-
Notifications
You must be signed in to change notification settings - Fork 1
/
BacAssembly.pl
194 lines (177 loc) · 7 KB
/
BacAssembly.pl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
#! /usr/bin/perl -w
use strict;
use Getopt::Long;
use File::Spec;
use POSIX qw(strftime);
use FindBin qw($Bin);
use File::Path;
my $usage="Pipeline for hybrid assembly using short and long reads
Usage:
Options:
-i <input> input txt_file contain 4 cols (sample_ID Path2raw.Long_reads.fq.gz Path2raw.short_readas.1.fq.gz Path2raw.short_readas.2.fq.gz )
-c <config> configure file
-o <opath> output path [./result]
-h|?Help!
Example:Perl $0 -i data.info -c cfg.file
";
my ($input,$cfg,$outpath,$help);
GetOptions(
'-i=s' => \$input,
'-c=s' => \$cfg,
'-o=s' => \$outpath,
'h|?'=> \$help,
);
if ($help or !$input){die "$usage\n";}
#$outpath ||= "./result";
$outpath ||= "./";
mkdir ("$outpath") unless (-d $outpath);
$outpath=File::Spec->rel2abs($outpath);
my $shellall="$outpath/shellall";
mkdir ($shellall) unless (-d $shellall);
### read config file ###
print strftime(">>>Generate shell scripts started at:%Y-%m-%d,%H:%M:%S\n\n",localtime(time));
my %config= &readConf($cfg);
sub readConf{
my $confFile=shift @_;
my %hash;
open IN,$confFile or die "Can't open file $confFile:$!\n";
while (<IN>){
chomp;
next if(/^\s*$/ || /^\s*\#/);
$_ =~ s/^\s*//;
$_ =~ s/#(.)*//;
$_ =~ s/\s*$//;
if (/^(\w+)\s*=\s*(.*)$/xms){
next if ($2 =~ /^\s*$/);
my $key = $1;
my $value = $2;
$value =~ s/\s*$//;
$hash{$key} = $value;
}
}
return %hash;
}
### read input data list ###
my %data;
my $dataNum;
my %sample;
my @sample;
open LIST,"$input" or die $!;
#open NP,">$outpath/input.np" or die $!;
while (<LIST>){
chomp;
next if (/^#/);
my ($name,$lpath,$spath1,$spath2)=(split/\s+/,$_)[0,1,2,3];
$lpath=File::Spec->rel2abs($lpath);
$spath1=File::Spec->rel2abs($spath1);
$spath2=File::Spec->rel2abs($spath2);
$data{$name}="$lpath $spath1 $spath2";
# print NP "$name\t$lpath\t$spath1\t$spath2\n";
push @sample,$name;
$dataNum++;
}
close LIST;
my @dependent;
###01.porechop
if ($config{Lreads_adapter_method} eq "porechop"){
my $outdir="$outpath/result/01.porechop";
mkpath ($outdir) unless (-d $outdir);
open SH, ">$shellall/01.porechop.sh" or dir $!;
foreach my $name (@sample){
mkdir ("$outdir/$name") unless (-d "$outdir/$name");
my $lpath=(split /\s+/,$data{$name})[0];
# print SH "$config{'porechop'} $config{'porechop_Parameters'} -i $lpath -o $outdir/$name/$name.porechop.reads.fq >$outdir/$name/$name.porechop.log && \n";
print SH "$config{'porechop'} -i $lpath -o $outdir/$name/$name.porechop.reads.fq >$outdir/$name/$name.porechop.log\n";
}
close SH;
}
###02.NanoFilt+NanoStat
if ($config{Lreads_filt_method} eq "NanoFilt"){
my $outdir="$outpath/result/02.NanoFilt";
mkpath ($outdir) unless (-d $outdir);
open SH, ">$shellall/02.nanofilt.sh" or dir $!;
foreach my $name (@sample){
mkdir ("$outdir/$name") unless (-d "$outdir/$name");
print SH "$config{'nanofilt'} $config{'nanofilt_Parameters'} --logfile $outdir/$name/$name.nanofilt.log $outpath/01.porechop/$name/$name.porechop.reads.fq |gzip >$outdir/$name/$name.nanofilt.fq.gz && $config{'nanostat'} --fastq $outdir/$name/$name.nanofilt.fq.gz >$outdir/$name/$name.nanofilt.fq.gz.nanostat\n";
}
close SH;
}
###01_2.short.clean.reads:fastp+soapnuke
if ($config{Sreads_filt_method} eq "fastp+soapnuke"){
my $outdir="$outpath/result/01_2.short.clean.reads";
mkpath ($outdir) unless (-d $outdir);
open SH,">$shellall/01_2.short.clean.reads.sh" or dir $!;
foreach my $name(@sample){
mkdir ("$outdir/$name") unless (-d "$outdir/$name");
my ($path1,$path2)=(split /\s+/,$data{$name})[1,2];
print SH "$config{'fastp'} $config{'fastp_Parameters'} -i $path1 -o $outdir/$name/$name.fastp.clean.1.fa.gz -I $path2 -O $outdir/$name/$name.fastp.clean.2.fa.gz -j $outdir/$name/$name.fastp.json -h $outdir/$name/$name.fastp.html -R $name && $config{'soapnuke'} $config{'soapnuke_Parameters'} -1 $outdir/$name/$name.fastp.clean.1.fq.gz -2 $outdir/$name/$name.fastp.clean.2.fq.gz -C $name.fastp.nodup.clean.1.fq.gz -D $name.fastp.nodup.clean.2.fq.gz -o $outdir/$name\n";
}
close SH;
}
###03.flye
if ($config{Lreads_assembly_method} eq "flye"){
my $outdir="$outpath/result/03.flye";
mkpath ($outdir) unless (-d $outdir);
open SH,">$shellall/03.flye.sh" or dir $!;
foreach my $name(@sample){
mkdir ("$outdir/$name") unless (-d "$outdir/$name");
print SH "$config{'flye'} $config{'flye_Parameters'} $outpath/02.NanoFilt/$name/$name.nanofilt.fq.gz -o $outdir/$name\n";
}
close SH;
}
###04.racon
if ($config{'Lreads_1st_polish_method'} eq "racon"){
my $outdir="$outpath/result/04.racon";
mkpath ($outdir) unless (-d $outdir);
open SH,">$shellall/04.racon.sh" or dir $!;
foreach my $name(@sample){
mkdir ("$outdir/$name") unless (-d "$outdir/$name");
print SH "$config{'bwa'} index $outpath/03.flye/$name/assembly.fasta\n$config{'bwa'} mem $outpath/03.flye/$name/assembly.fasta $outpath/02.NanoFilt/$name/$name.nanofilt.fq.gz >$outdir/$name/$name.sam\n$config{'racon'} $config{'racon_Parameters'} $outpath/02.NanoFilt/$name/$name.nanofilt.fq.gz $outpath/03.flye/$name/assembly.fasta >$outdir/$name/$name.racon.fasta\n";
}
close SH;
}
###05.medaka
if ($config{'Lreads_2nd_polish_method'} eq "medaka"){
my $outdir="$outpath/result/05.medaka";
mkpath ($outdir) unless (-d $outdir);
open SH,">$shellall/05.medaka.sh" or dir $!;
foreach my $name (@sample){
mkdir ("$outdir/$name") unless (-d "$outdir/$name");
print SH "$config{'medaka'} $config{'medaka_Parameters'} -i $outpath/02.NanoFilt/$name/$name.nanofilt.fq.gz -d $outpath/04.racon/$name/$name.racon.fasta -o $outdir/$name\n";
}
close SH;
}
###06.pilon
if ($config{'Sreads_polish_method'} eq "pilon"){
my $outdir="$outpath/result/06.pilon";
mkpath ($outdir) unless (-d $outdir);
open SH,">$shellall/06.pilon.sh" or dir $!;
foreach my $name (@sample){
mkdir ("$outdir/$name") unless (-d "$outdir/$name");
print SH "java -Xmx32G -jar $config{'pilon'} $config{'pilon_Parameters'} --genome $outpath/05.medaka/$name/consensus.fasta --frags $outdir/$name/mapping.sorted.bam --outdir $outdir/$name --output $name\n";
}
close SH;
}
###07.circlator
if ($config{'Lreads_circlator_method'} eq "circlator"){
my $outdir="$outpath/result/07.circlator";
mkpath ($outdir) unless (-d $outdir);
open SH,">$shellall/07.circlator.sh" or dir $!;
foreach my $name (@sample){
mkdir ("$outdir/$name") unless (-d "$outdir/$name");
print SH "$config{'circlator'} $config{circlator_Parameters} $outpath/06.pilon/$name/$name.fasta $outpath/02.NanoFilt/$name/$name.nanofilt.fq.gz $outdir/$name\n";
}
close SH;
}
###03_2.unicycler
if ($config{'Sreads_first_assembly_method'} eq "unicycler"){
my $outdir="$outpath/result/03_2.unicycler";
mkpath ($outdir) unless (-d $outdir);
open SH,">$shellall/03_2.unicycler.sh" or dir $!;
foreach my $name (@sample){
mkdir ("$outdir/$name") unless (-d "$outdir/$name");
my ($lpath,$spath1,$spath2)=(split /\s+/,$data{$name})[0,1,2];
print SH "$config{'unicycler'} $config{unicycler_Parameters} -1 $spath1 -2 $spath2 -l $lpath -o $outdir/$name\n";
}
close SH;
}