Updating README/Docker scripts

README.md

@@ -151,8 +151,38 @@ Finally, ViFi outputs several working files that can be deleted after a run.  Th
 7. \<prefix\>.fixed.trans.bam - A BAM file created by merging 6. and any human/viral paired end reads discovered by running the viral HMMs on 3.
 8. \<prefix\>.fixed.trans.cs.bam - A coordinate sorted BAM file of 7.
 
+## References
+1. Nguyen ND, Deshpande V, Luebeck J, Mischel PS, Bafna V (2018) ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer. Nucleic Acids Res (April):1–17.
+
+# [Advanced Notes](#advanced_notes)
+
+## Building evolutionary models
+
+ViFi can be run with and without evolutionary models (i.e., the HMMs).  We outline the steps in building the HMMs below.  However, we also include a Docker pipeline that will automatically build the HMMs for the users to use.  The pipeline only requires docker to be installed for use.
+
+## Using Docker pipeline to build HMMs for use in ViFi
+The following command will create HMMs from a set of unaligned sequences.  The sequences are assumed to share a common viral ancestor (i.e., don't mix viral families together when running the pipeline).  
+
+```
+bash $VIFI_DIR/scripts/build_references.sh <INPUT_SEQ> <OUTPUT_DIR> <PREFIX>
+```
+
+The output in the OUTPUT_DIR folder will be a set of HMMs (suffix with *.hmmbuild) and a file containing the list of HMMs.
+
+## Using customized reference 
+
+If you want to use a customized reference or a reference for a different organism, you can inform ViFi 
+of the reference sequences by supplying a chromosome file to ViFi using the **--chromosome_list**.  The file 
+format is a single line that has the sequence names delimited by spaces.  For example:
+
+```
+mouse_chr1 mouse_chr2
+```
 
-## Installation (Depreciated):
+would inform ViFi that any other sequences found in the BAM file that does not match mouse_chr1 and mouse_chr2 are
+considered viral sequences.
+
+## Installation from source code (Depreciated):
 We provide instructions for installing ViFi on Linux below.  
 
 1. ViFi download (if you have not already cloned this source code):
@@ -221,41 +251,3 @@ Note that this version defaults to searching for **HPV**.  To search for HBV, ru
 ```
 python run_vifi.py -f <input_R1.fq.gz> -r <input_R2.fq.gz> -o <output_dir> -v hbv
 ```
-
-## References
-1. Nguyen ND, Deshpande V, Luebeck J, Mischel PS, Bafna V (2018) ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer. Nucleic Acids Res (April):1–17.
-
-# [Advanced Notes](#advanced_notes)
-
-## Building evolutionary models
-
-ViFi can be run with and without evolutionary models (i.e., the HMMs).  The HMMs
-
-## Building Alignment and Tree on viral family of interest
-
-ViFi can build HMMs from any viral family if there is an existing FASTA alignment and NEWICK tree on the viral
-sequences.  Note that the sequences should be phylogenetically related to each other (i.e., do not mix HPV and HBV
-sequences).  Any standard alignment method and tree reconstruction method can be used.  In our paper, we used [PASTA](https://github.com/smirarab/pasta) to construct our alignment and tree and provide the steps in doing this below.
-Instructions on installing and running PASTA can be found [here](https://github.com/smirarab/pasta).
-
-## Building HMMs
-
-We created script to allow easy creation of the HMMs used within ViFi for a viral family of interesting.  To
-
-Requires:
-## 1) Python 2.7
-## 2) Dendropy verion 4.0.0 or higher (https://github.com/jeetsukumaran/DendroPy):
-sudo pip install dendropy
-
-## Using customized reference 
-
-If you want to use a customized reference or a reference for a different organism, you can inform ViFi 
-of the reference sequences by supplying a chromosome file to ViFi using the **--chromosome_list**.  The file 
-format is a single line that has the sequence names delimited by spaces.  For example:
-
-```
-mouse_chr1 mouse_chr2
-```
-
-would inform ViFi that any other sequences found in the BAM file that does not match mouse_chr1 and mouse_chr2 are
-considered viral sequences.

scripts/build_hmms.py

@@ -62,8 +62,8 @@ def build_hmms(tree_map, alignment_file, output_dir, prefix, keep_alignment):
 parser.add_argument('--prefix', dest='prefix',
                     help="prefix used to name HMM files (default=viral)", metavar='PREFIX', default = 'viral',
                     action='store', type=str)
-parser.add_argument('--max_size', dest='max_size',
-                    help="Maximum subtree size to decompose (default=10)", metavar='MAX_SIZE', default = 10,
+parser.add_argument('--max_size_fraction', dest='max_size',
+                    help="Maximum fraction of total size to decompose (default=.10)", metavar='MAX_SIZE', default = 0.10,
                     action='store', type=int)
 parser.add_argument('--keep_alignment', dest='keep_alignment',
                     help="Keep temporary ", default = False,
@@ -76,6 +76,7 @@ def build_hmms(tree_map, alignment_file, output_dir, prefix, keep_alignment):
 tree = Tree.get(file=open(arg.tree_file, 'r'), schema="newick", preserve_underscores=True)
 tree_map = {}
 print "Decomposing Tree"
-decompose_tree(tree, arg.max_size, tree_map = tree_map, decomposition=arg.decomposition)
+max_size = max(10, int(arg.max_size*len(tree.leaf_nodes())))
+decompose_tree(tree, max_size, tree_map = tree_map, decomposition=arg.decomposition)
 print "Building HMMs"
 build_hmms(tree_map, arg.alignment_file, arg.output_dir, arg.prefix, arg.keep_alignment)

scripts/build_references.sh

@@ -3,14 +3,31 @@ INPUT_FASTA=$1
 OUTPUT_DIR=$2
 PREFIX=$3
 
-#Build alignment/tree
-run_pasta.py --max-mem-mb=4000 -d dna -j $PREFIX -i $INPUT_FASTA  -o $OUTPUT_DIR
+mkdir -p $OUTPUT_DIR
+OUTPUT_DIR=`realpath $OUTPUT_DIR`
+INPUT_DIR=`dirname $INPUT_FASTA`
+if [ "$INPUT_DIR" == "." ]
+then
+  INPUT_DIR=`pwd`
+fi 
+INPUT_NAME=`basename $INPUT_FASTA`
+
+#Pull latest version of PASTA
+docker pull smirarab/pasta
+
+#Build alignment/tree, use 4GB for alignment
+docker run -v $INPUT_DIR/:/data/ -v $OUTPUT_DIR/:/output/ smirarab/pasta run_pasta.py  --max-mem-mb=4000 -d dna -j $PREFIX -i $INPUT_NAME  -o /output/
+
+cd $OUTPUT_DIR
 
 OUT_ALN=`grep "Writing resulting alignment" $PREFIX.out.txt | awk '{print $7}'`
+OUT_ALN=`basename $OUT_ALN`
 OUT_TREE=`grep "Writing resulting tree" $PREFIX.out.txt | awk '{print $7}'`
-
+OUT_TREE=`basename $OUT_TREE`
 #Decompose alignment/tree into HMMs
-python $VIFI_DIR/scripts/build_hmms.py --tree_file $OUT_TREE --alignment_file $OUT_ALN --prefix $PREFIX --output_dir $OUTPUT_DIR
+docker run -v $OUTPUT_DIR/:/output/ docker.io/namphuon/vifi python "scripts/build_hmms.py" --tree_file /output/$OUT_TREE --alignment_file /output/$OUT_ALN --prefix $PREFIX --output_dir /output/
+
+#python $VIFI_DIR/scripts/build_hmms.py --tree_file $OUT_TREE --alignment_file $OUT_ALN --prefix $PREFIX --output_dir $OUTPUT_DIR
 
 #Build HMM list
 ls $OUTPUT_DIR/*.hmmbuild > $OUTPUT_DIR/hmm_list.txt