Update gto_relative_complexity_profile pipeline and add gto_fasta_ali…

…gn_bwa pipeline
cobilab · Dec 1, 2020 · 3cf64d8 · 3cf64d8
1 parent f364f5f
commit 3cf64d8
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Showing 4 changed files with 337 additions and 43 deletions.
diff --git a/conda/build.sh b/conda/build.sh
@@ -25,7 +25,7 @@ cp pipelines/gto_sars_simulation_detection/gto_sars_simulation_detection.sh $PRE
 cp pipelines/gto_download_sars2/gto_download_sars2.sh $PREFIX/bin/
 cp pipelines/gto_find_best_sars2/gto_find_best_sars2.sh $PREFIX/bin/
 cp pipelines/gto_relative_complexity_profile/gto_relative_complexity_profile.sh $PREFIX/bin/
-
+cp pipelines/gto_fasta_align_bwa/gto_fasta_align_bwa.sh $PREFIX/bin/
 
 cp bin/gto $PREFIX/bin/
 cp bin/gto_amino_acid_compressor $PREFIX/bin/

diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -5,10 +5,10 @@
 
 package:
     name: gto
-    version: '1.5.4'
+    version: '1.5.6'
 
 source:
-    git_rev: v1.5.4
+    git_rev: v1.5.6
     git_url: https://github.com/cobilab/gto.git
 
 requirements:

diff --git a/pipelines/gto_fasta_align_bwa/gto_fasta_align_bwa.sh b/pipelines/gto_fasta_align_bwa/gto_fasta_align_bwa.sh
@@ -0,0 +1,177 @@
+#!/bin/bash
+#
+TAG="X";
+RUN="0";
+THREADS="4";
+REFERENCE="";
+FORWARD="o_fw_pr.fq";
+REVERSE="o_rv_pr.fq";
+UNPAIRED="o_fw_unpr.fq,o_rv_unpr.fq";
+#
+################################################################################
+#
+SHOW_MENU () {
+  echo " ------------------------------------------------------- ";
+  echo " ";
+  echo " gto_align_reads.sh >> FASTQ reads alignment pipeline     ";
+  echo "        with sort, duplications removal, and indexes. ";
+  echo " ";
+  echo " Program options --------------------------------------- ";
+  echo " ";
+  echo " -h, --help                     Show this, ";
+  echo " -c, --install                  Installation (w/ conda), ";
+  echo " ";
+  echo " -n <STR>, --name <STR>         TAG name for uniqueness,  ";
+  echo " -t <INT>, --threads <INT>      Number of threads.        ";
+  echo " ";
+  echo " Input options ----------------------------------------- ";
+  echo " ";
+  echo " -r <FILE>, --reference <FILE>  FASTA Reference filename, ";
+  echo " ";
+  echo " -1 <FILE>, --forward <FILE>    FASTQ forward filename,   ";
+  echo " -2 <FILE>, --reverse <FILE>    FASTQ reverse filename,   ";
+  echo " -U <FILE>, --unpaired <FILE>   FASTQ unpaired filename.  ";
+  echo " ";
+  echo " Example ----------------------------------------------- ";
+  echo " ";
+  echo " gto_align_reads.sh --threads 8 --reference B19.fa \\ ";
+  echo " --forward FW.fq --reverse RV.fq -U FW_U.fq,RV_U.fq ";
+  echo " ";
+  echo " ------------------------------------------------------- ";
+  }
+#
+################################################################################
+#
+CHECK_INPUT () {
+  FILE=$1
+  if [ -f "$FILE" ];
+    then
+    echo "Input filename: $FILE"
+    else
+    echo -e "\e[31mERROR: input file not found ($FILE)!\e[0m";
+    SHOW_MENU;
+    exit;
+    fi
+  }
+#
+################################################################################
+#
+PROGRAM_EXISTS () {
+  if ! [ -x "$(command -v $1)" ];
+    then
+    echo -e "\e[41mERROR\e[49m: $1 is not installed." >&2;
+    echo -e "\e[42mTIP\e[49m: Try: gto_align_reads.sh --install" >&2;
+    exit 1;
+    fi
+  }
+#
+################################################################################
+#
+if [[ "$#" -lt 1 ]];
+  then
+  HELP=1;
+  fi
+#
+POSITIONAL=();
+#
+while [[ $# -gt 0 ]]
+  do
+  i="$1";
+  case $i in
+    -h|--help|?)
+      HELP=1;
+      shift
+    ;;
+    -c|--install|--compile)
+      INSTALL=1;
+      shift
+    ;;
+    -n|--name|--tag)
+      TAG="$2";
+      shift 2;
+    ;;
+    -t|--threads)
+      THREADS="$2";
+      shift 2;
+    ;;
+    -r|--reference)
+      REFERENCE="$2";
+      RUN=1;
+      shift 2;
+    ;;
+    -1|--forward)
+      FORWARD="$2";
+      shift 2;
+    ;;
+    -2|--reverse)
+      REVERSE="$2";
+      shift 2;
+    ;;
+    -U|--unpaired)
+      UNPAIRED="$2";
+      shift 2;
+    ;;
+    -*) # unknown option with small
+    echo "Invalid arg ($1)!";
+    echo "For help, try: gto_align_reads.sh -h"
+    exit 1;
+    ;;
+  esac
+  done
+#
+set -- "${POSITIONAL[@]}" # restore positional parameters
+#
+################################################################################
+#
+if [[ "$HELP" -eq "1" ]];
+  then
+  SHOW_MENU;
+  exit;
+  fi
+#
+################################################################################
+#
+if [[ "$INSTALL" -eq "1" ]];
+  then
+  conda install -c bioconda samtools --yes
+  conda install -c bioconda bowtie2 --yes
+  exit;
+  fi
+#
+################################################################################
+#
+if [[ "$RUN" -eq "1" ]];
+  then
+  #
+  echo "Using $THREADS threads ...";
+  #
+  PROGRAM_EXISTS "bowtie2";
+  PROGRAM_EXISTS "samtools";
+  #
+  CHECK_INPUT "$REFERENCE";
+  #
+  CHECK_INPUT "$FORWARD";
+  CHECK_INPUT "$REVERSE";
+  CHECK_INPUT "$UNPAIRED";
+  #
+  rm -f index_file_$TAG* aligned_sorted-$TAG.bam aligned_sorted-$TAG.bam.bai aligned_sorted-$TAG.bam
+  #
+  bowtie2-build $REFERENCE index_file_$TAG
+  bowtie2 -a --threads $THREADS --very-sensitive -x index_file_$TAG -1 $FORWARD -2 $REVERSE -U $UNPAIRED > aligned-$TAG.sam
+  samtools sort --threads $THREADS aligned-$TAG.sam > aligned_sorted-$TAG.bam
+  samtools sort --threads $THREADS -n aligned_sorted-$TAG.bam > aligned_sorted_sorted-$TAG.bam
+  samtools fixmate --threads $THREADS -m aligned_sorted_sorted-$TAG.bam aligned_sorted_sorted-$TAG-fixmate.bam
+  samtools sort --threads $THREADS -o aligned_sorted_sorted-$TAG-fixmate-sort.bam aligned_sorted_sorted-$TAG-fixmate.bam
+  samtools markdup --threads $THREADS -r aligned_sorted_sorted-$TAG-fixmate-sort.bam aligned_sorted-$TAG.bam
+  samtools index -@ $THREADS aligned_sorted-$TAG.bam aligned_sorted-$TAG.bam.bai
+  samtools flagstat -@ $THREADS aligned_sorted-$TAG.bam > Alignments-Stats-$TAG.txt
+  #
+  rm -f *.bt2 aligned-$TAG.sam aligned_sorted_sorted-$TAG.bam aligned_sorted_sorted-$TAG-fixmate.bam aligned_sorted_sorted-$TAG-fixmate-sort.bam
+  #
+  echo "Reference  : $REFERENCE (index included)";
+  echo "Alignments : aligned_sorted-$TAG.bam (index included)";
+  #
+  fi
+#
+################################################################################
+#