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Merged
WilliamKMLai merged 6 commits into from
Jan 6, 2021
Merged

Last bug fixes and additions for v0.13 CLI release #50

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6709ebc
fix BAM format converter cli validation
owlang Jan 5, 2021
06859c9
allow FilterPIPseq to use multi-nucleotide strings
owlang Jan 5, 2021
0a44cae
fix extension check
owlang Jan 5, 2021
2cc0bc7
remove default title-setting
owlang Jan 5, 2021
5fe99f3
add basic checks to row/column options
owlang Jan 5, 2021
d2b6910
add validation for motif string input
owlang Jan 5, 2021
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4 changes: 3 additions & 1 deletion src/cli/BAM_Format_Converter/BAMtoBEDCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -86,6 +86,8 @@ private String validateInput() throws IOException {
else if(readType.midpoint) { STRAND=3; }
else if(readType.fragment) { STRAND=4; }
else { STRAND=0; }
// set PE defaults
if(STRAND==3 || STRAND==4) { matePair=true; }

//check inputs exist
if(!bamFile.exists()){
Expand Down Expand Up @@ -131,7 +133,7 @@ private String validateInput() throws IOException {
// validate insert sizes
if( MIN_INSERT<0 && MIN_INSERT!=-9999 ){ r += "MIN_INSERT must be a positive integer value: " + MIN_INSERT + "\n"; }
if( MAX_INSERT<0 && MAX_INSERT!=-9999 ){ r += "MAX_INSERT must be a positive integer value: " + MAX_INSERT + "\n"; }
if( MAX_INSERT<MIN_INSERT ){ r += "MAX_INSERT must be larger/equal to MIN_INSERT: " + MIN_INSERT + "," + MAX_INSERT + "\n"; }
if( MAX_INSERT<MIN_INSERT && MIN_INSERT!=-9999 && MAX_INSERT!=-9999){ r += "MAX_INSERT must be larger/equal to MIN_INSERT: " + MIN_INSERT + "," + MAX_INSERT + "\n"; }
// turn pair status boolean into int
PAIR = matePair ? 1 : 0;

Expand Down
4 changes: 3 additions & 1 deletion src/cli/BAM_Format_Converter/BAMtoGFFCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -86,6 +86,8 @@ private String validateInput() throws IOException {
else if(readType.midpoint) { STRAND=3; }
else if(readType.fragment) { STRAND=4; }
else { STRAND=0; }
// set PE defaults
if(STRAND==3 || STRAND==4) { matePair=true; }

//check inputs exist
if(!bamFile.exists()){
Expand Down Expand Up @@ -131,7 +133,7 @@ private String validateInput() throws IOException {
// validate insert sizes
if( MIN_INSERT<0 && MIN_INSERT!=-9999 ){ r += "MIN_INSERT must be a positive integer value: " + MIN_INSERT + "\n"; }
if( MAX_INSERT<0 && MAX_INSERT!=-9999 ){ r += "MAX_INSERT must be a positive integer value: " + MAX_INSERT + "\n"; }
if( MAX_INSERT<MIN_INSERT ){ r += "MAX_INSERT must be larger/equal to MIN_INSERT: " + MIN_INSERT + "," + MAX_INSERT + "\n"; }
if( MAX_INSERT<MIN_INSERT && MIN_INSERT!=-9999 && MAX_INSERT!=-9999){ r += "MAX_INSERT must be larger/equal to MIN_INSERT: " + MIN_INSERT + "," + MAX_INSERT + "\n"; }
// turn pair status boolean into int
PAIR = matePair ? 1 : 0;

Expand Down
4 changes: 3 additions & 1 deletion src/cli/BAM_Format_Converter/BAMtobedGraphCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -81,6 +81,8 @@ private String validateInput() throws IOException {
else if(readType.combined) { STRAND=2; }
else if(readType.midpoint) { STRAND=3; }
else { STRAND=0; }
// set PE defaults
if(STRAND==3) { matePair=true; }

//check inputs exist
if(!bamFile.exists()){
Expand Down Expand Up @@ -119,7 +121,7 @@ private String validateInput() throws IOException {
// validate insert sizes
if( MIN_INSERT<0 && MIN_INSERT!=-9999 ){ r += "MIN_INSERT must be a positive integer value: " + MIN_INSERT + "\n"; }
if( MAX_INSERT<0 && MAX_INSERT!=-9999 ){ r += "MAX_INSERT must be a positive integer value: " + MAX_INSERT + "\n"; }
if( MAX_INSERT<MIN_INSERT ){ r += "MAX_INSERT must be larger/equal to MIN_INSERT: " + MIN_INSERT + "," + MAX_INSERT + "\n"; }
if( MAX_INSERT<MIN_INSERT && MIN_INSERT!=-9999 && MAX_INSERT!=-9999){ r += "MAX_INSERT must be larger/equal to MIN_INSERT: " + MIN_INSERT + "," + MAX_INSERT + "\n"; }
// turn pair status boolean into int
PAIR = matePair ? 1 : 0;

Expand Down
4 changes: 3 additions & 1 deletion src/cli/BAM_Format_Converter/BAMtoscIDXCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -83,6 +83,8 @@ private String validateInput() throws IOException {
else if(readType.combined) { STRAND=2; }
else if(readType.midpoint) { STRAND=3; }
else { STRAND=0; }
// set PE defaults
if(STRAND==3) { matePair=true; }

//check inputs exist
if(!bamFile.exists()){
Expand Down Expand Up @@ -128,7 +130,7 @@ private String validateInput() throws IOException {
// validate insert sizes
if( MIN_INSERT<0 && MIN_INSERT!=-9999 ){ r += "MIN_INSERT must be a positive integer value: " + MIN_INSERT + "\n"; }
if( MAX_INSERT<0 && MAX_INSERT!=-9999 ){ r += "MAX_INSERT must be a positive integer value: " + MAX_INSERT + "\n"; }
if( MAX_INSERT<MIN_INSERT ){ r += "MAX_INSERT must be larger/equal to MIN_INSERT: " + MIN_INSERT + "," + MAX_INSERT + "\n"; }
if( MAX_INSERT<MIN_INSERT && MIN_INSERT!=-9999 && MAX_INSERT!=-9999){ r += "MAX_INSERT must be larger/equal to MIN_INSERT: " + MIN_INSERT + "," + MAX_INSERT + "\n"; }
// turn pair status boolean into int
PAIR = matePair ? 1 : 0;

Expand Down
2 changes: 1 addition & 1 deletion src/cli/BAM_Manipulation/FilterforPIPseqCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -107,7 +107,7 @@ private String validateInput() throws IOException {
}

//check filter string is valid ATCG
Pattern seqPat = Pattern.compile("[ATCG]");
Pattern seqPat = Pattern.compile("[ATCG]+");
Matcher m = seqPat.matcher( filterString );
if( !m.matches() ){
r += "(!)Filter string must be formatted as a nucleotide sequence.\n" + filterString +
Expand Down
4 changes: 2 additions & 2 deletions src/cli/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -70,8 +70,8 @@ private String validateInput() throws IOException {
}else{
//check ext
try{
if(!"gff".equals(ExtensionFileFilter.getExtension(output))){
r += "(!)Use GFF extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + ".gff\n";
if(!"bed".equals(ExtensionFileFilter.getExtension(output))){
r += "(!)Use BED extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + ".bed\n";
}
} catch( NullPointerException e){ r += "(!)Output filename must have extension: use GFF extension for output filename. Try: " + output + ".gff\n"; }
//check directory
Expand Down
4 changes: 1 addition & 3 deletions src/cli/Figure_Generation/CompositePlotCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -104,7 +104,7 @@ public Integer call() throws Exception {
// Save Composite Plot
OutputStream OUT = new FileOutputStream(output);
ChartUtilities.writeChartAsPNG(OUT, chart, pixelWidth, pixelHeight);

System.err.println( "Image Generated." );
return(0);
}
Expand Down Expand Up @@ -140,8 +140,6 @@ private String validateInput() throws IOException {
}
}

//set default title name
if(title!=null){ title = compositeData.getName(); }
//check pixel ranges are valid
if(pixelHeight<=0){ r += "(!)Cell height must be a positive integer value! check \"-y\" flag.\""; }
if(pixelWidth<=0) { r += "(!)Cell width must be a positive integer value! check \"-x\" flag.\""; }
Expand Down
4 changes: 4 additions & 0 deletions src/cli/Read_Analysis/AggregateDataCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -149,6 +149,10 @@ private String validateInput() throws IOException {
else if(aggr.max) { aggType = 5; }
else if(aggr.var) { aggType = 6; }

//validate row&column start indexes
if(startROW<0){ r += "(!)Row start must not be less than zero\n"; }
if(startCOL<0){ r += "(!)Column start must not be less than zero\n"; }

return(r);
}
}
10 changes: 10 additions & 0 deletions src/cli/Sequence_Analysis/SearchMotifCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,8 @@
import picocli.CommandLine.Parameters;

import java.util.concurrent.Callable;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import java.io.File;
import java.io.IOException;
Expand Down Expand Up @@ -83,6 +85,14 @@ private String validateInput() throws IOException {
}
}

//check filter string is valid ATCG
Pattern seqPat = Pattern.compile("[ATCG]+");
Matcher m = seqPat.matcher( motif );
if( !m.matches() ){
r += "(!)Motif string must be formatted as a nucleotide sequence.\n" + motif +
" is not a valid nucleotide sequence.\nExpected input string format: \"[ATCG]\"";
}

//check mismatch value
if(ALLOWED_MISMATCH<0){ r += "(!)Please use a non-negative integer for allowed mismatches."; }

Expand Down
25 changes: 13 additions & 12 deletions src/scripts/BAM_Manipulation/FilterforPIPseq.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,37 +24,38 @@ public class FilterforPIPseq {
File genome = null;
File output = null;
String SEQ = "";
private PrintStream PS;

private PrintStream PS = null;

public FilterforPIPseq(File in, File gen, File out, String s, PrintStream ps) {
bamFile = in;
genome = gen;
output = out;
SEQ = s.toUpperCase();
PS = ps;
}

public void run() throws IOException, InterruptedException {
IndexedFastaSequenceFile QUERY = new IndexedFastaSequenceFile(genome);

IOUtil.assertFileIsReadable(bamFile);
IOUtil.assertFileIsWritable(output);
final SamReader reader = SamReaderFactory.makeDefault().open(bamFile);
reader.getFileHeader().setSortOrder(SAMFileHeader.SortOrder.coordinate);
final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), false, output);

printBoth(bamFile.getName()); //output file name to textarea

//Code to get individual chromosome stats
AbstractBAMFileIndex bai = (AbstractBAMFileIndex) reader.indexing().getIndex();
for (int z = 0; z < bai.getNumberOfReferences(); z++) {
SAMSequenceRecord seq = reader.getFileHeader().getSequence(z);

printBoth(seq.getSequenceName());

CloseableIterator<SAMRecord> iter = reader.query(seq.getSequenceName(), 0, seq.getSequenceLength(), false);
while (iter.hasNext()) {
//Create the record object
//Create the record object
SAMRecord sr = iter.next();
if(sr.getReadPairedFlag()) {
if(sr.getProperPairFlag() && sr.getFirstOfPairFlag()) {
Expand All @@ -70,7 +71,7 @@ public void run() throws IOException, InterruptedException {
}
}
//System.out.println(sr.getReadString() + "\t" + seq.getSequenceName() + "\t" + sr.getUnclippedStart() + "\t" + sr.getUnclippedEnd() + "\t" + sr.getReadNegativeStrandFlag() + "\t" + filter);
if(filter.toUpperCase().equals(SEQ)) { writer.addAlignment(sr); }
if(filter.toUpperCase().equals(SEQ)) { writer.addAlignment(sr); }
}
} else {
String filter = "";
Expand All @@ -83,7 +84,7 @@ public void run() throws IOException, InterruptedException {
filter = FASTAUtilities.RevComplement(filter);
}
//System.out.println(sr.getReadString() + "\t" + seq.getSequenceName() + "\t" + sr.getUnclippedStart() + "\t" + sr.getUnclippedEnd() + "\t" + sr.getReadNegativeStrandFlag() + "\t" + filter);
if(filter.toUpperCase().equals(SEQ)) { writer.addAlignment(sr); }
if(filter.toUpperCase().equals(SEQ)) { writer.addAlignment(sr); }
}
}
iter.close();
Expand All @@ -93,7 +94,7 @@ public void run() throws IOException, InterruptedException {
reader.close();
bai.close();
}

private void printBoth(String message){
if(PS!=null){ PS.println(message); }
System.err.println(message);
Expand Down