From 622e57f27be511aa5db0855b040cebb6f7f6c58b Mon Sep 17 00:00:00 2001
From: criscuol <alexis.criscuolo@pasteur.fr>
Date: Sat, 13 Mar 2021 13:27:05 +0100
Subject: [PATCH] 2.0
---
README.md | 49 ++++++++++-
contig_info.sh | 222 ++++++++++++++++++++++++++++++++++---------------
2 files changed, 201 insertions(+), 70 deletions(-)
diff --git a/README.md b/README.md
index 46531a2..0f73f1a 100644
--- a/README.md
+++ b/README.md
@@ -1,11 +1,12 @@
# contig_info
_contig_info_ is a command line program written in [Bash](https://www.gnu.org/software/bash/) for quickly estimating several standard descriptive statistics from FASTA-formatted contig files inferred by _de novo_ genome assembly methods.
-Estimated statistics are sequence number, residue counts, AT- and GC-content, sequence lengths, [auN](https://lh3.github.io/2020/04/08/a-new-metric-on-assembly-contiguity) (also called E-size, Salzberg et al. 2012), [N50](https://en.wikipedia.org/wiki/N50,_L50,_and_related_statistics) (Lander et al. 2001), [NG50](https://en.wikipedia.org/wiki/N50,_L50,_and_related_statistics) (Earl et al. 2011), and the related N75, NG75, N90, NG90, L50, LG50, L75, LG75, L90, LG90.
+Estimated statistics are sequence number, residue counts, AT- and GC-content, sequence lengths, [auN](https://lh3.github.io/2020/04/08/a-new-metric-on-assembly-contiguity) (also called E-size, Salzberg et al. 2012), [N50](https://en.wikipedia.org/wiki/N50,_L50,_and_related_statistics) (Lander et al. 2001), [NG50](https://en.wikipedia.org/wiki/N50,_L50,_and_related_statistics) (Earl et al. 2011), and the related N(G)75, N(G)G90, L(G)50, L(G)75, L(G)90.
+_contig_info_ can also estimates nucleotide content statistics for each contig sequence.
## Installation and execution
-Give the execute permission to the file `contig_info.sh` by typing:
+Give the execute permission to the file `contig_info.sh` by typing:
```bash
chmod +x contig_info.sh
@@ -29,6 +30,8 @@ Run _contig_info_ without option to read the following documentation:
than this cutoff will be discarded (default: 1)
-g <int> expected genome size for computing auNG and {N,L}G{50,75,90}
values instead of auN and {N,L}{50,75,90} ones, respectively
+ -r residue content statistics for each contig sequence instead of
+ global statistics
-t tab-delimited output
```
@@ -126,7 +129,7 @@ Mucor.WJ11.fasta 28368 24148 12884 5672 429 898 1455
```
-Finally, the option `-g` can be used to set an expected genome size for obtaining auNG and {N,L}G{50,75,90} statistics instead of auN and {N,L}{50,75,90} ones:
+The option `-g` can be used to set an expected genome size for obtaining auNG and {N,L}G{50,75,90} statistics instead of auN and {N,L}{50,75,90} ones:
```bash
./contig_info.sh -t -g 36000000 Mucor.*.fasta | cut -f1,22-
@@ -142,6 +145,46 @@ Mucor.WJ11.fasta 26055 21799 9865 2445 493 1092 2146 36000000
```
+Finally, the option `-r` enables to obtain the residue details for each sequence within each input file.
+Option `-r` can be used together with option `-t` to obtain a global view of the residue composition:
+
+```bash
+./contig_info.sh -r -t Mucor.CBS277.49.fasta
+```
+
+```
+#File Seq Nres A C G T N %A %C %G %T %N %AT %GC Pval
+Mucor.CBS277.49.fasta AMYB01000001.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_01, whole genome shotgun sequence 6050249 1750309 1276313 1271843 1751784 0 28.92 21.09 21.02 28.95 0 57.89 42.11 1.0000
+Mucor.CBS277.49.fasta AMYB01000002.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_02, whole genome shotgun sequence 5009828 1445835 1059454 1055351 1449188 0 28.85 21.14 21.06 28.92 0 57.79 42.21 0.000
+Mucor.CBS277.49.fasta AMYB01000003.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_03, whole genome shotgun sequence 4868387 1404688 1027031 1026257 1410411 0 28.85 21.09 21.08 28.97 0 57.83 42.17 0.020
+Mucor.CBS277.49.fasta AMYB01000004.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_04, whole genome shotgun sequence 4318338 1250156 914240 913373 1240569 0 28.94 21.17 21.15 28.72 0 57.68 42.32 0.000
+Mucor.CBS277.49.fasta AMYB01000005.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_05, whole genome shotgun sequence 3239665 934794 681540 688359 934972 0 28.85 21.03 21.24 28.86 0 57.72 42.28 0.222
+Mucor.CBS277.49.fasta AMYB01000006.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_06, whole genome shotgun sequence 3187354 921853 671173 669308 925020 0 28.92 21.05 20.99 29.02 0 57.95 42.05 0.626
+Mucor.CBS277.49.fasta AMYB01000007.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_07, whole genome shotgun sequence 3096690 894782 653220 654088 894600 0 28.89 21.09 21.12 28.88 0 57.79 42.21 0.444
+Mucor.CBS277.49.fasta AMYB01000008.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_08, whole genome shotgun sequence 2213752 637973 467830 470692 637257 0 28.81 21.13 21.26 28.78 0 57.61 42.39 0.526
+Mucor.CBS277.49.fasta AMYB01000009.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_09, whole genome shotgun sequence 1074709 310418 227365 225234 311692 0 28.88 21.15 20.95 29.00 0 57.89 42.11 0.808
+Mucor.CBS277.49.fasta AMYB01000010.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_10, whole genome shotgun sequence 976311 285831 206369 203542 280569 0 29.27 21.13 20.84 28.73 0 58.02 41.98 0.792
+Mucor.CBS277.49.fasta AMYB01000011.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_11, whole genome shotgun sequence 934259 273240 195919 194769 270331 0 29.24 20.97 20.84 28.93 0 58.19 41.81 0.378
+Mucor.CBS277.49.fasta AMYB01000012.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_12, whole genome shotgun sequence 832466 240427 175344 173907 242788 0 28.88 21.06 20.89 29.16 0 58.05 41.95 0.720
+Mucor.CBS277.49.fasta AMYB01000013.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_13, whole genome shotgun sequence 423239 121227 88619 87831 125562 0 28.64 20.93 20.75 29.66 0 58.31 41.69 0.180
+Mucor.CBS277.49.fasta AMYB01000014.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_14, whole genome shotgun sequence 155282 45402 31673 31509 46698 0 29.23 20.39 20.29 30.07 0 59.32 40.68 0.000
+Mucor.CBS277.49.fasta AMYB01000015.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_15, whole genome shotgun sequence 97977 28739 20928 20035 28275 0 29.33 21.36 20.44 28.85 0 58.20 41.80 0.702
+Mucor.CBS277.49.fasta AMYB01000016.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_16, whole genome shotgun sequence 41542 11324 9228 9406 11584 0 27.25 22.21 22.64 27.88 0 55.15 44.85 0.000
+Mucor.CBS277.49.fasta AMYB01000017.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_17, whole genome shotgun sequence 17493 5063 3195 3919 5316 0 28.94 18.26 22.40 30.38 0 59.34 40.66 0.504
+Mucor.CBS277.49.fasta AMYB01000018.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_18, whole genome shotgun sequence 11355 3216 2365 2256 3518 0 28.32 20.82 19.86 30.98 0 59.31 40.69 0.486
+Mucor.CBS277.49.fasta AMYB01000019.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_19, whole genome shotgun sequence 9869 2972 2278 2160 2459 0 30.11 23.08 21.88 24.91 0 55.04 44.96 0.144
+Mucor.CBS277.49.fasta AMYB01000020.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_21, whole genome shotgun sequence 4662 1534 815 946 1367 0 32.90 17.48 20.29 29.32 0 62.23 37.77 0.216
+Mucor.CBS277.49.fasta AMYB01000021.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_22, whole genome shotgun sequence 4155 1247 1002 1116 790 0 30.01 24.11 26.85 19.01 0 49.03 50.97 0.036
+```
+
+Note that the last column `Pval` assesses the GC-content adequation between each contig and the longest one.
+When _Pval_ is close to 0, then the %GC of the corresponding contig is significantly different to the %GC of the longest one.
+This _p_-value can be used as an indicator when searching for particular replicons (e.g. plasmids, mitochondrion) or artefactual contigs, as such sequences often induce specific nucleotide compositions.
+Indeed, when considering a FASTA file outputted by a _de novo_ assembly program, the longest contig generally does not correspond to such replicon(s), therefore giving a good approximation of the expected GC-content within the hole chromosome.
+
+
+
+
## References
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol Ä°, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B (2011) _Assemblathon 1: a competitive assessment of de novo short read assembly methods_. **Genome Research**, 21(12):2224-2241. [doi:10.1101/gr.126599.111](https://genome.cshlp.org/content/21/12/2224).
diff --git a/contig_info.sh b/contig_info.sh
index c22e1c1..d279e13 100755
--- a/contig_info.sh
+++ b/contig_info.sh
@@ -4,7 +4,7 @@
# #
# contig_info: a BASH script to estimate standard statistics from FASTA contig files #
# #
-# Copyright (C) 2018-2021 Institut Pasteur #
+ COPYRIGHT="Copyright (C) 2018-2021 Institut Pasteur" #
# #
# This program is free software: you can redistribute it and/or modify it under the terms of the GNU #
# General Public License as published by the Free Software Foundation, either version 3 of the License, or #
@@ -33,7 +33,11 @@
# = VERSIONS = #
# ============ #
# #
- VERSION=1.1.201007ac #
+ VERSION=2.0.210312ac #
+# + adding option -r #
+# + adding trap when interrupting script #
+# #
+# VERSION=1.1.201007ac #
# + estimating auN (also called E-size) #
# #
# VERSION=1.0.190426ac #
@@ -69,10 +73,9 @@
# #
if [ "$1" = "-?" ] || [ $# -lt 1 ]
then
+ echo -e "\n\033[1m contig_info v$VERSION $COPYRIGHT\033[0m";
cat <<EOF
- contig_info v.$VERSION Copyright (C) 2018-2021 Institut Pasteur
-
USAGE: contig_info.sh [options] <contig_files>
where 'options' are:
@@ -81,11 +84,13 @@ then
than this cutoff will be discarded (default: 1)
-g <int> expected genome size for computing auNG and {N,L}G{50,75,90}
values instead of auN and {N,L}{50,75,90} ones, respectively
+ -r residue content statistics for each contig sequence instead of
+ global statistics
-t tab-delimited output
EOF
- exit #
-fi #
+ exit ;
+fi
# #
#############################################################################################################
@@ -110,21 +115,29 @@ randomfile() {
#### INITIALIZING PARAMETERS AND READING OPTIONS ####
#### ####
#############################################################################################################
+export LC_ALL=C;
+
MIN_CONTIG_LGT=1;
GENOME_SIZE=0;
+RES_CONTENT=false;
TSVOUT=false;
-while getopts m:g:t option
+
+while getopts m:g:tr option
do
case $option in
m) MIN_CONTIG_LGT=$OPTARG ;;
g) GENOME_SIZE=$OPTARG ;;
+ r) RES_CONTENT=true ;;
t) TSVOUT=true ;;
:) echo "option $OPTARG : missing argument" ; exit 1 ;;
\?) echo "$OPTARG : option invalide" ; exit 1 ;;
esac
done
-if [ $MIN_CONTIG_LGT -lt 1 ]; then echo " the min contig length threshold must be a positive integer (option -m)" ; exit 1 ; fi
-if [ $GENOME_SIZE -lt 0 ]; then echo " the expected genome size must be a positive integer (option -g)" ; exit 1 ; fi
+if ! [[ $MIN_CONTIG_LGT =~ ^[0-9]+$ ]]; then echo " incorrect value (option -m): $MIN_CONTIG_LGT" >&2 ; exit 1 ; fi
+if [ $MIN_CONTIG_LGT -lt 1 ]; then echo " the min contig length threshold must be a positive integer (option -m)" >&2 ; exit 1 ; fi
+if ! [[ $GENOME_SIZE =~ ^[0-9]+$ ]]; then echo " incorrect value (option -g): $GENOME_SIZE" >&2 ; exit 1 ; fi
+if [ $GENOME_SIZE -lt 0 ]; then echo " the expected genome size must be a positive integer (option -g)" >&2 ; exit 1 ; fi
+
#############################################################################################################
#### ####
@@ -133,81 +146,156 @@ if [ $GENOME_SIZE -lt 0 ]; then echo " the expected genome size must be a p
#############################################################################################################
if $TSVOUT
then
- CSVCAPT="#File\tNseq\tNres\tA\tC\tG\tT\tN\t%A\t%C\t%G\t%T\t%N\t%AT\t%GC\tMin\tQ25\tMed\tQ75\tMax\tAvg\tauN\tN50\tN75\tN90\tL50\tL75\tL90";
- [ $GENOME_SIZE -ne 0 ]&&CSVCAPT="$CSVCAPT\tExpSize";
+ if ! $RES_CONTENT
+ then
+ CSVCAPT="#File\tNseq\tNres\tA\tC\tG\tT\tN\t%A\t%C\t%G\t%T\t%N\t%AT\t%GC\tMin\tQ25\tMed\tQ75\tMax\tAvg\tauN\tN50\tN75\tN90\tL50\tL75\tL90";
+ [ $GENOME_SIZE -ne 0 ] && CSVCAPT="$CSVCAPT\tExpSize";
+ else
+ CSVCAPT="#File\tSeq\tNres\tA\tC\tG\tT\tN\t%A\t%C\t%G\t%T\t%N\t%AT\t%GC\tPval";
+ fi
echo -e "$CSVCAPT" ;
fi
+
SEQS=$(randomfile); ## txt file with one sequence per line
+trap "echo -n interrupting ; rm -f $SEQS &>/dev/null ; echo ; exit " SIGINT
+
for INFILE in "$@"
do
if [ ! -e $INFILE ] || [ ! -f $INFILE ] || [ ! -r $INFILE ]; then continue; fi
tr -d '\15\32' < $INFILE | awk -v thr=$MIN_CONTIG_LGT '/^>/{if(length(s)>=thr)print s;s="";next}{s=s$0}END{if(length(s)>=thr)print s}' | tr '[:lower:]' '[:upper:]' > $SEQS ;
- R=$(tr -d [:cntrl:] < $SEQS | wc -c); S=$(wc -l < $SEQS); AVG=$(bc -l<<<"scale=2;$R/$S" | sed 's/^\./0./');
- A=$(tr -cd A < $SEQS | wc -c); fA=$(bc -l <<<"scale=2;100*$A/$R" | sed 's/^\./0./');
- C=$(tr -cd C < $SEQS | wc -c); fC=$(bc -l <<<"scale=2;100*$C/$R" | sed 's/^\./0./');
- G=$(tr -cd G < $SEQS | wc -c); fG=$(bc -l <<<"scale=2;100*$G/$R" | sed 's/^\./0./');
- T=$(tr -cd T < $SEQS | wc -c); fT=$(bc -l <<<"scale=2;100*$T/$R" | sed 's/^\./0./');
- N=$(tr -cd N < $SEQS | wc -c); fN=$(bc -l <<<"scale=2;100*$N/$R" | sed 's/^\./0./');
- fGC=$(bc -l <<<"scale=2;100*($C+$G)/($A+$C+$G+$T)" | sed 's/^\./0./'); fAT=$(bc -l <<<"scale=2;100-$fGC" | sed 's/^\./0./');
- ER=$R; [ $GENOME_SIZE != 0 ] && ER=$GENOME_SIZE;
- STATS=$(awk '{print length}' $SEQS | sort -rn | awk -v g=$ER '{l[++n]=$0;aun+=$0*$0}END{g50=g/2;g75=3*g/4;g90=9*g/10;i=s=n50=n75=n90=0;while(++i<=n&&n90==0){s+=l[i];n50==0&&s>=g50&&n50=l[i]+(l50=i);n75==0&&s>=g75&&n75=l[i]+(l75=i);n90==0&&s>=g90&&n90=l[i]+(l90=i)}print (n50-l50)"\t"(n75-l75)"\t"(n90-l90)"\t"l50"\t"l75"\t"l90"\t"l[1]"\t"l[int(n/4+1)]"\t"l[int(n/2+1)]"\t"l[int(3*n/4+1)]"\t"l[n]"\t"int(0.5+aun/g)}');
- N50=$(cut -f1 <<<"$STATS"); N75=$(cut -f2 <<<"$STATS"); N90=$(cut -f3 <<<"$STATS");
- L50=$(cut -f4 <<<"$STATS"); L75=$(cut -f5 <<<"$STATS"); L90=$(cut -f6 <<<"$STATS");
- Q75=$(cut -f8 <<<"$STATS"); Q50=$(cut -f9 <<<"$STATS"); Q25=$(cut -f10 <<<"$STATS");
- MIN=$(cut -f11 <<<"$STATS"); MAX=$(cut -f7 <<<"$STATS"); AUN=$(cut -f12 <<<"$STATS");
-
- if ! $TSVOUT
+
+ if ! $RES_CONTENT
then
- echo ;
- echo "File $(basename $INFILE)" ;
- echo ;
- echo "Number of sequences $S" ;
- echo ;
- echo "Residue counts:" ;
- echo " Number of A's $A $fA %" ;
- echo " Number of C's $C $fC %" ;
- echo " Number of G's $G $fG %" ;
- echo " Number of T's $T $fT %" ;
- echo " Number of N's $N $fN %" ;
- echo " Total $R" ;
- echo ;
- echo " %AT $fAT %" ;
- echo " %GC $fGC %" ;
- echo ;
- echo "Sequence lengths:" ;
- echo " Minimum $MIN" ;
- echo " Quartile 25% $Q25" ;
- echo " Median $Q50" ;
- echo " Quartile 75% $Q75" ;
- echo " Maximum $MAX" ;
- echo " Average $AVG" ;
- echo ;
- echo "Contiguity statistics:" ;
- echo " auN $AUN" ;
- echo " N50 $N50" ;
- echo " N75 $N75" ;
- echo " N90 $N90" ;
- echo " L50 $L50" ;
- echo " L75 $L75" ;
- echo " L90 $L90" ;
- if [ $GENOME_SIZE -ne 0 ]; then echo " Expected genome size $GENOME_SIZE"; fi
- echo ;
- else
- CSVLINE="$(basename $INFILE)\t$S\t$R\t$A\t$C\t$G\t$T\t$N\t$fA%\t$fC%\t$fG%\t$fT%\t$fN%\t$fAT%\t$fGC%\t$MIN\t$Q25\t$Q50\t$Q75\t$MAX\t$AVG\t$AUN\t$N50\t$N75\t$N90\t$L50\t$L75\t$L90";
- [ $GENOME_SIZE -ne 0 ]&&CSVLINE="$CSVLINE\t$ER";
- echo -e "$CSVLINE" ;
+ R=$(tr -d [:cntrl:] < $SEQS | wc -c); S=$(wc -l < $SEQS); AVG=$(bc -l<<<"scale=2;$R/$S" | sed 's/^\./0./');
+ A=$(tr -cd A < $SEQS | wc -c); fA=$(bc -l <<<"scale=2;100*$A/$R" | sed 's/^\./0./');
+ C=$(tr -cd C < $SEQS | wc -c); fC=$(bc -l <<<"scale=2;100*$C/$R" | sed 's/^\./0./');
+ G=$(tr -cd G < $SEQS | wc -c); fG=$(bc -l <<<"scale=2;100*$G/$R" | sed 's/^\./0./');
+ T=$(tr -cd T < $SEQS | wc -c); fT=$(bc -l <<<"scale=2;100*$T/$R" | sed 's/^\./0./');
+ N=$(tr -cd N < $SEQS | wc -c); fN=$(bc -l <<<"scale=2;100*$N/$R" | sed 's/^\./0./');
+ ACGT=$(( $A + $C + $G + $T ));
+ fGC=$(bc -l <<<"scale=2;100*($C+$G)/$ACGT" | sed 's/^\./0./'); fAT=$(bc -l <<<"scale=2;100-$fGC" | sed 's/^\./0./');
+ ER=$R; [ $GENOME_SIZE != 0 ] && ER=$GENOME_SIZE;
+ STATS=$(awk '{print length}' $SEQS | sort -rn | awk -v g=$ER '{l[++n]=$0;aun+=$0*$0}
+ END{OFMT="%f";g50=g/2;g75=3*g/4;g90=9*g/10;i=s=n50=n75=n90=0;
+ while(++i<=n&&n90==0){s+=l[i];n50==0&&s>=g50&&n50=l[i]+(l50=i);n75==0&&s>=g75&&n75=l[i]+(l75=i);n90==0&&s>=g90&&n90=l[i]+(l90=i)}
+ n90==0&&n90=l[n]+(l90=n);n75==0&&n75=l[n]+(l75=n);n50==0&&n50=l[n]+(l50=n);
+ iq1=int(n/4+1);iq2=int(n/2+1);iq3=int(3*n/4+1);
+ print(n50-l50)"\t"(n75-l75)"\t"(n90-l90)"\t"l50"\t"l75"\t"l90"\t"l[1]"\t"l[iq1]"\t"l[iq2]"\t"l[iq3]"\t"l[n]"\t"int(0.5+aun/g)}');
+ N50=$(cut -f1 <<<"$STATS"); N75=$(cut -f2 <<<"$STATS"); N90=$(cut -f3 <<<"$STATS");
+ L50=$(cut -f4 <<<"$STATS"); L75=$(cut -f5 <<<"$STATS"); L90=$(cut -f6 <<<"$STATS");
+ Q75=$(cut -f8 <<<"$STATS"); Q50=$(cut -f9 <<<"$STATS"); Q25=$(cut -f10 <<<"$STATS");
+ MIN=$(cut -f11 <<<"$STATS"); MAX=$(cut -f7 <<<"$STATS"); AUN=$(cut -f12 <<<"$STATS");
+
+ if ! $TSVOUT
+ then
+ echo ;
+ echo "File $(basename $INFILE)" ;
+ echo ;
+ echo "Number of sequences $S" ;
+ echo ;
+ echo "Residue counts:" ;
+ echo " Number of A's $A $fA %" ;
+ echo " Number of C's $C $fC %" ;
+ echo " Number of G's $G $fG %" ;
+ echo " Number of T's $T $fT %" ;
+ echo " Number of N's $N $fN %" ;
+ echo " Total $R" ;
+ echo ;
+ echo " %AT $fAT %" ;
+ echo " %GC $fGC %" ;
+ echo ;
+ echo "Sequence lengths:" ;
+ echo " Minimum $MIN" ;
+ echo " Quartile 25% $Q25" ;
+ echo " Median $Q50" ;
+ echo " Quartile 75% $Q75" ;
+ echo " Maximum $MAX" ;
+ echo " Average $AVG" ;
+ echo ;
+ echo "Contiguity statistics:" ;
+ echo " auN $AUN" ;
+ echo " N50 $N50" ;
+ echo " N75 $N75" ;
+ echo " N90 $N90" ;
+ echo " L50 $L50" ;
+ echo " L75 $L75" ;
+ echo " L90 $L90" ;
+ if [ $GENOME_SIZE -ne 0 ]; then echo " Expected genome size $GENOME_SIZE"; fi
+ echo ;
+ else
+ CSVLINE="$(basename $INFILE)\t$S\t$R\t$A\t$C\t$G\t$T\t$N\t$fA%\t$fC%\t$fG%\t$fT%\t$fN%\t$fAT%\t$fGC%\t$MIN\t$Q25\t$Q50\t$Q75\t$MAX\t$AVG\t$AUN\t$N50\t$N75\t$N90\t$L50\t$L75\t$L90";
+ [ $GENOME_SIZE -ne 0 ]&&CSVLINE="$CSVLINE\t$ER";
+ echo -e "$CSVLINE" ;
+ fi
+
+ continue ;
fi
-done
-rm -f $SEQS ;
+
+ ## residue details
-exit
+ lseq="$(awk '(length()>max){s=$0;max=length()}END{print s}' $SEQS)"; # lseq = the longest contig
+ wslseq="$(tr -cd ACGT <<<"$lseq" | tr ACGT WSSW)"; # the longest contig with only AT/CG replaced by W/S
+ tr -d '\15\32' < $INFILE | awk '!/^>/{s=s$0;next}(s!=""){print toupper(s);s=""}{print}END{print toupper(s)}' | paste - - > $SEQS ; ## tsv file: FASTA header \t contig
+ FTMP=$(randomfile); ## $REP GC% observed from substrings of length $R of the longest contig
+ trap "echo -n interrupting ; rm -f $SEQS $FTMP &>/dev/null ; echo ; exit " SIGINT
+ while IFS=$'\t' read -r fh seq
+ do
+ R=${#seq};
+ if [ $R -lt $MIN_CONTIG_LGT ]; then continue; fi
+ NAME=$(tr -d '>' <<<"$fh");
+ A=$(tr -cd A <<<"$seq" | wc -c); fA=$(bc -l <<<"scale=2;100*$A/$R" | sed 's/^\./0./');
+ C=$(tr -cd C <<<"$seq" | wc -c); fC=$(bc -l <<<"scale=2;100*$C/$R" | sed 's/^\./0./');
+ G=$(tr -cd G <<<"$seq" | wc -c); fG=$(bc -l <<<"scale=2;100*$G/$R" | sed 's/^\./0./');
+ T=$(tr -cd T <<<"$seq" | wc -c); fT=$(bc -l <<<"scale=2;100*$T/$R" | sed 's/^\./0./');
+ N=$(tr -cd N <<<"$seq" | wc -c); fN=$(bc -l <<<"scale=2;100*$N/$R" | sed 's/^\./0./');
+ ACGT=$(( $A + $C + $G + $T ));
+ fGC=$(bc -l <<<"scale=2;100*($C+$G)/$ACGT" | sed 's/^\./0./'); fAT=$(bc -l <<<"scale=2;100-$fGC" | sed 's/^\./0./');
+ REP=111; [ $R -gt 1000000 ] && REP=99; [ $R -gt 10000000 ] && REP=77;
+ [ "$seq" != "$lseq" ] && awk -v l=$R -v r=$REP '{srand(l-r);x=length()-l;while(--r>=0){s=substr($0,1+int(x*rand()),l);printf("%.6f\n",gsub("S","S",s)/length(s))}}' <<<"$wslseq" > $FTMP ;
+ gc=$(awk -v gc=$(( $C + $G )) -v acgt=$ACGT 'BEGIN{printf("%.6f\n",gc/acgt)}');
+ #echo "$gc $(tr '\n' ' ' <$FTMP)" ;
+ [ -e $FTMP ] && pv=$(awk -v x=$gc '{++n;(x<=$0)&&++p}END{printf("%.3f",p/n)}' $FTMP) || pv=0.500;
+ pv=$(awk '{p=(($0<0.5)?0.5-$0:$0-0.5);printf("%.3f",1-2*p)}' <<<"$pv");
+ [ ! -e $FTMP ] && pv=$pv"0";
+ rm -f $FTMP ;
+
+ if ! $TSVOUT
+ then
+ echo ;
+ echo "File $(basename $INFILE)" ;
+ echo ;
+ echo "Sequence $NAME" ;
+ echo ;
+ echo "Residue counts:" ;
+ echo " Number of A's $A $fA %" ;
+ echo " Number of C's $C $fC %" ;
+ echo " Number of G's $G $fG %" ;
+ echo " Number of T's $T $fT %" ;
+ echo " Number of N's $N $fN %" ;
+ echo " Total $R" ;
+ echo ;
+ echo " %AT $fAT %" ;
+ echo " %GC $fGC %" ;
+ echo ;
+ echo "Composition test p-value: $pv" ;
+ echo ;
+ else
+ CSVLINE="$(basename $INFILE)\t$NAME\t$R\t$A\t$C\t$G\t$T\t$N\t$fA\t$fC\t$fG\t$fT\t$fN\t$fAT\t$fGC\t$pv";
+ echo -e "$CSVLINE" ;
+ fi
+ done < $SEQS
+
+done
+rm -f $SEQS $FTMP ;
+exit ;
+
--
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