updates to v1.5.2; add score 500 to genemark-ET intron hints

Author: Jon Palmer

dockerbuild/Dockerfile-base

@@ -100,5 +100,5 @@ RUN wget --quiet https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86
 
 COPY pasa_conf.txt /home/linuxbrew/PASApipeline/pasa_conf/conf.txt
 
-RUN wget https://github.com/nextgenusfs/funannotate/archive/1.5.1.tar.gz && \
-    tar -zxvf 1.5.1.tar.gz && rm 1.5.1.tar.gz && mv funannotate-1.5.1 funannotate
+RUN wget https://github.com/nextgenusfs/funannotate/archive/1.5.2.tar.gz && \
+    tar -zxvf 1.5.2.tar.gz && rm 1.5.2.tar.gz && mv funannotate-1.5.2 funannotate

funannotate.py

@@ -237,6 +237,7 @@ def fmtcols(mylist, cols):
            --rna_bam                RNA-seq mapped to genome to train Augustus/GeneMark-ET 
            --stringtie              StringTie GTF result
            --augustus_species       Augustus species config. Default: uses species name
+           --min_training_models    Minimum number of models to train Augustus. Default: 200
            --genemark_mode          GeneMark mode. Default: ES [ES,ET]
            --genemark_mod           GeneMark ini mod file
            --busco_seed_species     Augustus pre-trained species to start BUSCO. Default: anidulans

lib/library.py

@@ -4180,6 +4180,7 @@ def RunGeneMarkET(command, input, ini, evidence, maxintron, softmask, cpus, tmpd
         with open(evidence, 'rU') as evid:
             for line in evid:
                 if '\tintron\t' in line and '\tb2h\t' in line:
+                    line[5] = 500 # for intron hint score to be 500
                     hints.write(line)
     log.info("Running GeneMark-ET on assembly")
     cmd = [command, '--ET', os.path.abspath(hintsfile), '--max_intron', str(maxintron), '--soft_mask', str(softmask), '--cores', str(cpus), '--sequence', contigs]