質問編集履歴
3
systemが指定している最初のファイルのコードを追加
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@@ -20,19 +20,192 @@
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use warnings;
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system "perl ./Scripts/1_Preprocessing.pl";
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23
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-
system "perl ./Scripts/1_4_Rarefaction.pl";
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24
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-
system "perl ./Scripts/2_1_Find_unique.pl";
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25
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-
system "perl ./Scripts/2_2_Denoise.pl";
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26
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-
system "perl ./Scripts/2_3_Separate_chimera.pl";
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-
system "perl ./Scripts/3_1_Usearch_global.pl";
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28
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-
system "perl ./Scripts/4_1_Annotation.pl";
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-
system "perl ./Scripts/5_1_Fasta_for_Phylogenetic_Analysis.pl";
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30
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-
system "perl ./Scripts/5_2_Summary_table.pl";
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31
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-
system "perl ./Scripts/5_3_Fasta_classified_by_family.pl";
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32
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-
system "perl ./Scripts/6_1_Portal.pl";
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33
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-
system "perl ./Scripts/6_2_Phylogenetic_trees.pl";
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-
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以下略
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24
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以下1_Preprocessing.plのコード
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#!/usr/bin/perl
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use strict;
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use warnings;
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29
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+
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30
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#2018/12/04 1_2 Strip_primers change to use the Primer_Cleaner.pl
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31
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#2018/07/01 1_2_Strip_primers.pl were changed to permit no primer seq
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32
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#2018/01/29 change Blast to Usearch_global
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33
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#2018/01/20 output a log file at 1_1 step
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34
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#2018/01/05 add compress option
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#This script execute below scripts in each sample
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#1_1 Merge_paird_reads.pl
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#1_2_Strip_primers.pl
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#1_3_Quality_filter.pl
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#Setting
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my ($db, $primer, $diff, $separate, $depth, $size, $identity, $identity2, $dictionary, $family, $temporary, $compress, $trim);
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open (SET, "<", "Setting.txt") or die("error:$!");
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45
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while(<SET>){
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46
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if($_ =~ /^DB\s*=\s*(\S+)/){$db = $1;}
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47
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elsif($_ =~ /^Primers\s*=\s*(\S+)/){my $temp = $1;if($temp =~ /^no$/i){$primer = "No";}else{$primer = $temp;}}
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48
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elsif($_ =~ /^MaxDiff\s*=\s*(\S+)/){$diff = $1;}
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49
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elsif($_ =~ /^Divide\s*=\s*(\S+)/){$separate = $1;}
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elsif($_ =~ /^Depth\s*=\s*(\S+)/){$depth = $1;}
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elsif($_ =~ /^Length\s*=\s*(\d+)/){$size = $1;}
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elsif($_ =~ /^UIdentity\s*=\s*(\S+)/){$identity = $1;}
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elsif($_ =~ /^LIdentity\s*=\s*(\S+)/){$identity2 = $1;}
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elsif($_ =~ /^Dictionary\s*=\s*(\S+)/){$dictionary = $1;}
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elsif($_ =~ /^Family\s*=\s*(\S+)/){$family = $1;}
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elsif($_ =~ /^Temporary\s*=\s*(\S+)/){$temporary = $1;}
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elsif($_ =~ /^Compress\s*=\s*(\S+)/){$compress = $1;}
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}
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close(SET);
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if($diff =~ /^length$/i){$trim = 1;}
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unless($diff =~ /\d+/){$diff = 2;}
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unless($separate){$separate = 0;}
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if($separate =~ /^yes$/i){$separate = 1;}
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else{$separate = 0;}
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unless($db){print "Error!! Check the DB name in Setting.txt.\n"; exit;}
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unless($primer){print "Error!! Check the Primer file name in Setting.txt.\n"; exit;}
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unless($depth){print "Error!! Check the number of Depth in Setting.txt.\n"; exit;}
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unless($size){print "Error!! Check the number of Length in Setting.txt.\n"; exit;}
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unless($identity){print "Error!! Check the upper cut line of Homology Search in Setting.txt.\n"; exit;}
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unless($identity2){print "Error!! Check the lower cut line of Homology Search in Setting.txt.\n"; exit;}
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unless($temporary){$temporary = "YES";}
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unless($compress){$compress = "YES";}
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unless(-f "./DataBase/$db"){print "No DataBase file or DataBase name didn't match in Setting.txt\n"; exit;}
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unless($primer =~ /^no$/i){
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unless(-f "./DataBase/$primer"){print "No Primers file or file name didn't match in Setting.txt\n"; exit;}
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}
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unless(-f "./Dictionary/$dictionary"){
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if($dictionary =~ /^no$/i){undef($dictionary);}
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else{print "The file of Dictionary for common name isn't or don't match the name in Setting.txt\n"; exit;}
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}
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unless(-f "./Dictionary/$family"){
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if($family =~ /^no$/i){undef($family);}
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else{print "The file of Dictionary for Family name isn't or don't match the name in Setting.txt\n"; exit;}
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}
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#Get primer sequences
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my $countp = 0;
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my (%forward, %reverse, $namep);
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my ($primerF, $primerR);
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unless($primer =~ /^no$/i){
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open (DATA2, "<", "./DataBase/$primer") or die("error:$!");
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while(<DATA2>){
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if($_ =~ /\#/){next;}
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chomp($_);
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if($_ =~ /Forward/){$countp = 1;next;}
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if($_ =~ /Reverse/){$countp = 2;next;}
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if($countp == 1){
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if($_ =~ /^>(.+)/){$namep = $1;}
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elsif($_ =~ /^[a-z]/i){$_ =~ tr/[a-z]/[A-Z]/; $forward{$namep} = $_;}
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}
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if($countp == 2){
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if($_ =~ /^>(.+)/){$namep = $1;}
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elsif($_ =~ /^[a-z]/i){
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my $rev = reverse($_);
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$rev =~ tr/ATGCURYMKDHBV/TACGAYRKMHDVB/;
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$reverse{$namep} = $rev;}
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}
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}
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close(DATA2);
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unless(%forward){print "Error!! No primer seqeunce in $primer\n"; exit;}
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unless(%reverse){print "Error!! No primer seqeunce in $primer\n"; exit;}
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foreach(keys %forward){
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unless($reverse{$_}){print "Error!! Paird primer need to be the same name!\nCheck $primer\n"; exit;}
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}
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foreach(keys %reverse){
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unless($forward{$_}){print "Error!! Paird primer need to be the same name!\nCheck $primer\n"; exit;}
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}
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my $primer_num = keys %forward;
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if($primer_num == 1){$separate = 0;}
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if($trim and $primer_num == 1){
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foreach(keys %forward){$primerF = length($forward{$_}); $primerR = length($reverse{$_});}
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}elsif($trim and $primer_num > 1){
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print "Error! \"MaxDiff = length\" in Setting.txt can use when primer pair is one pair\n"; exit;
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}
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if($trim){$separate = 0;}
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}
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#Database and Usearch check
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opendir (DIR, "./DataBase") or die ("error:$!");
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my @database = readdir DIR;
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my $dbcheck = 0;
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foreach(@database){
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if ($_ =~ /${db}.udb/){$dbcheck++;}
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}
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closedir DIR;
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opendir (DIR, "./Tools") or die ("error:$!");
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my @tool = readdir DIR;
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my $usearch;
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foreach (@tool) {
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if ($_ =~ /(usearch.+)/){$usearch = $1;}
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}
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closedir DIR;
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unless($usearch){print "Error!! Please put an usearch exectable file in Tools directory!\n"; exit;}
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unless($dbcheck){
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my $command = "./Tools/$usearch -makeudb_usearch \"./DataBase/$db\" -output \"./DataBase/${db}.udb\"";
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system $command;
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}
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152
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153
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#Decompressing files
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opendir (DIR, "./Run") or die ("error:$!");
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my @run = readdir DIR;
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157
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my $gzip = 0;
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158
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foreach (@run) {
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159
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if ($_ =~ /.gz$/){$gzip++;}
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}
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closedir DIR;
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163
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if($gzip){
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print "Decompressing gz file to fastq file...\n";
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foreach (@run) {
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if ($_ =~ /.gz$/){
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my $comand = "gzip -d \"./Run/$_\"";
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168
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system $comand;
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}
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170
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}
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}
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172
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173
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#Get data names
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174
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opendir (DIR, "./Run") or die ("error:$!");
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175
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my @read = readdir DIR;
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my $read_count = 0;
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177
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my %file;
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178
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foreach (@read) {
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179
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if ($_ =~ /(.+)_R1/){$file{$1}++; $read_count++;}
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180
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if ($_ =~ /(.+)_R2/){$file{$1}++; $read_count++;}
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}
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182
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closedir DIR;
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183
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unless(%file){print "None of fastq files in Run file!!\n"; exit;}
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184
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foreach(keys %file){
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185
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if($file{$_} < 2){print "Error!! Check the Run directory!The analysis needs both R1 and R2 fastq files.\nR1 or R2 fastq files of $_ is not.\n"; exit;}
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}
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unless(-d "./Results"){mkdir "./Results";}
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188
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189
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190
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print "============================================================\n";
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191
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print " 1_Preprocessing \n";
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192
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print "============================================================\n";
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193
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#assemble pair seqs
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194
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mkdir "./Results/1_1_Merge_paird_reads";
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195
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unless($primer =~ /^no$/i){mkdir "./Results/1_2_Strip_primers";}
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196
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mkdir "./Results/1_3_Quality_filter";
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197
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open (LOG, ">", "./Results/log.txt") or die("error:$!");
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198
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my (%log, %raw);
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199
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200
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my @youbi = ('Sun', 'Mon', 'Tue', 'Wed', 'Thu', 'Fri', 'Sat');
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201
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my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
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202
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$year += 1900;
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203
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$mon += 1;
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204
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if($min < 10){$min = "0$min";}
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205
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print LOG "Start: $year/$mon/$mday ($youbi[$wday]) $hour:$min\n";
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206
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207
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以下略
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208
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36
209
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### 試したこと
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37
210
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38
211
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Active perlのインストールしなおし、環境変数の確認
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2
画像追加
title
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File without changes
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body
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@@ -1,4 +1,4 @@
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1
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-
](848a977b10b17ad124d14d2a8e66bf0e.png)### 前提・実現したいこと
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1
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+
](848a977b10b17ad124d14d2a8e66bf0e.png)### 前提・実現したいこと
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2
2
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3
3
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windows powershellでperlのプログラムを動かしたいが、一行目で以下のエラーが出て上手く動作しません
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4
4
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1
画像、コード追加
title
CHANGED
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File without changes
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body
CHANGED
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@@ -1,4 +1,4 @@
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1
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-
### 前提・実現したいこと
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1
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](848a977b10b17ad124d14d2a8e66bf0e.png)### 前提・実現したいこと
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2
2
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3
3
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windows powershellでperlのプログラムを動かしたいが、一行目で以下のエラーが出て上手く動作しません
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4
4
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@@ -13,6 +13,24 @@
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13
13
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14
14
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```ここに言語名を入力
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15
15
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perl PMiFish.pl
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16
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+
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17
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+
以下PMiFish.plコード
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18
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#!/usr/bin/perl
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19
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use strict;
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20
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use warnings;
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21
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+
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22
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system "perl ./Scripts/1_Preprocessing.pl";
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23
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+
system "perl ./Scripts/1_4_Rarefaction.pl";
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24
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+
system "perl ./Scripts/2_1_Find_unique.pl";
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25
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+
system "perl ./Scripts/2_2_Denoise.pl";
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26
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+
system "perl ./Scripts/2_3_Separate_chimera.pl";
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27
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system "perl ./Scripts/3_1_Usearch_global.pl";
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28
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+
system "perl ./Scripts/4_1_Annotation.pl";
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29
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+
system "perl ./Scripts/5_1_Fasta_for_Phylogenetic_Analysis.pl";
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30
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+
system "perl ./Scripts/5_2_Summary_table.pl";
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31
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+
system "perl ./Scripts/5_3_Fasta_classified_by_family.pl";
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32
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+
system "perl ./Scripts/6_1_Portal.pl";
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33
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+
system "perl ./Scripts/6_2_Phylogenetic_trees.pl";
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16
34
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```
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17
35
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18
36
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### 試したこと
|