[med-svn] [transdecoder] branch upstream updated (7460a4a -> 9d2e299)

[Michael Crusoe]

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misterc-guest pushed a change to branch upstream
in repository transdecoder.

      from  7460a4a   Imported Upstream version 2.0.1+dfsg
      adds  9d2e299   Imported Upstream version 2.1.0+dfsg

No new revisions were added by this update.

Summary of changes:
 Release.Notes => Changelog.txt                     |   8 ++
 PerlLib/Fasta_retriever.pm                         |  93 ++++++++++++++
 PerlLib/Longest_orf.pm                             |  69 ++++++++++-
 TransDecoder.LongOrfs                              |  14 +++
 TransDecoder.Predict                               |   9 +-
 sample_data/README.md                              |  12 ++
 .../blastp.results.outfmt6.gz                      | Bin
 sample_data/{ => cufflinks_example}/cleanme.pl     |   0
 .../{ => cufflinks_example}/pfam.domtblout.gz      | Bin
 sample_data/{ => cufflinks_example}/runMe.sh       |  17 ++-
 .../{ => cufflinks_example}/test.genome.fasta.gz   | Bin
 .../{ => cufflinks_example}/test.tophat.sam.gz     | Bin
 .../{ => cufflinks_example}/transcripts.gtf.gz     | Bin
 sample_data/{ => pasa_example}/cleanme.pl          |  18 ++-
 sample_data/pasa_example/genome.fasta.gz           | Bin 0 -> 852337 bytes
 sample_data/pasa_example/pasa_assemblies.fasta.gz  | Bin 0 -> 304896 bytes
 sample_data/pasa_example/pasa_assemblies.gff3.gz   | Bin 0 -> 55455 bytes
 sample_data/pasa_example/runMe.sh                  |  21 ++++
 .../simple_transcriptome_target/Trinity.fasta.gz   | Bin 0 -> 359112 bytes
 .../{ => simple_transcriptome_target}/cleanme.pl   |  16 +--
 sample_data/simple_transcriptome_target/runMe.sh   |  11 ++
 util/cdna_alignment_orf_to_genome_orf.pl           |  43 +++++--
 util/create_start_PSSM.pl                          | 131 ++++++++++++++++++++
 util/cufflinks_gtf_to_alignment_gff3.pl            |  10 +-
 util/cufflinks_gtf_to_bed.pl                       |   4 +-
 util/extract_FL_subset.pl                          | 134 +++++++++++++++++++++
 util/get_FL_accs.pl                                |  31 +++++
 util/get_longest_ORF_per_transcript.pl             |  63 ++++++++++
 28 files changed, 652 insertions(+), 52 deletions(-)
 rename Release.Notes => Changelog.txt (77%)
 create mode 100755 PerlLib/Fasta_retriever.pm
 create mode 100644 sample_data/README.md
 rename sample_data/{ => cufflinks_example}/blastp.results.outfmt6.gz (100%)
 copy sample_data/{ => cufflinks_example}/cleanme.pl (100%)
 rename sample_data/{ => cufflinks_example}/pfam.domtblout.gz (100%)
 rename sample_data/{ => cufflinks_example}/runMe.sh (59%)
 rename sample_data/{ => cufflinks_example}/test.genome.fasta.gz (100%)
 rename sample_data/{ => cufflinks_example}/test.tophat.sam.gz (100%)
 rename sample_data/{ => cufflinks_example}/transcripts.gtf.gz (100%)
 copy sample_data/{ => pasa_example}/cleanme.pl (58%)
 create mode 100644 sample_data/pasa_example/genome.fasta.gz
 create mode 100644 sample_data/pasa_example/pasa_assemblies.fasta.gz
 create mode 100644 sample_data/pasa_example/pasa_assemblies.gff3.gz
 create mode 100755 sample_data/pasa_example/runMe.sh
 create mode 100644 sample_data/simple_transcriptome_target/Trinity.fasta.gz
 rename sample_data/{ => simple_transcriptome_target}/cleanme.pl (58%)
 create mode 100755 sample_data/simple_transcriptome_target/runMe.sh
 create mode 100755 util/create_start_PSSM.pl
 create mode 100755 util/extract_FL_subset.pl
 create mode 100755 util/get_FL_accs.pl
 create mode 100755 util/get_longest_ORF_per_transcript.pl

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