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v.1.4.0
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@tomas-fer
tomas-fer authored Mar 9, 2017
1 parent 5b804dd commit 1da5bb9
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6 changes: 3 additions & 3 deletions HybPhyloMaker0a_preparedata.sh
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# ********************************************************************************
# * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building *
# * Script 00a - Download & prepare data *
# * v.1.3.0 *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
# * Script 0a - Download & prepare data *
# * v.1.4.0 *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
# * [email protected] *
# ********************************************************************************

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4 changes: 2 additions & 2 deletions HybPhyloMaker0b_preparereference.sh
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# ********************************************************************************
# * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building *
# * Script 0b - Prepare pseudoreference *
# * v.1.3.1 *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
# * v.1.4.0 *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
# * [email protected] *
# ********************************************************************************

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6 changes: 3 additions & 3 deletions HybPhyloMaker0c_Rsetup_MetaCentrum.sh
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# ********************************************************************************
# * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building *
# * Setup R packages *
# * v.1.3.1 *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
# * Script 0c - Setup R packages on Metacentrum *
# * v.1.4.0 *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
# * [email protected] *
# ********************************************************************************

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6 changes: 3 additions & 3 deletions HybPhyloMaker1_rawprocess.sh
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#!/bin/bash
#----------------MetaCentrum----------------
#PBS -l walltime=1d
#PBS -l nodes=1:ppn=1:debian8
#PBS -l nodes=1:ppn=1:debian8:minspec=29
#PBS -j oe
#PBS -l mem=4gb
#PBS -l scratch=80gb
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# ********************************************************************************
# * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building *
# * Script 01 - Raw data processing *
# * v.1.3.3 *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
# * v.1.4.0 *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
# * [email protected] *
# * based on Weitemier et al. (2014), Applications in Plant Science 2(9): 1400042*
# ********************************************************************************
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25 changes: 16 additions & 9 deletions HybPhyloMaker2_readmapping.sh
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#!/bin/bash
#----------------MetaCentrum----------------
#PBS -l walltime=2d
#PBS -l nodes=1:ppn=4
#PBS -l nodes=1:ppn=4:minspec=29
#PBS -j oe
#PBS -l mem=4gb
#PBS -l scratch=80gb
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# ********************************************************************************
# * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building *
# * Script 02 - Read mapping using bowtie2 *
# * v.1.3.2 *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
# * v.1.4.0 *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
# * [email protected] *
# ********************************************************************************

Expand All @@ -43,6 +43,7 @@ if [[ $PBS_O_HOST == *".cz" ]]; then
module add samtools-1.3
module add perl-5.10.1
module add gcc-4.8.4
module add python34-modules-gcc
module add ococo-2016-11
elif [[ $HOSTNAME == compute-*-*.local ]]; then
echo -e "\nHybPhyloMaker2 is running on Hydra...\n"
Expand All @@ -57,6 +58,7 @@ elif [[ $HOSTNAME == compute-*-*.local ]]; then
#Add necessary modules
module load bioinformatics/bowtie2/2.2.6
module load bioinformatics/samtools/1.3
module load bioinformatics/ococo/ #???
else
echo -e "\nHybPhyloMaker2 is running locally...\n"
#settings for local run
Expand Down Expand Up @@ -222,19 +224,24 @@ for file in $(cat SamplesFileNames.txt); do
echo "Copying BAM..."
cp $path/$type/21mapped/${file}.bam .
fi
#CONSENSUS USING OCOCO
echo "Making consensus with OCOCO..."
ococo -i ${file}.bam -c $mincov -F ${file}.fasta 2>/dev/null
#CONSENSUS USING KINDEL/OCOCO
if [[ $conscall =~ "ococo" ]]; then
echo "Making consensus with OCOCO..."
ococo -i ${file}.bam -x ococo64 -c $mincov -F ${file}.fasta 2>/dev/null
else
echo "Making consensus with kindel..."
kindel -m $mincov -t $majthres ${file}.bam > ${file}.fasta
fi
#change name in fasta file
sed -i '1d' ${file}.fasta #delete first line
sed -i "1i >$file" ${file}.fasta #insert fasta header as a first line
sed -i.bak '1d' ${file}.fasta #delete first line
sed -i.bak "1i >$file" ${file}.fasta #insert fasta header as a first line
#Remove line breaks from fasta file
awk '!/^>/ { printf "%s", $0; n = "\n" } /^>/ { print n $0; n = "" } END { printf "%s", n }' ${file}.fasta > tmp && mv tmp ${file}.fasta
#put $nrns Ns to variable 'a' and $nrns ?s to variable 'b'
a=$(printf "%0.sN" $(seq 1 $nrns))
b=$(printf "%0.s?" $(seq 1 $nrns))
#replace all Ns separating exons by '?'
sed -i "s/$a/$b/g" ${file}.fasta
sed -i.bak "s/$a/$b/g" ${file}.fasta
#copy results to home
cp ${file}.fasta $path/$type/21mapped
#delete BAM
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4 changes: 2 additions & 2 deletions HybPhyloMaker3_generatepslx.sh
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# ********************************************************************************
# * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building *
# * Script 03 - Process consensus after mapping, make pslx files *
# * v.1.3.2 *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2016 *
# * v.1.4.0 *
# * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 *
# * [email protected] *
# * based on Weitemier et al. (2014), Applications in Plant Science 2(9): 1400042*
# ********************************************************************************
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