Notebook

Visualizing Emma's Proteomic Data in Genome Browser¶

In [ ]:

!java -jar samifier.jar -r /Volumes/web/oyster/bioinformatics/xml_files/interact-20120821_103B_251_QE_02.pep.mzid -m /Volumes/web/oyster/bioinformatics/103B_251_02_mappingfile.txt -g /Volumes/web/oyster/bioinformatics/oyster.v9.glean.final.rename.fixed.gff -c /Volumes/web/oyster/bioinformatics/Crassostrea_gigas.GCA_000297895.1.21.dna.genome.fa.fa -o /Users/emmatimminsschiffman/Documents/winter_2014/Bioinformatics/Cg_samifier_out20140220 -l /Users/emmatimminsschiffman/Documents/winter_2014/Bioinformatics/log_20140220 -b /Users/emmatimminsschiffman/Documents/winter_2014/Cg_20140220.bed 

In [2]:

!java -jar /Users/sr320/Desktop/ap11_samifier-master/dist/samifier.jar -r

org.apache.commons.cli.MissingOptionException: Missing required options: r, m, g, c, o
Version = 1.0.9
usage: samifier [-b <bedFile>] -c <chromosomeDir> -g <genomeFile> [-l
       <logFile>] -m <mappingFile> -o <outputFile> -r <searchResultsFile>
       [-s <Confidence Score thresold>]
 -b <bedFile>                     Filename to write IGV regions of
                                  interest (BED) file to
 -c <chromosomeDir>               Directory containing the chromosome
                                  files in FASTA format for the given
                                  genome
 -g <genomeFile>                  Genome file in gff format
 -l <logFile>                     Filename to write the log into
 -m <mappingFile>                 File mapping protein identifier to
                                  ordered locus name
 -o <outputFile>                  Filename to write the SAM format file to
 -r <searchResultsFile>           Mascot search results file in txt format
 -s <Confidence Score thresold>   Minimum confidence score for peptides to
                                  be included

In [5]:

# -r <searchResultsFile>           Mascot search results file in txt format
!head -50 /Volumes/web/oyster/bioinformatics/xml_files/interact-20120821_103B_251_QE_02.pep.mzid

<?xml version="1.0" encoding="ISO-8859-1"?>
<MzIdentML id="" creationDate="2012-09-20T03:13:18" version="1.1.0" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://psidev.info/files/mzIdentML1.1.0.xsd" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <cvList>
    <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.53.0" uri="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
    <cv id="UNIMOD" fullName="UNIMOD" version="2013-05-31" uri="http://www.unimod.org/obo/unimod.obo"/>
    <cv id="UO" fullName="Unit Ontology" version="12:10:2011" uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
  </cvList>
  <AnalysisSoftwareList>
    <AnalysisSoftware id="AS_peptideprophet_" name="peptideprophet">
      <SoftwareName><cvParam cvRef="MS" accession="MS:1001456" name="analysis software" value="peptideprophet"/></SoftwareName>
    </AnalysisSoftware>
    <AnalysisSoftware id="AS_database_refresh_" name="database_refresh">
      <SoftwareName><cvParam cvRef="MS" accession="MS:1001456" name="analysis software" value="database_refresh"/></SoftwareName>
    </AnalysisSoftware>
    <AnalysisSoftware id="AS_interact_" name="interact">
      <SoftwareName><cvParam cvRef="MS" accession="MS:1001456" name="analysis software" value="interact"/></SoftwareName>
    </AnalysisSoftware>
    <AnalysisSoftware id="AS_Sequest" name="Sequest">
      <SoftwareName><cvParam cvRef="MS" accession="MS:1001208" name="SEQUEST" value=""/></SoftwareName>
    </AnalysisSoftware>
    <AnalysisSoftware id="pwiz_3.0.5519" name="ProteoWizard MzIdentML" version="3.0.5519">
      <ContactRole contact_ref="ORG_PWIZ">
        <Role><cvParam cvRef="MS" accession="MS:1001267" name="software vendor" value=""/></Role>
      </ContactRole>
      <SoftwareName><cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/></SoftwareName>
    </AnalysisSoftware>
  </AnalysisSoftwareList>
  <AuditCollection>
    <Organization id="ORG_PWIZ" name="ProteoWizard">
      <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="support@proteowizard.org"/>
    </Organization>
  </AuditCollection>
  <SequenceCollection>
    <DBSequence id="DBSeq_CGI_10027476" accession="CGI_10027476" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10022468" accession="CGI_10022468" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10008057" accession="CGI_10008057" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10008062" accession="CGI_10008062" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10008068" accession="CGI_10008068" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10008073" accession="CGI_10008073" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10008078" accession="CGI_10008078" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10008083" accession="CGI_10008083" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10011811" accession="CGI_10011811" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10028133" accession="CGI_10028133" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10014966" accession="CGI_10014966" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10024399" accession="CGI_10024399" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10020326" accession="CGI_10020326" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10024572" accession="CGI_10024572" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10024579" accession="CGI_10024579" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10021674" accession="CGI_10021674" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10003490" accession="CGI_10003490" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>

http://eagle.fish.washington.edu/oyster/bioinformatics/xml_files/interact-20120821_103B_251_QE_02.pep.mzid

In [9]:

!java -jar /Users/sr320/Desktop/ap11_samifier-master/dist/samifier.jar -r /Volumes/web/oyster/bioinformatics/xml_files/interact-20120821_103B_251_QE_02.pep.mzid -m /Volumes/we!b/oyster/bioinformatics/103B_251_02_mappingfile.txt -g /Volumes/web/oyster/bioinformatics/oyster.v9.glean.final.rename.fixed.gff -c /Volumes/web/oyster/bioinformatics/Crassostrea_gigas.GCA_000297895.1.21.dna.genome.fa.fa -o /Users/sr320/Desktop/Cg_samifier_out20140220 -l /Users/sr320/Desktop/log_20140220 -b /Users/sr320/Desktop/Cg_20140220.bed 

Version = 1.0.9
au.org.intersect.samifier.parser.GenomeFileParsingException: Error in /Volumes/web/oyster/bioinformatics/oyster.v9.glean.final.rename.fixed.gff:23 C19392	GLEAN	CDS	452	610	.	+	0	Parent=CGI_10000015;
 > Stop of sequence in gene CGI_10000015 overflows gene
usage: samifier [-b <bedFile>] -c <chromosomeDir> -g <genomeFile> [-l
       <logFile>] -m <mappingFile> -o <outputFile> -r <searchResultsFile>
       [-s <Confidence Score thresold>]
 -b <bedFile>                     Filename to write IGV regions of
                                  interest (BED) file to
 -c <chromosomeDir>               Directory containing the chromosome
                                  files in FASTA format for the given
                                  genome
 -g <genomeFile>                  Genome file in gff format
 -l <logFile>                     Filename to write the log into
 -m <mappingFile>                 File mapping protein identifier to
                                  ordered locus name
 -o <outputFile>                  Filename to write the SAM format file to
 -r <searchResultsFile>           Mascot search results file in txt format
 -s <Confidence Score thresold>   Minimum confidence score for peptides to
                                  be included
au.org.intersect.samifier.parser.GenomeFileParsingException: Error in /Volumes/web/oyster/bioinformatics/oyster.v9.glean.final.rename.fixed.gff:23 C19392	GLEAN	CDS	452	610	.	+	0	Parent=CGI_10000015;
 > Stop of sequence in gene CGI_10000015 overflows gene
	at au.org.intersect.samifier.parser.GenomeParserImpl.throwParsingException(GenomeParserImpl.java:98)
	at au.org.intersect.samifier.parser.GenomeParserImpl.processSequence(GenomeParserImpl.java:181)
	at au.org.intersect.samifier.parser.GenomeParserImpl.doParsing(GenomeParserImpl.java:84)
	at au.org.intersect.samifier.parser.GenomeParserImpl.parseGenomeFile(GenomeParserImpl.java:46)
	at au.org.intersect.samifier.runner.SamifierRunner.run(SamifierRunner.java:84)
	at au.org.intersect.samifier.Samifier.main(Samifier.java:125)

In [10]:

!head -50 /Volumes/web/oyster/bioinformatics/oyster.v9.glean.final.rename.fixed.gff

C16582	GLEAN	mRNA	35	385	0.555898	-	.	ID=CGI_10000001;
C16582	GLEAN	CDS	35	385	.	-	0	Parent=CGI_10000001;
C17212	GLEAN	mRNA	31	363	0.999572	+	.	ID=CGI_10000002;
C17212	GLEAN	CDS	31	363	.	+	0	Parent=CGI_10000002;
C17316	GLEAN	mRNA	30	257	0.555898	+	.	ID=CGI_10000003;
C17316	GLEAN	CDS	30	257	.	+	0	Parent=CGI_10000003;
C17998	GLEAN	mRNA	196	387	1	-	.	ID=CGI_10000005;
C17998	GLEAN	CDS	196	387	.	-	0	Parent=CGI_10000005;
C18346	GLEAN	mRNA	174	551	1	+	.	ID=CGI_10000009;
C18346	GLEAN	CDS	174	551	.	+	0	Parent=CGI_10000009;
C18428	GLEAN	mRNA	286	546	0.555898	-	.	ID=CGI_10000010;
C18428	GLEAN	CDS	286	546	.	-	0	Parent=CGI_10000010;
C18964	GLEAN	mRNA	203	658	0.999572	-	.	ID=CGI_10000011;
C18964	GLEAN	CDS	203	658	.	-	0	Parent=CGI_10000011;
C18980	GLEAN	mRNA	30	674	0.555898	+	.	ID=CGI_10000012;
C18980	GLEAN	CDS	30	674	.	+	0	Parent=CGI_10000012;
C19100	GLEAN	mRNA	160	681	0.999955	-	.	ID=CGI_10000013;
C19100	GLEAN	CDS	160	681	.	-	0	Parent=CGI_10000013;
C19356	GLEAN	mRNA	355	597	1	+	.	ID=CGI_10000014;
C19356	GLEAN	CDS	355	597	.	+	0	Parent=CGI_10000014;
C19392	GLEAN	mRNA	46	610	1	+	.	ID=CGI_10000015;
C19392	GLEAN	CDS	46	183	.	+	0	Parent=CGI_10000015;
C19392	GLEAN	CDS	452	610	.	+	0	Parent=CGI_10000015;
C19510	GLEAN	mRNA	451	702	1	+	.	ID=CGI_10000016;
C19510	GLEAN	CDS	451	702	.	+	0	Parent=CGI_10000016;
C19532	GLEAN	mRNA	155	601	0.575455	-	.	ID=CGI_10000017;
C19532	GLEAN	CDS	155	601	.	-	0	Parent=CGI_10000017;
C19570	GLEAN	mRNA	208	411	0.555898	-	.	ID=CGI_10000018;
C19570	GLEAN	CDS	208	411	.	-	0	Parent=CGI_10000018;
C19626	GLEAN	mRNA	347	814	0.999572	-	.	ID=CGI_10000019;
C19626	GLEAN	CDS	347	814	.	-	0	Parent=CGI_10000019;
C19672	GLEAN	mRNA	132	464	1	+	.	ID=CGI_10000021;
C19672	GLEAN	CDS	132	464	.	+	0	Parent=CGI_10000021;
C20188	GLEAN	mRNA	437	967	0.999572	-	.	ID=CGI_10000024;
C20188	GLEAN	CDS	437	967	.	-	0	Parent=CGI_10000024;
C20262	GLEAN	mRNA	222	1005	1	-	.	ID=CGI_10000025;
C20262	GLEAN	CDS	872	1005	.	-	0	Parent=CGI_10000025;
C20262	GLEAN	CDS	642	649	.	-	1	Parent=CGI_10000025;
C20262	GLEAN	CDS	222	538	.	-	2	Parent=CGI_10000025;
C20282	GLEAN	mRNA	330	980	1	+	.	ID=CGI_10000026;
C20282	GLEAN	CDS	330	980	.	+	0	Parent=CGI_10000026;
scaffold1224	GLEAN	mRNA	107	775	0.639435	-	.	ID=CGI_10000027;
scaffold1224	GLEAN	CDS	107	775	.	-	0	Parent=CGI_10000027;
C20334	GLEAN	mRNA	273	1027	1	-	.	ID=CGI_10000028;
C20334	GLEAN	CDS	868	1027	.	-	0	Parent=CGI_10000028;
C20334	GLEAN	CDS	273	523	.	-	2	Parent=CGI_10000028;
C20412	GLEAN	mRNA	73	776	1	-	.	ID=CGI_10000029;
C20412	GLEAN	CDS	706	776	.	-	0	Parent=CGI_10000029;
C20412	GLEAN	CDS	410	463	.	-	1	Parent=CGI_10000029;
C20412	GLEAN	CDS	73	214	.	-	1	Parent=CGI_10000029;

In [13]:

!sed 's/CDS/exon/g' </Volumes/web/oyster/bioinformatics/oyster.v9.glean.final.rename.fixed.gff> /Volumes/web/cnidarian/ets_v9.gff

In [14]:

!head /Volumes/web/cnidarian/ets_v9.gff

C16582	GLEAN	mRNA	35	385	0.555898	-	.	ID=CGI_10000001;
C16582	GLEAN	exon	35	385	.	-	0	Parent=CGI_10000001;
C17212	GLEAN	mRNA	31	363	0.999572	+	.	ID=CGI_10000002;
C17212	GLEAN	exon	31	363	.	+	0	Parent=CGI_10000002;
C17316	GLEAN	mRNA	30	257	0.555898	+	.	ID=CGI_10000003;
C17316	GLEAN	exon	30	257	.	+	0	Parent=CGI_10000003;
C17998	GLEAN	mRNA	196	387	1	-	.	ID=CGI_10000005;
C17998	GLEAN	exon	196	387	.	-	0	Parent=CGI_10000005;
C18346	GLEAN	mRNA	174	551	1	+	.	ID=CGI_10000009;
C18346	GLEAN	exon	174	551	.	+	0	Parent=CGI_10000009;

In [16]:

!sed 's/mRNA/CDS/g' </Volumes/web/cnidarian/ets_v9.gff> /Volumes/web/cnidarian/ets_v9_b.gff

In [17]:

!head /Volumes/web/cnidarian/ets_v9_b.gff

C16582	GLEAN	CDS	35	385	0.555898	-	.	ID=CGI_10000001;
C16582	GLEAN	exon	35	385	.	-	0	Parent=CGI_10000001;
C17212	GLEAN	CDS	31	363	0.999572	+	.	ID=CGI_10000002;
C17212	GLEAN	exon	31	363	.	+	0	Parent=CGI_10000002;
C17316	GLEAN	CDS	30	257	0.555898	+	.	ID=CGI_10000003;
C17316	GLEAN	exon	30	257	.	+	0	Parent=CGI_10000003;
C17998	GLEAN	CDS	196	387	1	-	.	ID=CGI_10000005;
C17998	GLEAN	exon	196	387	.	-	0	Parent=CGI_10000005;
C18346	GLEAN	CDS	174	551	1	+	.	ID=CGI_10000009;
C18346	GLEAN	exon	174	551	.	+	0	Parent=CGI_10000009;

In [20]:

!sed 's/ID=/PGUUID=/g' </Volumes/web/cnidarian/ets_v9_b.gff> /Volumes/web/cnidarian/ets_v9_c.gff

In [21]:

!head /Volumes/web/cnidarian/ets_v9_c.gff

C16582	GLEAN	CDS	35	385	0.555898	-	.	PGUUID=CGI_10000001;
C16582	GLEAN	exon	35	385	.	-	0	Parent=CGI_10000001;
C17212	GLEAN	CDS	31	363	0.999572	+	.	PGUUID=CGI_10000002;
C17212	GLEAN	exon	31	363	.	+	0	Parent=CGI_10000002;
C17316	GLEAN	CDS	30	257	0.555898	+	.	PGUUID=CGI_10000003;
C17316	GLEAN	exon	30	257	.	+	0	Parent=CGI_10000003;
C17998	GLEAN	CDS	196	387	1	-	.	PGUUID=CGI_10000005;
C17998	GLEAN	exon	196	387	.	-	0	Parent=CGI_10000005;
C18346	GLEAN	CDS	174	551	1	+	.	PGUUID=CGI_10000009;
C18346	GLEAN	exon	174	551	.	+	0	Parent=CGI_10000009;

In [22]:

!sed 's/Parent=/ID=/g' </Volumes/web/cnidarian/ets_v9_c.gff> /Volumes/web/cnidarian/ets_v9_d.gff

In [23]:

!head /Volumes/web/cnidarian/ets_v9_d.gff

C16582	GLEAN	CDS	35	385	0.555898	-	.	PGUUID=CGI_10000001;
C16582	GLEAN	exon	35	385	.	-	0	ID=CGI_10000001;
C17212	GLEAN	CDS	31	363	0.999572	+	.	PGUUID=CGI_10000002;
C17212	GLEAN	exon	31	363	.	+	0	ID=CGI_10000002;
C17316	GLEAN	CDS	30	257	0.555898	+	.	PGUUID=CGI_10000003;
C17316	GLEAN	exon	30	257	.	+	0	ID=CGI_10000003;
C17998	GLEAN	CDS	196	387	1	-	.	PGUUID=CGI_10000005;
C17998	GLEAN	exon	196	387	.	-	0	ID=CGI_10000005;
C18346	GLEAN	CDS	174	551	1	+	.	PGUUID=CGI_10000009;
C18346	GLEAN	exon	174	551	.	+	0	ID=CGI_10000009;

In [24]:

!sed 's/PGUUID=/Parent=/g' </Volumes/web/cnidarian/ets_v9_d.gff> /Volumes/web/cnidarian/ets_v9_f.gff

In [25]:

!head /Volumes/web/cnidarian/ets_v9_f.gff

C16582	GLEAN	CDS	35	385	0.555898	-	.	Parent=CGI_10000001;
C16582	GLEAN	exon	35	385	.	-	0	ID=CGI_10000001;
C17212	GLEAN	CDS	31	363	0.999572	+	.	Parent=CGI_10000002;
C17212	GLEAN	exon	31	363	.	+	0	ID=CGI_10000002;
C17316	GLEAN	CDS	30	257	0.555898	+	.	Parent=CGI_10000003;
C17316	GLEAN	exon	30	257	.	+	0	ID=CGI_10000003;
C17998	GLEAN	CDS	196	387	1	-	.	Parent=CGI_10000005;
C17998	GLEAN	exon	196	387	.	-	0	ID=CGI_10000005;
C18346	GLEAN	CDS	174	551	1	+	.	Parent=CGI_10000009;
C18346	GLEAN	exon	174	551	.	+	0	ID=CGI_10000009;

Fixed gff issue¶

In [27]:

!java -jar /Users/sr320/Desktop/ap11_samifier-master/dist/samifier.jar -r /Volumes/web/oyster/bioinformatics/xml_files/interact-20120821_103B_251_QE_02.pep.mzid -m /Volumes/web/oyster/bioinformatics/103B_251_02_mappingfile.txt -g /Volumes/web/cnidarian/ets_v9_f.gff -c /Volumes/web/oyster/bioinformatics/Crassostrea_gigas.GCA_000297895.1.21.dna.genome.fa.fa -o /Users/sr320/Desktop/Cg_samifier_out20140220 -l /Users/sr320/Desktop/log_20140220 -b /Users/sr320/Desktop/Cg_20140220.bed 

Start document
End document!
Run exception thrown
java.lang.NumberFormatException: null
	at java.lang.Integer.parseInt(Integer.java:454)
	at java.lang.Integer.parseInt(Integer.java:527)
	at au.org.intersect.samifier.parser.mzidentml.MzidReader.build(MzidReader.java:113)
	at au.org.intersect.samifier.parser.mzidentml.MzidReader.processEvidence(MzidReader.java:137)
	at au.org.intersect.samifier.parser.mzidentml.MzidReader.run(MzidReader.java:54)
	at au.org.intersect.samifier.parser.PeptideSearchResultsParserImpl.parseMascotPeptideSearchResultsMzidentMLFormat(PeptideSearchResultsParserImpl.java:129)
	at au.org.intersect.samifier.parser.PeptideSearchResultsParserImpl.parseResults(PeptideSearchResultsParserImpl.java:79)
	at au.org.intersect.samifier.parser.PeptideSearchResultsParserImpl.parseResults(PeptideSearchResultsParserImpl.java:56)
	at au.org.intersect.samifier.runner.SamifierRunner.run(SamifierRunner.java:90)
	at au.org.intersect.samifier.Samifier.main(Samifier.java:125)
Version = 1.0.9
java.lang.NullPointerException
usage: samifier [-b <bedFile>] -c <chromosomeDir> -g <genomeFile> [-l
       <logFile>] -m <mappingFile> -o <outputFile> -r <searchResultsFile>
       [-s <Confidence Score thresold>]
 -b <bedFile>                     Filename to write IGV regions of
                                  interest (BED) file to
 -c <chromosomeDir>               Directory containing the chromosome
                                  files in FASTA format for the given
                                  genome
 -g <genomeFile>                  Genome file in gff format
 -l <logFile>                     Filename to write the log into
 -m <mappingFile>                 File mapping protein identifier to
                                  ordered locus name
 -o <outputFile>                  Filename to write the SAM format file to
 -r <searchResultsFile>           Mascot search results file in txt format
 -s <Confidence Score thresold>   Minimum confidence score for peptides to
                                  be included
java.lang.NullPointerException
	at java.util.ArrayList.addAll(ArrayList.java:559)
	at au.org.intersect.samifier.parser.PeptideSearchResultsParserImpl.parseResults(PeptideSearchResultsParserImpl.java:56)
	at au.org.intersect.samifier.runner.SamifierRunner.run(SamifierRunner.java:90)
	at au.org.intersect.samifier.Samifier.main(Samifier.java:125)

!java -jar /Users/sr320/Desktop/ap11_samifier-master/dist/samifier.jar -r /Volumes/web/oyster/bioinformatics/xml_files/interact-20120821_103B_251_QE_02.pep.mzid -m /Volumes/web/oyster/bioinformatics/103B_251_02_mappingfile.txt -g /Volumes/web/cnidarian/ets_v9_f.gff -c /Volumes/web/cnidarian/v9_multi -o /Users/sr320/Desktop/Cg_samifier_out20140220 -l /Users/sr320/Desktop/log_20140220 -b /Users/sr320/Desktop/Cg_20140220.bed

In [29]:

!head /Volumes/web/cnidarian/oyster.v9.fa

>scaffold360
TATTCATATATCATTGAGAATGACAGTTTAAAACAGGATTTTTAATTGTGTTTAATAGGCGACCAACATTTAAGTGTCATTTGTTGAGTTATAAGCGAGTTAAAAAGCTTGTAGTTCTTCGCTATGGAAACAAAACTTTACATTTTGTTTACATTTCAGTTTTAGACCTCAAATGAATGTTTTTATCGTTAGGAACTGTTTATTTATGCTTTAAATTGATAAGAAGATTGACAAATCAGCTTGAAAAAGATTTTTTACTGGTGTATTGAACCCAGATGTA
>scaffold18356
TTAAACTGGTACAACAGTATATCCAAGAGAAAAAGGACTTTATAAACAATTTAGAACAACATTGTGGGTCGGATCGGAATTCAAGAACACAGGATCCATTGATGGCTTCTACTATGAAGGGCGATACTACCGCTTGGGGTGACGTCAAATACACTCCGTCATCGACAAAATCTCCTGGATTGTATCCATTACAGGAATTGAAGAAATAACTTTCAATGTAAACAATTTACAAAGATATACATATCTTACGTGAATATCTGGCATGGAAACAACACCTACATGATAGAATAAGACAATATTTCCTACGATACATCCATGGGACATGAAGAAAGTGAAACAGTGTATATCCATATTTAAATTATTATTATAACCGTGTAATCCAAAATGAATTTTATTCCTTCTCATCAGTAAGTACACTGAAAATTGACTACTAAGAAGAGGAAAACACAGAAACGCTAGTTACAACCGATGACCGTTATGAACATAATGCGATTATTTCAGTGAACCGTGTATTAGTGATTTCCTATGTAGGAAGGATTAATATAATTTGCTTCCTATTAGTGTAAT
>scaffold20428
AGAAATTATCCAGGGGTATATTCAGTAATTAAATTTGAAAAAAAAATTGGTTTCAACATATTTTATTGAATAAGGAAAATAGTTTGTATAACTTTAGTTACAAGTTCCTCTTTCTCAATTACTAGAAACTGAATACAACATGATAGAAGAAAATTAGATTTACAGGAATCAATTTTAATTGAGACACACTTGCTATATTGGGGTAGTGACACTTTCTTATAACACAAACTGCTTTTATTTTTTCAGCAGTTCAAAACTTTATTTAAGAGTCTGGAAGATTTTTAAATAATTAATTTTCTTTTTGTTATGGCTATTCTTACACCGTATATCACTCTATTTACCATACAATCACATTTTGTTTTGTTAATGCATGTTTAGGAATATAATTACTATAAAGTCAATATCTACAAATATAATGCATTATCACTATGGCAGTTGTATATATTATACATATTATAATCAAGAGAGAAACATGTAAGTTAAAAGAACTTGTTACCCACCCTCTTGTCCAATAACAATAAAATATGTTCAAATCAAATCAAACAAGAATTGATATACATGTACTAGTATATGGAATTTTTGTTCCTTTTGATGATGTATAGTGAAGAGTTTTTTAACCGCGTCACCTTTCGAATTGAACGTGAAAACCAGCAGGTTGTAAATTTCCTCTACACCATTCTTTTATATTTTTTAATTTTCAAATTTATTGTTGTGATGTTGGCTAAGAATCCTCATTTCAATCCCTTAATTATAATGGTACATGTAAATAAAATGGCGAGTGTCTATCTATGACGTACAAAGGAAGAAGCACTTTCCGGTGACGTAGTTATCACAATGCCCATACAGTGCTTGTCGATTTTATCAACTTTGATAAATAGGTTAAGTTGTATGTATACTGTATAGAATTCATGGATCCAAGGTCATGTAATAATCAACGCAAATTCCATATTGTGTTGAACATCAATTTAGTTTGTGTTATAAATTTGTAAAAGTTTATACATTCATACAAGCACCTGCTGTA
>scaffold18720
TCATGCCGATGATTTATCATACAAACATACGAGAGAAGTATTTAATAAAGCTGCATTTAGGATAATTATATCATTTTGCCATGCCATGACATATTCTGATCATCTCACATCATTGATAAAAAATTGTGCCTTTAATTCCTACCCTAAAATTAAATATTGAATATTATCATAATATTAAATTCAGTTACCTTAGATGTTCCTTTACTTGAGCCGATAAACTGCATGGTTCTATTCATCTTCACAAATAATATAGGAGACAGCCATGTCACCGAGTTTGAACGTCAGCAGGAGGATGTCTGTACAAAAAAATTGCCTTTAATTTGCTTTCAAATTTTCATTTTAAAGTATTGAGAACATTATTGTATAATAATCACCCATATATAATAAAAATCTGTAAAAGAACATCTGCATACTTACATTATTCCTACAGGCAGCCATGATGATAGCATAAGATCAAGTTACTCTGATGGATTTGTCAAAAATGACATCACAGTTCTTTTGGCGGTAATGTTTCATTCACGAGTGCAGAAAAGTTACTATGCATTGATACTGCATTTCATAAATAGTGTAGACAAGTAAAATGCTTCATGATGGACACACATAATATAGTCATGTACATTTAAAAAAA
>scaffold23246
GAATTGATTTGCCACAATTTTTTGTGTGGTCAATCTAAACTAGGTTCCTCAGCTCTGTTTCTAAATTAGCATTCTGTCCTTTTTCAGAATAAAATTTTGCACAACTAACCAGGATCTTGTTAACAATTTTGAGTTAAGTCTAAATATAAATTCAAAAAATCATTTAGAGTTATTAGTAACATGATATACTAGTGTAAGTCATTTTTTGAGAATTCCCAAATGTTCTTTCTGTTGAGTGAAGATACATGTAGGTCACGAATCTGGCACGTTTCCATTTTTTGTAAACTTGTAAAATAAAACATTTTAAAAATTTTTAAAGTAAAAAGGTGGCATTTACAAAATCTGTTTTTAGTTATAAAGAACAATCATATTTAAAATATATAAAAATGCTGTCTTTGGACTCCGAATAATATTCCAAATATATTGTCTGAAAGTTGGACAATTTTCTACTTCAAATATATTATAATACGTACGTGTATTTCCGAATCTGTAGTCTAGCAATGGGTTAACATTGTCACATAAAATTGCATGTTATGGGAAAAACCGGACATTCTATATTTTACTAAACTGTACGGTTGCTTCAACCCATATTGTTTAAAAGCAATGCGATTAAATCAAAGGAAAGCATGGTCAAATGGGAATTCAAATATATAAGTTAAAGAGGAAAAAACAAAACCATTTTATAAACTCGTATATATTTCACTATTAATGAAATAAAAAATAAGCAGTCTCACATGCCCACACACCCCATGACTTGGCAATGCTACACATTACAAATGGCAGAGTACCCTTTATATACCCTTAATAATAACATGGACATAACCACAAAAATCAAAGTACTGAAGTACTTAAACCCGGACTCTTTCGGTGTAATTATGCACATAGTGTAGTTAAATATTCTCTCTCTCTCTCTCTCTCTCTCTTATAATGCTTTGTAAAGAAGTTCATTGAATTAAGAAGAAATTAAACAATAGGAAATAAAAGGAAATTTTAAAAGTTCAGCATGATTCTAAGTTGCTCATGGCTACAGAAAAATGTATAAACTTACCTTTTGATGATGTAACGAAAGCACAGACTGCAAATGTAAAGATTACACCCTTCATTCTATATGAATGTCTATAACTAGGAAGACAGGCTATTTAAATACAAACCTGTTTATGTGATTTTATTTTTAGAAATAACTAAAGTTAGAGCAATACGCAAGTTAAACATGTGGGTGATAGAAATGCATGCAAAACACAGTTACGTCTCTTCAAGCCTTATCAGGCCTTCTCGGCAAAGTTTAGAAAGCATTTTAAATGCATCTGGCATATTCACTTGGTTTTACTTTCCACCTCTTGTATACTGACTGTTGTGATACATTGTACAGTTTAAAATTTAGATAAACTTTTCTTATTATTTGGACTTGATTTCATTTCCAAGAATAATTCTATCCTGTTTTGATTAGCACTGCATATTGAATATTTTCACAAAGTGTTTTATTGTTGCGCGTGTATCTATAGTCTGTTCCAAGTTACACTGACTTTTTTTAATGATTTTGAACAAAAACATGTATACACATATACGTATAACAATACAAGTAAAGTAATAAAGCAAACGTTATTGAAATTAATGATAAAAAAGTGCAAAGACTATTTGTAAAAATACATGTAATCATCAAAAGAACACTATACAGTATAGTCATATGCATAAAAAAAATCAATGGTGTTACTCGTTTATTCTGGAATCTGATATGTAAACTTAAAAAGTCATGAATGTTATAAAACTGTTGATTTTTATTGCTTGATTTTTAATTGGACGATAGTATTAACATGCATTATTACTCTGTTATGTTGAGTATTTATTTTATTTATTCATTTGGTCGAAATTTATCGGCATAATTTGTCGTTATTTTCAAATTTCTGGCGGCATTATTATTCAGTGTTTTAAAATGATTATCACATGACCAA

In [34]:

!/Users/sr320/Desktop/pl.pl /Volumes/web/cnidarian/oyster.v9.fa /Volumes/web/cnidarian/v9_multi

  SplitMultiFasta
  -------------------------------------------------
  Splits multi fasta into single sequences
 
  Usage:
  splitMultiFasta.pl InputFile OutputDirectory
  -------------------------------------------------
^C

In [3]:

!head  C8443.fna

>C8443
CTGGCATCTGGCAAGTTTCTGTAAAAGTAATTTGCAGTACATGCATTGCAAGTACTGGTAATGCACAGACCTTATTGTGATTATGGTAAATGTACTATCGTCCTGTTTAATACAGTATAGTACGCATCCTGCCTATGAC

In [63]:

!java -jar /Users/sr320/Desktop/ap11_samifier-master/dist/samifier.jar \
-r /Volumes/web/oyster/bioinformatics/xml_files/interact-20120821_103B_251_QE_02.pep.mzid \
-m /Users/sr320/Desktop/103B_251_02_mappingfile.txt \
-g /Volumes/web/cnidarian/ets_v9_f.gff \
-c /Users/sr320/Desktop/multi_fasta \
-o /Users/sr320/Desktop/Cg_samifier_out20140220 \
-l /Users/sr320/Desktop/log_20140220 \
-b /Users/sr320/Desktop/Cg_20140220.bed 

Start document
End document!
Run exception thrown
java.lang.NumberFormatException: null
	at java.lang.Integer.parseInt(Integer.java:454)
	at java.lang.Integer.parseInt(Integer.java:527)
	at au.org.intersect.samifier.parser.mzidentml.MzidReader.build(MzidReader.java:113)
	at au.org.intersect.samifier.parser.mzidentml.MzidReader.processEvidence(MzidReader.java:137)
	at au.org.intersect.samifier.parser.mzidentml.MzidReader.run(MzidReader.java:54)
	at au.org.intersect.samifier.parser.PeptideSearchResultsParserImpl.parseMascotPeptideSearchResultsMzidentMLFormat(PeptideSearchResultsParserImpl.java:129)
	at au.org.intersect.samifier.parser.PeptideSearchResultsParserImpl.parseResults(PeptideSearchResultsParserImpl.java:79)
	at au.org.intersect.samifier.parser.PeptideSearchResultsParserImpl.parseResults(PeptideSearchResultsParserImpl.java:56)
	at au.org.intersect.samifier.runner.SamifierRunner.run(SamifierRunner.java:90)
	at au.org.intersect.samifier.Samifier.main(Samifier.java:125)
Version = 1.0.9
java.lang.NullPointerException
usage: samifier [-b <bedFile>] -c <chromosomeDir> -g <genomeFile> [-l
       <logFile>] -m <mappingFile> -o <outputFile> -r <searchResultsFile>
       [-s <Confidence Score thresold>]
 -b <bedFile>                     Filename to write IGV regions of
                                  interest (BED) file to
 -c <chromosomeDir>               Directory containing the chromosome
                                  files in FASTA format for the given
                                  genome
 -g <genomeFile>                  Genome file in gff format
 -l <logFile>                     Filename to write the log into
 -m <mappingFile>                 File mapping protein identifier to
                                  ordered locus name
 -o <outputFile>                  Filename to write the SAM format file to
 -r <searchResultsFile>           Mascot search results file in txt format
 -s <Confidence Score thresold>   Minimum confidence score for peptides to
                                  be included
java.lang.NullPointerException
	at java.util.ArrayList.addAll(ArrayList.java:559)
	at au.org.intersect.samifier.parser.PeptideSearchResultsParserImpl.parseResults(PeptideSearchResultsParserImpl.java:56)
	at au.org.intersect.samifier.runner.SamifierRunner.run(SamifierRunner.java:90)
	at au.org.intersect.samifier.Samifier.main(Samifier.java:125)

Lets Try Example Data¶

java -jar samifier.jar \
-c cconcisus_ref/genome_dir \
-r Mascot_Result/Glimmer/F188715.dat \
-g pipeline_glimmer.gff \
-m pipeline_glimmer.accession \
-l pipeline_glimmer.log \
-o pipeline_glimmer.sam \
-b pipeline_glimmer.bed

In [38]:

!java -jar /Users/sr320/Desktop/ap11_samifier-master/dist/samifier.jar \
-c /Users/sr320/Desktop/wiki_test_cases/cconcisus_ref/genome_dir \
-r /Users/sr320/Desktop/wiki_test_cases/Mascot_Result/Glimmer/F188715.dat \
-g /Users/sr320/Desktop/wiki_test_cases/pipeline_glimmer.gff \
-m /Users/sr320/Desktop/wiki_test_cases/pipeline_glimmer.accession \
-l /Users/sr320/Desktop/pipeline_glimmer.log \
-o /Users/sr320/Desktop/pipeline_glimmer.sam \
-b /Users/sr320/Desktop/pipeline_glimmer.bed

In [64]:

!head /Users/sr320/Desktop/wiki_test_cases/pipeline_glimmer.accession

orf00002 orf00002 orf00002
orf00003 orf00003 orf00003
orf00004 orf00004 orf00004
orf00005 orf00005 orf00005
orf00006 orf00006 orf00006
orf00007 orf00007 orf00007
orf00008 orf00008 orf00008
orf00009 orf00009 orf00009
orf00011 orf00011 orf00011
orf00012 orf00012 orf00012

In [62]:

!head 103B_251_02_mappingfile.txt

CGI_10000050	CGI_10000050	CGI_10000050
CGI_10000055	CGI_10000055	CGI_10000055
CGI_10000067	CGI_10000067	CGI_10000067
CGI_10000075	CGI_10000075	CGI_10000075
CGI_10000077	CGI_10000077	CGI_10000077
CGI_10000174	CGI_10000174	CGI_10000174
CGI_10000235	CGI_10000235	CGI_10000235
CGI_10000237	CGI_10000237	CGI_10000237
CGI_10000384	CGI_10000384	CGI_10000384
CGI_10000492	CGI_10000492	CGI_10000492

Likely -r file ( Mascot search results file in txt format ) is wrong format¶

In [48]:

!head -50 /Volumes/web/oyster/bioinformatics/xml_files/interact-20120821_103B_251_QE_02.pep.mzid

<?xml version="1.0" encoding="ISO-8859-1"?>
<MzIdentML id="" creationDate="2012-09-20T03:13:18" version="1.1.0" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://psidev.info/files/mzIdentML1.1.0.xsd" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <cvList>
    <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.53.0" uri="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
    <cv id="UNIMOD" fullName="UNIMOD" version="2013-05-31" uri="http://www.unimod.org/obo/unimod.obo"/>
    <cv id="UO" fullName="Unit Ontology" version="12:10:2011" uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
  </cvList>
  <AnalysisSoftwareList>
    <AnalysisSoftware id="AS_peptideprophet_" name="peptideprophet">
      <SoftwareName><cvParam cvRef="MS" accession="MS:1001456" name="analysis software" value="peptideprophet"/></SoftwareName>
    </AnalysisSoftware>
    <AnalysisSoftware id="AS_database_refresh_" name="database_refresh">
      <SoftwareName><cvParam cvRef="MS" accession="MS:1001456" name="analysis software" value="database_refresh"/></SoftwareName>
    </AnalysisSoftware>
    <AnalysisSoftware id="AS_interact_" name="interact">
      <SoftwareName><cvParam cvRef="MS" accession="MS:1001456" name="analysis software" value="interact"/></SoftwareName>
    </AnalysisSoftware>
    <AnalysisSoftware id="AS_Sequest" name="Sequest">
      <SoftwareName><cvParam cvRef="MS" accession="MS:1001208" name="SEQUEST" value=""/></SoftwareName>
    </AnalysisSoftware>
    <AnalysisSoftware id="pwiz_3.0.5519" name="ProteoWizard MzIdentML" version="3.0.5519">
      <ContactRole contact_ref="ORG_PWIZ">
        <Role><cvParam cvRef="MS" accession="MS:1001267" name="software vendor" value=""/></Role>
      </ContactRole>
      <SoftwareName><cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/></SoftwareName>
    </AnalysisSoftware>
  </AnalysisSoftwareList>
  <AuditCollection>
    <Organization id="ORG_PWIZ" name="ProteoWizard">
      <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="support@proteowizard.org"/>
    </Organization>
  </AuditCollection>
  <SequenceCollection>
    <DBSequence id="DBSeq_CGI_10027476" accession="CGI_10027476" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10022468" accession="CGI_10022468" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10008057" accession="CGI_10008057" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10008062" accession="CGI_10008062" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10008068" accession="CGI_10008068" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10008073" accession="CGI_10008073" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10008078" accession="CGI_10008078" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10008083" accession="CGI_10008083" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10011811" accession="CGI_10011811" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10028133" accession="CGI_10028133" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10014966" accession="CGI_10014966" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10024399" accession="CGI_10024399" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10020326" accession="CGI_10020326" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10024572" accession="CGI_10024572" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10024579" accession="CGI_10024579" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10021674" accession="CGI_10021674" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>
    <DBSequence id="DBSeq_CGI_10003490" accession="CGI_10003490" searchDatabase_ref="oyster.v9.glean.final.rename.gff.pep"/>

example¶

In [41]:

!head -50 /Users/sr320/Desktop/wiki_test_cases/Mascot_Result/Glimmer/F188715.dat

MIME-Version: 1.0 (Generated by Mascot version 1.0)
Content-Type: multipart/mixed; boundary=gc0p4Jq0M2Yt08jU534c0p

--gc0p4Jq0M2Yt08jU534c0p
Content-Type: application/x-Mascot; name="parameters"

LICENSE=Licensed to: Australian Proteomics Computational Facility, (51 processors).
MP=
NM=
COM=Submitted from Test virtual protein by Mascot Daemon on WIN-V0L2R2U0DVL
IATOL=
IA2TOL=
IASTOL=
IBTOL=
IB2TOL=
IBSTOL=
IYTOL=
IY2TOL=
IYSTOL=
SEG=
SEGT=
SEGTU=
LTOL=
TOL=4
TOLU=ppm
ITH=
ITOL=0.4
ITOLU=Da
PFA=1
DB=contaminants
DB2=Campylobacter_PR
MODS=
MASS=Monoisotopic
CLE=Trypsin
FILE=C:\Users\ignatius\Documents\PostDoc\2012\ANDS data integration project\Sample Data\Cconcisus Reference proteome\RawSpectra\BAA-1457 Reference\mzML\Nadeem_29_7_10_1.mzML
PEAK=
QUE=
TWO=
SEARCH=MIS
USERNAME=Carlos Aya
USEREMAIL=carlos@intersect.org.au
CHARGE=2+ and 3+
INTERMEDIATE=
REPORT=AUTO
OVERVIEW=
FORMAT=mzML (.mzML)
FORMVER=1.01
FRAG=
IT_MODS=Carbamidomethyl (C),Oxidation (M)
USER00=

In [47]:

!head /Users/sr320/Desktop/wiki_test_cases/pipeline_glimmer.accession

orf00002 orf00002 orf00002
orf00003 orf00003 orf00003
orf00004 orf00004 orf00004
orf00005 orf00005 orf00005
orf00006 orf00006 orf00006
orf00007 orf00007 orf00007
orf00008 orf00008 orf00008
orf00009 orf00009 orf00009
orf00011 orf00011 orf00011
orf00012 orf00012 orf00012

In [ ]:

Fixing GFF¶

In [9]:

!wget http://eagle.fish.washington.edu/oyster/bioinformatics/oyster.v9.glean.final.rename.gff

--2014-03-12 09:08:26--  http://eagle.fish.washington.edu/oyster/bioinformatics/oyster.v9.glean.final.rename.gff
Resolving eagle.fish.washington.edu... 128.95.149.81
Connecting to eagle.fish.washington.edu|128.95.149.81|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 14179523 (14M) [text/plain]
Saving to: `oyster.v9.glean.final.rename.gff'

100%[======================================>] 14,179,523  45.9M/s   in 0.3s    

2014-03-12 09:08:26 (45.9 MB/s) - `oyster.v9.glean.final.rename.gff' saved [14179523/14179523]

In [7]:

cd Desktop

/Users/sr320/Desktop

In [ ]:

In [10]:

!head /Volumes/web/cnidarian/ets_v9_f.gff

C16582	GLEAN	CDS	35	385	0.555898	-	.	Parent=CGI_10000001;
C16582	GLEAN	exon	35	385	.	-	0	ID=CGI_10000001;
C17212	GLEAN	CDS	31	363	0.999572	+	.	Parent=CGI_10000002;
C17212	GLEAN	exon	31	363	.	+	0	ID=CGI_10000002;
C17316	GLEAN	CDS	30	257	0.555898	+	.	Parent=CGI_10000003;
C17316	GLEAN	exon	30	257	.	+	0	ID=CGI_10000003;
C17998	GLEAN	CDS	196	387	1	-	.	Parent=CGI_10000005;
C17998	GLEAN	exon	196	387	.	-	0	ID=CGI_10000005;
C18346	GLEAN	CDS	174	551	1	+	.	Parent=CGI_10000009;
C18346	GLEAN	exon	174	551	.	+	0	ID=CGI_10000009;

In [11]:

!head /Volumes/web/cnidarian/ets_v9_g.gff

C16582	GLEAN	CDS	35	385	0.555898	-	.	Parent=CGI_10000001;
C16582	GLEAN	exon	35	385	.	-	0	ID=CGI_10000001;
C16582	GLEAN	gene	35	385	0.555898	-	.	Name=CGI_10000001;
C17212	GLEAN	CDS	31	363	0.999572	+	.	Parent=CGI_10000002;
C17212	GLEAN	exon	31	363	.	+	0	ID=CGI_10000002;
C17212	GLEAN	gene	31	363	0.999572	+	.	Name=CGI_10000002;
C17316	GLEAN	CDS	30	257	0.555898	+	.	Parent=CGI_10000003;
C17316	GLEAN	exon	30	257	.	+	0	ID=CGI_10000003;
C17316	GLEAN	gene	30	257	0.555898	+	.	Name=CGI_10000003;
C17998	GLEAN	CDS	196	387	1	-	.	Parent=CGI_10000005;

In [12]:

!head /Volumes/web/cnidarian/ets_cgigas_v9_11.gff

C16582	GLEAN	mRNA	35	385	0.555898	-	.	ID=CGI_10000001;
C16582	GLEAN	CDS	35	385	.	-	0	Parent=CGI_10000001;
C16582	GLEAN	gene	35	385	.	-	0	Name=CGI_10000001;
C17212	GLEAN	mRNA	31	363	0.999572	+	.	ID=CGI_10000002;
C17212	GLEAN	CDS	31	363	.	+	0	Parent=CGI_10000002;
C17212	GLEAN	gene	31	363	.	+	0	Name=CGI_10000002;
C17316	GLEAN	mRNA	30	257	0.555898	+	.	ID=CGI_10000003;
C17316	GLEAN	CDS	30	257	.	+	0	Parent=CGI_10000003;
C17316	GLEAN	gene	30	257	.	+	0	Name=CGI_10000003;
C17476	GLEAN	mRNA	34	257	0.998947	-	.	ID=CGI_10000004;

In [13]:

!sed 's/ID/Parent/g' </Volumes/web/cnidarian/ets_cgigas_v9_11.gff> /Volumes/web/cnidarian/ets_cgigas_v9_12.gff

In [14]:

!head /Volumes/web/cnidarian/ets_cgigas_v9_12.gff

C16582	GLEAN	mRNA	35	385	0.555898	-	.	Parent=CGI_10000001;
C16582	GLEAN	CDS	35	385	.	-	0	Parent=CGI_10000001;
C16582	GLEAN	gene	35	385	.	-	0	Name=CGI_10000001;
C17212	GLEAN	mRNA	31	363	0.999572	+	.	Parent=CGI_10000002;
C17212	GLEAN	CDS	31	363	.	+	0	Parent=CGI_10000002;
C17212	GLEAN	gene	31	363	.	+	0	Name=CGI_10000002;
C17316	GLEAN	mRNA	30	257	0.555898	+	.	Parent=CGI_10000003;
C17316	GLEAN	CDS	30	257	.	+	0	Parent=CGI_10000003;
C17316	GLEAN	gene	30	257	.	+	0	Name=CGI_10000003;
C17476	GLEAN	mRNA	34	257	0.998947	-	.	Parent=CGI_10000004;

In [20]:

!sed 's/CDS/mRNA/g' </Volumes/web/cnidarian/ets_v9_h.gff> /Volumes/web/cnidarian/ets_v9_i.gff

In [22]:

!head /Volumes/web/cnidarian/ets_v9_i.gff

C16582	GLEAN	mRNA	35	385	0.555898	-	.	Parent=CGI_10000001;
C16582	GLEAN	exon	35	385	.	-	0	Parent=CGI_10000001;
C16582	GLEAN	gene	35	385	0.555898	-	.	Name=CGI_10000001;
C17212	GLEAN	mRNA	31	363	0.999572	+	.	Parent=CGI_10000002;
C17212	GLEAN	exon	31	363	.	+	0	Parent=CGI_10000002;
C17212	GLEAN	gene	31	363	0.999572	+	.	Name=CGI_10000002;
C17316	GLEAN	mRNA	30	257	0.555898	+	.	Parent=CGI_10000003;
C17316	GLEAN	exon	30	257	.	+	0	Parent=CGI_10000003;
C17316	GLEAN	gene	30	257	0.555898	+	.	Name=CGI_10000003;
C17998	GLEAN	mRNA	196	387	1	-	.	Parent=CGI_10000005;

In [ ]:

!sed 's/ID/Parent/g' </Volumes/web/cnidarian/ets_v9_g.gff> /Volumes/web/cnidarian/ets_v9_h.gff

In [26]:

!head -50 /Volumes/web/cnidarian/ets_v9_f.gff

C16582	GLEAN	CDS	35	385	0.555898	-	.	Parent=CGI_10000001;
C16582	GLEAN	exon	35	385	.	-	0	ID=CGI_10000001;
C17212	GLEAN	CDS	31	363	0.999572	+	.	Parent=CGI_10000002;
C17212	GLEAN	exon	31	363	.	+	0	ID=CGI_10000002;
C17316	GLEAN	CDS	30	257	0.555898	+	.	Parent=CGI_10000003;
C17316	GLEAN	exon	30	257	.	+	0	ID=CGI_10000003;
C17998	GLEAN	CDS	196	387	1	-	.	Parent=CGI_10000005;
C17998	GLEAN	exon	196	387	.	-	0	ID=CGI_10000005;
C18346	GLEAN	CDS	174	551	1	+	.	Parent=CGI_10000009;
C18346	GLEAN	exon	174	551	.	+	0	ID=CGI_10000009;
C18428	GLEAN	CDS	286	546	0.555898	-	.	Parent=CGI_10000010;
C18428	GLEAN	exon	286	546	.	-	0	ID=CGI_10000010;
C18964	GLEAN	CDS	203	658	0.999572	-	.	Parent=CGI_10000011;
C18964	GLEAN	exon	203	658	.	-	0	ID=CGI_10000011;
C18980	GLEAN	CDS	30	674	0.555898	+	.	Parent=CGI_10000012;
C18980	GLEAN	exon	30	674	.	+	0	ID=CGI_10000012;
C19100	GLEAN	CDS	160	681	0.999955	-	.	Parent=CGI_10000013;
C19100	GLEAN	exon	160	681	.	-	0	ID=CGI_10000013;
C19356	GLEAN	CDS	355	597	1	+	.	Parent=CGI_10000014;
C19356	GLEAN	exon	355	597	.	+	0	ID=CGI_10000014;
C19392	GLEAN	CDS	46	610	1	+	.	Parent=CGI_10000015;
C19392	GLEAN	exon	46	183	.	+	0	ID=CGI_10000015;
C19392	GLEAN	exon	452	610	.	+	0	ID=CGI_10000015;
C19510	GLEAN	CDS	451	702	1	+	.	Parent=CGI_10000016;
C19510	GLEAN	exon	451	702	.	+	0	ID=CGI_10000016;
C19532	GLEAN	CDS	155	601	0.575455	-	.	Parent=CGI_10000017;
C19532	GLEAN	exon	155	601	.	-	0	ID=CGI_10000017;
C19570	GLEAN	CDS	208	411	0.555898	-	.	Parent=CGI_10000018;
C19570	GLEAN	exon	208	411	.	-	0	ID=CGI_10000018;
C19626	GLEAN	CDS	347	814	0.999572	-	.	Parent=CGI_10000019;
C19626	GLEAN	exon	347	814	.	-	0	ID=CGI_10000019;
C19672	GLEAN	CDS	132	464	1	+	.	Parent=CGI_10000021;
C19672	GLEAN	exon	132	464	.	+	0	ID=CGI_10000021;
C20188	GLEAN	CDS	437	967	0.999572	-	.	Parent=CGI_10000024;
C20188	GLEAN	exon	437	967	.	-	0	ID=CGI_10000024;
C20262	GLEAN	CDS	222	1005	1	-	.	Parent=CGI_10000025;
C20262	GLEAN	exon	872	1005	.	-	0	ID=CGI_10000025;
C20262	GLEAN	exon	642	649	.	-	1	ID=CGI_10000025;
C20262	GLEAN	exon	222	538	.	-	2	ID=CGI_10000025;
C20282	GLEAN	CDS	330	980	1	+	.	Parent=CGI_10000026;
C20282	GLEAN	exon	330	980	.	+	0	ID=CGI_10000026;
scaffold1224	GLEAN	CDS	107	775	0.639435	-	.	Parent=CGI_10000027;
scaffold1224	GLEAN	exon	107	775	.	-	0	ID=CGI_10000027;
C20334	GLEAN	CDS	273	1027	1	-	.	Parent=CGI_10000028;
C20334	GLEAN	exon	868	1027	.	-	0	ID=CGI_10000028;
C20334	GLEAN	exon	273	523	.	-	2	ID=CGI_10000028;
C20412	GLEAN	CDS	73	776	1	-	.	Parent=CGI_10000029;
C20412	GLEAN	exon	706	776	.	-	0	ID=CGI_10000029;
C20412	GLEAN	exon	410	463	.	-	1	ID=CGI_10000029;
C20412	GLEAN	exon	73	214	.	-	1	ID=CGI_10000029;

In [27]:

!sed 's/CDS/gene/g' </Volumes/web/cnidarian/ets_v9_f.gff> /Volumes/web/cnidarian/ets_v9_j.gff

In [28]:

!sed 's/Parent/Name/g' </Volumes/web/cnidarian/ets_v9_j.gff> /Volumes/web/cnidarian/ets_v9_k.gff

In [29]:

!head /Volumes/web/cnidarian/ets_v9_k.gff

C16582	GLEAN	gene	35	385	0.555898	-	.	Name=CGI_10000001;
C16582	GLEAN	exon	35	385	.	-	0	ID=CGI_10000001;
C17212	GLEAN	gene	31	363	0.999572	+	.	Name=CGI_10000002;
C17212	GLEAN	exon	31	363	.	+	0	ID=CGI_10000002;
C17316	GLEAN	gene	30	257	0.555898	+	.	Name=CGI_10000003;
C17316	GLEAN	exon	30	257	.	+	0	ID=CGI_10000003;
C17998	GLEAN	gene	196	387	1	-	.	Name=CGI_10000005;
C17998	GLEAN	exon	196	387	.	-	0	ID=CGI_10000005;
C18346	GLEAN	gene	174	551	1	+	.	Name=CGI_10000009;
C18346	GLEAN	exon	174	551	.	+	0	ID=CGI_10000009;

In [30]:

!sed 's/ID/Parent/g' </Volumes/web/cnidarian/ets_v9_k.gff> /Volumes/web/cnidarian/ets_v9_l.gff

In [31]:

!head /Volumes/web/cnidarian/ets_v9_l.gff

C16582	GLEAN	gene	35	385	0.555898	-	.	Name=CGI_10000001;
C16582	GLEAN	exon	35	385	.	-	0	Parent=CGI_10000001;
C17212	GLEAN	gene	31	363	0.999572	+	.	Name=CGI_10000002;
C17212	GLEAN	exon	31	363	.	+	0	Parent=CGI_10000002;
C17316	GLEAN	gene	30	257	0.555898	+	.	Name=CGI_10000003;
C17316	GLEAN	exon	30	257	.	+	0	Parent=CGI_10000003;
C17998	GLEAN	gene	196	387	1	-	.	Name=CGI_10000005;
C17998	GLEAN	exon	196	387	.	-	0	Parent=CGI_10000005;
C18346	GLEAN	gene	174	551	1	+	.	Name=CGI_10000009;
C18346	GLEAN	exon	174	551	.	+	0	Parent=CGI_10000009;

In [32]:

!sed 's/exon/CDS/g' </Volumes/web/cnidarian/ets_v9_l.gff> /Volumes/web/cnidarian/ets_v9_m.gff

In [35]:

!tail -50 /Volumes/web/cnidarian/ets_v9_o.gff

scaffold998	GLEAN	CDS	116508	117557	.	-	0	Parent=CGI_10006465;
scaffold998	GLEAN	mRNA	3874	24837	0.410057	+	.	Parent=CGI_10006458;
scaffold998	GLEAN	mRNA	25310	28141	0.813029	+	.	Parent=CGI_10006459;
scaffold998	GLEAN	mRNA	43399	61271	0.812368	+	.	Parent=CGI_10006460;
scaffold998	GLEAN	mRNA	67122	73547	0.999674	+	.	Parent=CGI_10006461;
scaffold998	GLEAN	mRNA	73620	80841	0.721465	+	.	Parent=CGI_10006462;
scaffold998	GLEAN	mRNA	89231	90958	0.999202	+	.	Parent=CGI_10006463;
scaffold998	GLEAN	mRNA	91399	104169	0.99895	-	.	Parent=CGI_10006464;
scaffold998	GLEAN	mRNA	116508	131912	0.996071	-	.	Parent=CGI_10006465;
scaffold999	GLEAN	gene	23147	24888	0.654733	+	.	Name=CGI_10006969;
scaffold999	GLEAN	CDS	23147	23288	.	+	0	Parent=CGI_10006969;
scaffold999	GLEAN	CDS	24070	24204	.	+	2	Parent=CGI_10006969;
scaffold999	GLEAN	CDS	24468	24581	.	+	2	Parent=CGI_10006969;
scaffold999	GLEAN	CDS	24695	24888	.	+	2	Parent=CGI_10006969;
scaffold999	GLEAN	gene	39254	45360	1	-	.	Name=CGI_10006970;
scaffold999	GLEAN	CDS	45195	45360	.	-	0	Parent=CGI_10006970;
scaffold999	GLEAN	CDS	39995	40053	.	-	2	Parent=CGI_10006970;
scaffold999	GLEAN	CDS	39701	39892	.	-	0	Parent=CGI_10006970;
scaffold999	GLEAN	CDS	39254	39460	.	-	0	Parent=CGI_10006970;
scaffold999	GLEAN	gene	47971	57911	0.937649	-	.	Name=CGI_10006971;
scaffold999	GLEAN	CDS	57819	57911	.	-	0	Parent=CGI_10006971;
scaffold999	GLEAN	CDS	56427	56498	.	-	0	Parent=CGI_10006971;
scaffold999	GLEAN	CDS	53710	53847	.	-	0	Parent=CGI_10006971;
scaffold999	GLEAN	CDS	52115	52144	.	-	0	Parent=CGI_10006971;
scaffold999	GLEAN	CDS	51101	51218	.	-	0	Parent=CGI_10006971;
scaffold999	GLEAN	CDS	48506	48655	.	-	2	Parent=CGI_10006971;
scaffold999	GLEAN	CDS	47971	48086	.	-	2	Parent=CGI_10006971;
scaffold999	GLEAN	gene	88395	99702	0.482874	-	.	Name=CGI_10006972;
scaffold999	GLEAN	CDS	99690	99702	.	-	0	Parent=CGI_10006972;
scaffold999	GLEAN	CDS	96192	96278	.	-	2	Parent=CGI_10006972;
scaffold999	GLEAN	CDS	95628	95712	.	-	2	Parent=CGI_10006972;
scaffold999	GLEAN	CDS	93995	94089	.	-	1	Parent=CGI_10006972;
scaffold999	GLEAN	CDS	88395	88534	.	-	2	Parent=CGI_10006972;
scaffold999	GLEAN	gene	107744	126675	0.391684	+	.	Name=CGI_10006973;
scaffold999	GLEAN	CDS	107744	107798	.	+	0	Parent=CGI_10006973;
scaffold999	GLEAN	CDS	115160	115384	.	+	2	Parent=CGI_10006973;
scaffold999	GLEAN	CDS	116967	117221	.	+	2	Parent=CGI_10006973;
scaffold999	GLEAN	CDS	118234	118362	.	+	2	Parent=CGI_10006973;
scaffold999	GLEAN	CDS	120708	120818	.	+	2	Parent=CGI_10006973;
scaffold999	GLEAN	CDS	121053	121184	.	+	2	Parent=CGI_10006973;
scaffold999	GLEAN	CDS	122398	122535	.	+	2	Parent=CGI_10006973;
scaffold999	GLEAN	CDS	123424	123555	.	+	2	Parent=CGI_10006973;
scaffold999	GLEAN	CDS	124859	124996	.	+	2	Parent=CGI_10006973;
scaffold999	GLEAN	CDS	126012	126143	.	+	2	Parent=CGI_10006973;
scaffold999	GLEAN	CDS	126617	126675	.	+	2	Parent=CGI_10006973;
scaffold999	GLEAN	mRNA	23147	24888	0.654733	+	.	Parent=CGI_10006969;
scaffold999	GLEAN	mRNA	39254	45360	1	-	.	Parent=CGI_10006970;
scaffold999	GLEAN	mRNA	47971	57911	0.937649	-	.	Parent=CGI_10006971;
scaffold999	GLEAN	mRNA	88395	99702	0.482874	-	.	Parent=CGI_10006972;
scaffold999	GLEAN	mRNA	107744	126675	0.391684	+	.	Parent=CGI_10006973;

In [36]:

!head /Volumes/web/oyster/bioinformatics/oyster.v9.glean.final.rename.fixed.gff

C16582	GLEAN	mRNA	35	385	0.555898	-	.	ID=CGI_10000001;
C16582	GLEAN	CDS	35	385	.	-	0	Parent=CGI_10000001;
C17212	GLEAN	mRNA	31	363	0.999572	+	.	ID=CGI_10000002;
C17212	GLEAN	CDS	31	363	.	+	0	Parent=CGI_10000002;
C17316	GLEAN	mRNA	30	257	0.555898	+	.	ID=CGI_10000003;
C17316	GLEAN	CDS	30	257	.	+	0	Parent=CGI_10000003;
C17998	GLEAN	mRNA	196	387	1	-	.	ID=CGI_10000005;
C17998	GLEAN	CDS	196	387	.	-	0	Parent=CGI_10000005;
C18346	GLEAN	mRNA	174	551	1	+	.	ID=CGI_10000009;
C18346	GLEAN	CDS	174	551	.	+	0	Parent=CGI_10000009;

In [37]:

!head /Volumes/web/cnidarian/ets_v9_p.gff

C16582	GLEAN	mRNA	35	385	0.555898	-	.	Parent=CGI_10000001;
C16582	GLEAN	gene	35	385	.	-	.	Name=CGI_10000001;
C16582	GLEAN	CDS	35	385	.	-	0	Parent=CGI_10000001;
C17212	GLEAN	mRNA	31	363	0.999572	+	.	Parent=CGI_10000002;
C17212	GLEAN	gene	31	363	.	+	.	Name=CGI_10000002;
C17212	GLEAN	CDS	31	363	.	+	0	Parent=CGI_10000002;
C17316	GLEAN	mRNA	30	257	0.555898	+	.	Parent=CGI_10000003;
C17316	GLEAN	gene	30	257	.	+	.	Name=CGI_10000003;
C17316	GLEAN	CDS	30	257	.	+	0	Parent=CGI_10000003;
C17998	GLEAN	mRNA	196	387	1	-	.	Parent=CGI_10000005;

In [38]:

!head /Volumes/web/cnidarian/Crassostrea_gigas.GCA_000297895.1.21.gff3

##gff-version 3
scaffold1611	protein_coding	gene	1263	9963	.	-	.	ID=CGI_10014322;Name=CGI_10014322
scaffold1611	protein_coding	mRNA	1263	9963	.	-	.	ID=EKC25967;Parent=CGI_10014322
scaffold1611	protein_coding	start_codon	9961	9963	.	-	0	ID=start_codon:EKC25967:1;Parent=EKC25967
scaffold1611	protein_coding	exon	9922	9963	.	-	.	ID=exon:EKC25967:1;Parent=EKC25967
scaffold1611	protein_coding	exon	8502	8667	.	-	.	ID=exon:EKC25967:2;Parent=EKC25967
scaffold1611	protein_coding	exon	7374	7534	.	-	.	ID=exon:EKC25967:3;Parent=EKC25967
scaffold1611	protein_coding	exon	3861	4046	.	-	.	ID=exon:EKC25967:4;Parent=EKC25967
scaffold1611	protein_coding	exon	1635	1742	.	-	.	ID=exon:EKC25967:5;Parent=EKC25967
scaffold1611	protein_coding	exon	1263	1268	.	-	.	ID=exon:EKC25967:6;Parent=EKC25967

In [1]:

!head /Volumes/web/whale/wiki_test_cases/pipeline_glimmer.gff

##gff-version 3
NC_009802	Glimmer	gene	1	1311	16.88	+	0	Name=orf00002;ID=orf00002;
NC_009802	Glimmer	CDS	1	1311	16.88	+	0	Name=orf00002;Parent=orf00002;
NC_009802	Glimmer	gene	1319	1465	1.61	+	0	Name=orf00003;ID=orf00003;
NC_009802	Glimmer	CDS	1319	1465	1.61	+	0	Name=orf00003;Parent=orf00003;
NC_009802	Glimmer	gene	1465	2532	15.89	+	0	Name=orf00004;ID=orf00004;
NC_009802	Glimmer	CDS	1465	2532	15.89	+	0	Name=orf00004;Parent=orf00004;
NC_009802	Glimmer	gene	2550	4859	16.58	+	0	Name=orf00005;ID=orf00005;
NC_009802	Glimmer	CDS	2550	4859	16.58	+	0	Name=orf00005;Parent=orf00005;
NC_009802	Glimmer	gene	4878	5474	16.37	+	0	Name=orf00006;ID=orf00006;

In [ ]: