#Writes the aggregated fitness file\n-\n-\twith open(arguments.summary, "wb") as csvfile:\n-\t\twriter = csv.writer(csvfile)\n-\t\twriter.writerows(output)\n-\n-#If finding missing genes is not requested, just finds the aggregate w / count / standard deviation / standard error of the insertions within each gene, and writes them to a file, plus marks the genes requested\n-#This is never called through Galaxy since finding missing genes is just better than not finding them.\n-\n-else:\n-\toutput = [["Locus","W","Count","SD","SE","M\\n"]]\n-\tfor gene in gene_summary.keys():\n-\t\tsum = 0\n-\t\tnum = 0\n-\t\taverage = 0\n-\t\tif "w" not in gene_summary[gene]:\n-\t\t\tcontinue\n-\t\tfor i in gene_summary[gene]["w"]:\n-\t\t\tsum += i\n-\t\t\tnum += 1\n-\t\taverage = sum/num\n-\t\txminusxbars = 0\n-\t\tfor i in w:\n-\t\t\txminusxbars += (i-average)**2\n-\t\tif num > 1:\n-\t\t\tsd = math.sqrt(xminusxbars/(num-1))\n-\t\t\tse = sd / math.sqrt(num)\n-\t\tif (arguments.marked and locus in marked_set):\n-\t\t\toutput.append([gene, average, num, sd, se, "M", "\\n"])\n-\t\telse:\n-\t\t\toutput.append([gene, average, num, sd, se, "\\n"])\n-\twith open(arguments.summary, "wb") as csvfile:\n-\t\twriter = csv.writer(csvfile)\n-\t\twriter.writerows(output)\n\\ No newline at end of file\n' |
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| diff -r b24ed1fb8fde -r 6587180179b6 aggregate.xml --- a/aggregate.xml Mon Feb 13 22:05:15 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,102 +0,0 @@ -<tool id="aggregate" name="Aggregate"> - <description>fitness calculations by gene</description> - <requirements> - <requirement type="package" version="1.64">biopython</requirement> - </requirements> - <command interpreter="python"> - aggregate.py - #if $mark.certain == "yes": - -m $mark.genes - #end if - #if $weighted.algorithms == "yes": - -w 1 - #end if - -x $cutoff - -l $weightceiling - #if $blank.count == "yes": - -b $blank.custom_blanks - #end if - #if $blank.count == "no": - -f $blank.txt_blanks - #end if - -c $ref - -o $output - $input - #for $a in $additionalcsv - ${a.input2} - #end for - </command> - <inputs> - <param name="input" type="data" label="csv fitness file"/> - <repeat name="additionalcsv" title="Additional csv fitness file(s)"> - <param name="input2" type="data" label="Select" /> - </repeat> - <param name="ref" type="data" label="GenBank reference genome"/> - <conditional name="mark"> - <param name="certain" type="select" label="Mark certain genes?"> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <when value="no"> - <!-- do nothing --> - </when> - <when value="yes"> - <param name="genes" type="data" label="Genes to mark" /> - </when> - </conditional> - <conditional name="weighted"> - <param name="algorithms" type="select" label="Use weighted algorithms?"> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <when value="-w 1 "/> - <when value=""/> - </conditional> - <param name="weightceiling" type="float" value="50.0" label="Weight ceiling"/> - <param name="cutoff" type="float" value="10.0" label="Cutoff3"/> - <conditional name="blank"> - <param name="count" type="select" label="Enter custom bottleneck correction value?"> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <when value="no"> - <param name="txt_blanks" type="data" label="txt output from Calc_fit or Consol_fit"/> - </when> - <when value="yes"> - <param name="custom_blanks" type="float" value="0.0" label="bottleneck value (a number from 0.0 to 1.0)"/> - </when> - </conditional> - </inputs> - <outputs> - <data name="output" format="csv"/> - </outputs> - <help> - -**What it does** - -This tool calculates the aggregate fitness values of mutations by gene. - -**The options explained** - -The csv fitness file(s): These are the csv (comma separated values) files containing the fitness values you want to aggregate by gene. Since they should have been produced by the "Calculate Fitness" tool, each line besides the header should represent the following information for an insertion location: position,strand,count_1,count_2,ratio,mt_freq_t1,mt_freq_t2,pop_freq_t1,pop_freq_t2,gene,D,W,nW - -GenBank reference genome: the reference genome of whatever model you're working with, which needs to be in standard genbank format. For more on that format see the genbank website. - -Marking certain genes: If you chose to mark certain genes, those genes will have an "M" under the M column of the resulting aggregate file. - -Using weighted algorithms: Recommended. If you chose to use weighted algorithms, scores will be weighted by the number of reads their insertion location has, as insertions with more reads tend to be more accurate. - -Weight ceiling: This value lets you set a weight ceiling for the weights of fitness values. It's only relevant if you're using weighted algorithms. - -Cutoff3: This value lets you ignore the fitness scores of any insertion locations with an average count (the number of counts from t1 and t2 divided by 2) less than it. - -Bottleneck value: The percentage of insertions randomly lost, which will be discounted for all genes (for example, 20% would be entered as 0.20; default 0 if entered by hand). You can just use the blank % calculated from the normalization genes by calc_fit by entering its txt output file - -The name of your output file: self-explanatory. Remember to have it end in ".csv". - -**Additional notes** - -The output file should have each line (besides the header) represent the following information for a particular gene: locus,mean,var,sd,se,gene,Total,Blank,Not Blank,Blank Removed,M - -</help> -</tool> \ No newline at end of file |