From 73e07d707194809d372a68d2786ac4a65c573130 Mon Sep 17 00:00:00 2001
From: bart <bart.nijsse@wur.nl>
Date: Mon, 16 May 2022 16:43:02 +0200
Subject: [PATCH] moved to metagenomics

---
 bin_assembly_stats.sh   | 19 -------------------
 get_unbinned_contigs.sh |  7 -------
 2 files changed, 26 deletions(-)
 delete mode 100755 bin_assembly_stats.sh
 delete mode 100755 get_unbinned_contigs.sh

diff --git a/bin_assembly_stats.sh b/bin_assembly_stats.sh
deleted file mode 100755
index 93fd72c..0000000
--- a/bin_assembly_stats.sh
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/bin/bash
-
-# Loops through a folder of fasta files and calculates #contigs, total length, N50, largst contig and GC%.
-# (also works on gzipped fasta files)
-#
-# The raw_n50 executeable comes from the idba_ud assembler.
-
-echo -e 'bin\tcontigs\ttotal_length\tN50\tlargest\tGC%'
-for filepath in `ls $1/*.fa*`; do
-  bin=$(basename $filepath | sed s'/.fa.*//'g)
-  raw_n50_stats=$(/unlock/infrastructure/binaries/raw_n50 $filepath)
-  
-  GC=$(grep -v ">" $filepath | sed -e 's/\(.\)/\1\n/g' | grep -c "G\|C")
-  size=$(echo $raw_n50_stats | awk '{print $11}')
-  GCcontent=$(echo | awk -v GC=$GC -v size=$size '{printf "%.2f", GC/size*100}')
-  
-  stats=$(echo $raw_n50_stats | awk '{print $2"\t"$11"\t"$4"\t"$6}')
-  echo -e $bin"\t"$stats"\t"$GCcontent | sed 's/ /\t/g'
-done
diff --git a/get_unbinned_contigs.sh b/get_unbinned_contigs.sh
deleted file mode 100755
index 22ab695..0000000
--- a/get_unbinned_contigs.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/bin/bash
-
-# sh get_unbinned_contigs.sh <contigs.fasta> <folder containing .fa bins> <identifier>
-
-cat $2/*.fa  | grep "^>" | sed 's/>//g' | sort > binned.headers
-/unlock/infrastructure/binaries/faTools/faSomeRecords $1 -exclude binned.headers $3_unbinned.fasta
-pigz -p $4 $3_unbinned.fasta
-- 
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