https://chk.ipmb.sinica.edu.tw/wiki/ 2026-04-06T06:20:11+00:00 https://chk.ipmb.sinica.edu.tw/wiki/ https://chk.ipmb.sinica.edu.tw/wiki/lib/exe/fetch.php/wiki/logo.png text/html 2012-06-14T16:29:31+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/cmd_blast_.1.pl?rev=1339691371&do=diff #!/usr/bin/perl -w my $script_name = 'cmd_blast+.1.pl'; # Chih-Horng Kuo # generate commands for running NCBI blast+ # v1 2010/07/13 use strict; use warnings; use Getopt::Long; use File::Basename; my $exe; my $in_dir; my $out_dir; my $sh_dir; my $in_file_ext; my $out_file_ext; my $sh_prefix; my $opt; my $n_job; my $debug; GetOptions( "exe=s" => \$exe, "in_dir=s" => \$in_dir, "out_dir=s" => \$out_dir, "sh_dir=s" => \$sh_dir, "in_file_ext=s" =>… text/html 2012-06-14T16:36:50+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/combine_files.pl?rev=1339691810&do=diff # combine_files.pl # The opposite of write_lines_to_files; # obtain an input directory and an output file # from the command line, read the files in the # input directory and write their content to # one single output file. # Note that we want to exclude hidden files # in the input directory. my $in_dir = shift; my $out_file = shift; open OUT, ">$out_file"; opendir( DIR, $in_dir ) or die "can't open $in_dir: $!\n"; foreach $in_file ( sort readdir(DIR) ) { next if ( $in_file =~ /^\./ )… text/html 2012-06-14T16:32:19+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/correct_fasta_orientation.1.pl?rev=1339691539&do=diff #!/usr/bin/perl -w my $script_name = 'correct_fasta_orientation.1.pl'; # Chih-Horng Kuo <chkuo@lifedev.org> # correct sequence orientation in a .fasta file # v1 2010/12/31 use strict; use warnings; use Getopt::Long; use File::Basename; my $in_file; my $in_fasta; my $out_file; my $verbose; my $debug; GetOptions( "in_file=s" => \$in_file, "in_fasta=s" => \$in_fasta, "out_file=s" => \$out_file, "verbose=i" => \$verbose, "debug=i" => \$debug, ); my $out_dir = dirname(… text/html 2012-06-14T16:38:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/count_ecori_site.pl?rev=1339691892&do=diff # count_EcoRI_site.pl # Read a fasta file and count the number of # EcoRI restriction sites in each sequence. my $in_file = shift; my $seq_hash; # key = seq_name, value = seq; { # redefine the record separator local $/ = ">"; open IN, "<$in_file"; my $in_line = <IN>; # toss the first record while ( $in_line = <IN> ) { chomp $in_line; # remove the ">" character in the end my ( $seq_name, $seq ) = split( /\n/, $in_line, 2 ); $seq =~ tr/ \t\n\r//d; # Remove whitespace $seq_hash{… text/html 2012-06-14T16:36:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/count_first_name.pl?rev=1339691777&do=diff # count_first_name.pl # Read an input file that contains several names # (assuming one name in each line, the first name # and the last name are separate by a space). # Count how the number of times each first name appeared # in the input. Print the result to STDOUT, # sort the names alphabetically. my $in_file = shift; my %count_hash; # key = first_name, value = count open IN, "<$in_file"; while ( my $line = <IN> ) { chomp $line; my ( $first_name, $last_name ) = split /\s/, $line; $c… text/html 2012-06-14T16:37:48+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/display_codon_1.pl?rev=1339691868&do=diff # display_codon_1.pl # Read a fasta file that contain protein-coding sequences. # Re-format the sequences to show codons (10 codons per line) # in the output file. # this version uses substr function to get the codons my $in_file = shift; my $out_file = shift; my $seq_hash; # key = seq_name, value = seq; { # redefine the record separator local $/ = ">"; open IN, "<$in_file"; my $in_line = <IN>; # toss the first record while ( $in_line = <IN> ) { chomp $in_line; # remove the ">" charact… text/html 2012-06-14T16:38:24+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/display_codon_2.pl?rev=1339691904&do=diff # display_codon_2.pl # Read a fasta file that contain protein-coding sequences. # Re-format the sequences to show codons (10 codons per line) # in the output file. # this version uses regular expression to obtain the codons my $in_file = shift; my $out_file = shift; my $seq_hash; # key = seq_name, value = seq; { # redefine the record separator local $/ = ">"; open IN, "<$in_file"; my $in_line = <IN>; # toss the first record while ( $in_line = <IN> ) { chomp $in_line; # remove the ">" c… text/html 2012-06-14T16:29:52+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/execute.3.pl?rev=1339691392&do=diff #!/usr/bin/perl -w my $script_name = 'execute.3.pl'; # Chih-Horng Kuo <chkuo@lifedev.org> # execute all .sh in the in_dir # v3 2010/02/04 # style change # v2 2009/06/18 # v1 2006/05/03 use strict; use warnings; use Getopt::Long; my $in_dir; my $exe_dir; my $in_file_ext; my $batch_file_ext; my $log_file_ext; my $prefix; # prefix of batch files my $n_job; # split into n batch files my $debug; GetOptions( "in_dir=s" => \$in_dir, "exe_dir=s" => \$exe_dir, "i… text/html 2017-04-12T06:45:27+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/find_empty_file.2.pl?rev=1491979527&do=diff #!/usr/bin/perl -w my $script_name = 'find_empty_file.2.pl'; # Chih-Horng Kuo <chkuo@lifedev.org> # find empty files in the "--in_dir" # use the "--regex" option to set search regex (e.g., --regex="*.txt") # set "--opt_rm=1" to remove those files # v2 2010/07/12 # style change # v1 2007/05/25 use strict; use warnings; use Getopt::Long; my $in_dir; my $regex; my $opt_rm; my $verbose; my $debug; GetOptions( "in_dir=s" => \$in_dir, "regex=s" => \$regex, "opt_rm=i" => \$opt_r… text/html 2012-06-14T16:32:04+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/find_homopolymer.3.pl?rev=1339691524&do=diff #!/usr/bin/perl -w my $script_name = 'find_homopolymer.3.pl'; # Chih-Horng Kuo <chkuo@lifedev.org> # read fasta file, find homopolymeric regions in the seqs # v3 2010/07/13 # bug fix: process the last base # change output format # v2 2009/09/29 # report the position of homopolyers in GFF3 format # v1 2009/09/22 use strict; use warnings; use Getopt::Long; use File::Basename; my $in_file; my $out_file; my $min; my $verbose; my $debug; GetOptions( "in_file=s" => \$in_file, … text/html 2012-06-14T16:31:27+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/parse_blast_hsp.4.pl?rev=1339691487&do=diff #!/usr/bin/perl my $script_name = 'parse_blast_hsp.4.pl'; # parse blast results # output = parsed format for sequence similarity, 1 hsp per line # v4 2010/09/20 # bug fix: hsp length (should be 'total', not 'query') # output format change # v3 2010/08/05 # add strand info # v2 2010/07/15 # style change # change output format # v1 2007/04/16 use strict; use warnings; use Getopt::Long; use Bio::SearchIO; my $in_file; my $out_file; my $format; my $print_seq; my $debug; GetOptions( … text/html 2012-06-14T16:30:09+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/parse_blast_sim.6.pl?rev=1339691409&do=diff #!/usr/bin/perl my $script_name = 'parse_blast_sim.6.pl'; # Chih-Horng Kuo <chkuo@lifedev.org> # parse blast results # input = blast # output = parsed format for sequence similarity, 1 hit per line # v6 2010/11/05 # add format opt, use xml as the default # the query_id is now obtained from query_description, not query_name # v5 2010/07/15 # style change # v4 2008/09/10 # change output format # v3 2007/02/26 # bug fix: correct calculation of frac_HSP # v2 2007/02/09 # set max(frac_H… text/html 2012-06-14T16:35:44+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/parse_first_name.pl?rev=1339691744&do=diff # parse_first_name.pl # Read from an input file # (containing a list of full names) # and write the first names to an output file. # Assume the two filenames are provided in the command line. my $in_file = shift; my $out_file = shift; open IN, "<$in_file"; open OUT, ">$out_file"; while ( my $line = <IN> ) { chomp $line; my ( $first_name, $last_name ) = split /\s/, $line; print OUT "$first_name\n"; } close OUT; close IN; text/html 2012-06-13T04:21:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/read_and_write.pl?rev=1339561270&do=diff # read_and_write.pl # read from an input file # and write the content to an output file. # Assume the two filenames are provided in the command line. my $in_file = shift; my $out_file = shift; open IN, "<$in_file"; open OUT, ">$out_file"; while ( my $line = <IN> ) { print OUT "$line"; } close OUT; close IN; text/html 2017-04-12T09:27:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/rename_file_by_regex.3.pl?rev=1491989254&do=diff #!/usr/bin/perl -w my $script_name = 'rename_file_by_regex.3.pl'; # Chih-Horng Kuo <chkuo@lifedev.org> # rename files by regex # v3 2013/09/14 # add prefix, suffix option # v2 2010/12/31 # add in_file_ext, out_file_ext option # v1 2009/06/23 use strict; use warnings; use Getopt::Long; my $in_dir; my $out_dir; my $in_file_ext; my $out_file_ext; my $regex; my $prefix; my $suffix; my $mode; my $verbose; my $debug; GetOptions( "in_dir=s" => \$in_dir, "out_dir=s" => \$out… text/html 2012-06-14T16:32:42+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/trim_lucy.2.pl?rev=1339691562&do=diff #!/usr/bin/perl -w my $script_name = 'trim_lucy.2.pl'; # Chih-Horng Kuo <chkuo@lifedev.org> # trim lucy output # v2 2011/01/12 # add min_start opt # v1 2010/12/31 use strict; use warnings; use Getopt::Long; my $in_fasta_dir; my $in_qual_dir; my $out_fasta_dir; my $out_qual_dir; my $in_fasta_file_ext; my $out_fasta_file_ext; my $in_qual_file_ext; my $out_qual_file_ext; my $min_start; my $verbose; my $debug; GetOptions( "in_fasta_dir=s" => \$in_fasta_dir, "in_qual_dir=s" … text/html 2012-06-14T16:34:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/trim_seq_by_regex.1.pl?rev=1339691650&do=diff Usage: perl ~/plscript/trim_seq_by_regex.1.pl \ --in_file=INPUT_FILE \ --out_dir=OUTPUT_DIR \ --regex="AAACT[CT]AAA[GT]GAATTGACGG(\w+)$" \ --verbose=1 #!/usr/bin/perl -w my $script_name = 'trim_seq_by_regex.1.pl'; # Chih-Horng Kuo <chkuo@lifedev.org> # trim seqs in a fasta file by provided regex # v1 2011/01/13 use strict; use warnings; use Getopt::Long; use File::Basename; my $in_file; my $out_dir; my $regex; my $verbose; my $debug; GetOptions( "in_file=s" => \$in_file… text/html 2012-06-14T16:37:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/unwrap_fasta.pl?rev=1339691825&do=diff # unwrap_fasta.pl # Read a fasta file, unwrap the sequences # (i.e., remove all extra line breaks), # and save the result to an output file. my $in_file = shift; my $out_file = shift; my %seq_hash; # key = seq_name, value = seq; { # redefine the record separator local $/ = ">"; open IN, "<$in_file"; my $in_line = <IN>; # toss the first record while ( $in_line = <IN> ) { chomp $in_line; # remove the ">" character in the end my ( $seq_name, $seq ) = split( /\n/, $in_line, 2 ); $seq … text/html 2012-06-14T16:31:47+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/unwrap_seq_fasta.1.pl?rev=1339691507&do=diff #!/usr/bin/perl -w my $script_name = 'unwrap_seq_fasta.1.pl'; # Chih-Horng Kuo <chkuo@lifedev.org> # remove extra line-breaks (in the sequences) in fasta files # v1 2010/03/04 use strict; use warnings; use Getopt::Long; use File::Basename; my $in_dir; my $in_file_ext; my $out_dir; my $out_file_ext; my $verbose; my $debug; GetOptions( "in_dir=s" => \$in_dir, "in_file_ext=s" => \$in_file_ext, "out_dir=s" => \$out_dir, "out_file_ext=s" => \$out_… text/html 2012-06-14T16:36:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://chk.ipmb.sinica.edu.tw/wiki/doku.php/tutorials/perl/write_lines_to_files.pl?rev=1339691794&do=diff # write_lines_to_files.pl # Obtain an input file and # an output directory from the command line. # Produce one output file for each line in # the input file, use the line number # (i.e., 1, 2, 3, etc) as the filenames. my $in_file = shift; my $out_dir = shift; system "mkdir -p $out_dir" unless -e $out_dir; my $count_line = 0; open IN, "<$in_file"; while ( my $line = <IN> ) { $count_line++; my $out_file = $out_dir . $count_line; open OUT, ">$out_file"; print OUT "$line"; close OUT; }…