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type alignment {
string basename;
}
type tsv;
type textfile;
app (textfile t) version_goby() {
goby "1g" "version" stdout=@filename(t);
}
(textfile result) tr(textfile text, string from, string to) {
app {
tr from to stdin=@filename(text) stdout=@filename(result);
}
}
(string result) replace(string text, string from, string to) {
textfile f <concurrent_mapper;prefix="string-input", suffix=".txt">;
f=writeData(text);
textfile replacedText <concurrent_mapper;prefix="replace-string", suffix=".txt">;
replacedText=tr(f,from,to);
result=readData(replacedText);
}
app (tsv stats) alignment_to_annotation_counts(
string groupId1,
string group1_basenames,
string groupId2,
string group2_basenames,
string fullPathEntries[],
string annotationFile,
string useWeights,
string adjustGCBias) {
goby "3g" "alignment-to-annotation-counts" fullPathEntries
"--groups" @strcat(groupId1,"=",group1_basenames,"/",groupId2,"=",group2_basenames )
"--compare" @strcat(groupId1,"/",groupId2)
"--annotation" annotationFile
"--use-weights" useWeights
"--adjust-gc-bias" adjustGCBias
"--normalization-methods" "aligned-count"
"--include-annotation-types" "gene" "--write-annotation-counts" "false"
"--eval" "group-averages"
"--stats" @stats;
}
(tsv t) call_de( string groupId1,
string group1_basenames,
string groupId2,
string group2_basenames,
string annotationFile,
string useWeights,
string adjustGCBias) {
// string spaceSeparatedBasename1 = @regexp(group1_basenames, "[,]"," ");
string spaceSeparatedBasename1 = replace(group1_basenames, "[,]","[ ]");
// trace(spaceSeparatedBasename1);
string spaceSeparatedBasename2 = replace(group2_basenames, "[,]","[ ]");
// trace(spaceSeparatedBasename2);
string allBasenames = @strcat(spaceSeparatedBasename1," ",spaceSeparatedBasename2);
string statsFilename=@strcat(groupId1 ,"-",groupId2 ,"-",useWeights ,"-",adjustGCBias);
tsv stats <concurrent_mapper;prefix=statsFilename, suffix=".tsv">;
trace(@filename(stats));
// trace(replace("AAABBBCCC","[B]","[Z]"));
string fullPathEntries[];
string spaceSeparatedBasenames=allBasenames;
string entries[]=@strsplit(spaceSeparatedBasenames,"\\s");
string currentDirectory="/data/helicos-ILM-SOLID/";
foreach entry,i in entries {
fullPathEntries[i]=@strcat(currentDirectory,entry);
}
stats= alignment_to_annotation_counts(groupId1=groupId1, group1_basenames,
groupId2=groupId2, group2_basenames=group2_basenames,
fullPathEntries=fullPathEntries,
annotationFile,
useWeights, adjustGCBias);
}
string helicos_HBR_Basenames= "UMTVLVQ-helicos-brain.entries";
string bullard_HBR_Basenames= "DLTTEJH-Bullard-HBR-SRR037439.entries,DOWTGPI-Bullard-HBR-SRR037444.entries,HHNVSNR-Bullard-HBR-SRR037440.entries,ORVQUWJ-Bullard-HBR-SRR035678.entries,RRTFBOP-Bullard-HBR-SRR037443.entries,WKQCRQC-Bullard-HBR-SRR037442.entries,ZOBXCNB-Bullard-HBR-SRR037441.entries";
string illumina_HBR_Basenames="ALTZLBT-Illumina-brains_2_sequence.entries,DWFWKHJ-Illumina-brains_4_sequence.entries,FZCSFFY-Illumina-brains_8_sequence.entries,LNZIGRF-Illumina-brains_1_sequence.entries,QNDPONW-Illumina-brains_3_sequence.entries,SYXULGD-Illumina-brains_7_sequence.entries,UUBMNUK-Illumina-brains_6_sequence.entries";
string solid_HBR_Basenames= "LHFEDQE-solid-HBR.entries";
// textfile out <"output.txt">;
foreach adjustBias in ["false","formula2","formula3","formula4"] {
foreach useWeights in ["false","gc"] {
if (!(adjustBias=="true" && useWeights !="gc")) {
// adjustBias requires gc weights
tsv stats;
stats=call_de(groupId1="Bullard-ILM-HBR",
bullard_HBR_Basenames,
groupId2="Helicos-HBR",
helicos_HBR_Basenames,
"/Users/fac2003/IdeaProjects/goby/data/biomart_human_exon_esmbl57genes_NCBI_GRCh37.txt",
useWeights,
adjustBias );
}
}
}
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