removing default de novo assembly, split vcf variants, and several kr…

…aken2 requirements. Also, allow refseq alignment to be used ONLY instead of relying on kraken2 and assembly pulling. Fixing up some merged naming conventions. Added fuzzy matching parameters

bin/append_GCF.sh

@@ -0,0 +1,92 @@
+
+#!/usr/bin/env bash
+##############################################################################################
+# Copyright 2022 The Johns Hopkins University Applied Physics Laboratory LLC
+# All rights reserved.
+# Permission is hereby granted, free of charge, to any person obtaining a copy of this
+# software and associated documentation files (the "Software"), to deal in the Software
+# without restriction, including without limitation the rights to use, copy, modify,
+# merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+# permit persons to whom the Software is furnished to do so.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+# INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
+# PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+# LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE
+# OR OTHER DEALINGS IN THE SOFTWARE.
+#
+#    FUNCTIONS
+usage()
+{
+cat << EOF
+
+Help message for make_gcf_mapping.sh:
+
+DESCRIPTION:
+    Optionally merge assembly refseq on a gcf assembly pull FASTA file. FASTA file must be in format >chr GCF description (3 columns) where first 2 are a space and the third is anything after
+
+NOTES:
+
+
+OPTIONS:
+    -h    help    show this message
+    -i    FILE    a fasta file/dir of gcf references pulled. Appends the filename's GCF to the middle of the accession (between chr accession and description)
+    -d    FILE    optional. If called, it is a directory of GCF files (*fna, *fasta, *faa, *fa)
+    -o    FILE        full path to output  file
+
+USAGE:
+
+bash append_GCF.sh -i GCF_020735385.1.fasta -o test.fasta -t (looks at all fasta files in dir)
+bash append_GCF.sh -i GCF_020735385.1.fasta -o test.fasta  (appends base assembly accession to center of contig/chromosome header)
+
+EOF
+}
+
+DIR="FALSE"
+
+#    ARGUMENTS
+# parse args
+while getopts "hi:do:" OPTION
+do
+    case $OPTION in
+        h) usage; exit 1 ;;
+        i) fasta=$OPTARG ;;
+        d) DIR="TRUE" ;;
+        o) output=$OPTARG ;;
+        ?) usage; exit ;;
+    esac
+done
+
+
+# make a function to append the GCF to the middle of the accession
+# if the file is GCF_102310239.1_aSDGM I want only GCF. Split on the _ and get first 2 elements
+# now get all lines that start with ">" in the filename, and append the gcf to the middle of the accession between NC_12123 and "djaskdjasdklj" (random description). It should be $1 then $gcf then everything AFTER $1
+# use sed after first space
+append_f(){
+    filename=$1
+    # echo "Name BEGINS with GCF: ${basen}"
+    # get the basename of the file removing extension
+    basen=$(basename $filename | sed 's/\.[^.]*$//')
+    # if the file is GCF_102310239.1_aSDGM I want only GCF. Split on the _ and get first 2 elements
+    gcf=$(echo $basen | awk -F '_' '{print $1"_"$2}')
+    # now get all lines that start with ">" in the filename, and append the gcf to the middle of the accession between NC_12123 and "djaskdjasdklj" (random description). It should be $1 then $gcf then everything AFTER $1
+    # use sed after first space
+    sed -e "s/ / $gcf /" $filename
+}
+
+
+if [[ $DIR == "TRUE" ]]; then
+    echo "Directory detected"
+    for filename in $(find $fasta  \( -name "*.fasta" -o -name "*fna" -o -name "*faa" -o -name "*fa" \) -type f ); do
+        basen=$(basename $filename)
+        if [[ $basen =~ "GCF" ]]; then
+            append_f $filename
+        fi
+
+    done
+
+else
+    append_f $fasta
+fi
+

bin/determine_priority_assembly.py

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+import re
+def determine_priority_assembly(line):
+    cols = line.strip().split("\t")
+    if len(cols) > 7:
+        name = cols[7]
+        level = cols[4]
+        if level == "representative genome" :
+            return 0
+        elif cols[4] == "reference genome"  :
+            return 1
+        elif cols[11] == "Complete Genome"  :
+            return 2
+        else:
+            return 3
+def format_description(id, description):
+    delimiters = "[ ]"  # Split on underscore or comma
+    description = description.split(',', 1)[0]
+    linesplit = re.split(delimiters, description)
+    id = id.replace(">", "")
+    # remove all after first comma
+
+    if len(linesplit) > 1:
+        return id, " ".join(linesplit[1:])
+    else:
+        return id, description
+def extract_strain_from_description(description):
+    delimiters = "[ ]"  # Split on underscore or comma
+    # regex match for strain, get value after space until next space
+def parse_fasta_header(header):
+    parts = header.split()
+    organism_parts = []
+    strain = None
+    for part in parts:
+        if part.lower() == "strain":
+            strain_index = parts.index(part) + 1
+            if strain_index < len(parts):
+                strain = parts[strain_index]
+            break
+        organism_parts.append(part)
+    organism_name = " ".join(organism_parts)
+    return organism_name, strain