- Perl Program To Calculate Gc Content Analysis
- Perl Program To Calculate Gc Content Level
- Perl Program To Calculate Gc Content Analysis
- Perl Program To Calculate Gc Content Formula
- Perl Program To Calculate Gc Content Inventory
- Perl Script To Calculate Gc Content
May 06, 2021 The guanine-cytosine content, or GC-content, of a DNA sequence indicates the percentage of nucleotide base pairs where guanine is bonded to cytosine. DNA with a higher GC-content will be harder to break apart. GC content is usually calculated as a percentage value and sometimes called G+C ratio or GC-ratio. GC-content percentage is calculated as Count(G + C)/Count(A + T + G + C). 100%. The GC content calculation algorithm has been integrated into our Codon Optimization Software, which serves our protein expression services. Welcome back, Perl (GC content) I coded in Perl for 1-2 weeks in my life 7 months ago, then shifted to Python –and PHP for sometime– for the previous 7 months. Now, I am back to Perl –somehow! Started by this GC content calculator. /usr/bin/perl -w.
CpG_calculator.pl
A script to calculate observed vs expected CpG dinucleotides
CpG_calculator.pl --fasta <directory|filename> [--options...]
CpG_calculator.pl --db <text> [--options...]
The command line flags and descriptions:
Perl Program To Calculate Gc Content Analysis
Provide the name of a Bio::DB::SeqFeature::Store database from which to collect the genomic sequence. Alternatively, provide the name of an uncompressed Fasta file (multi-fasta is ok) or directory containing multiple fasta files representing the genomic sequence. The directory must be writeable for a small index file to be written. For more information about using databases, see https://code.google.com/p/biotoolbox/wiki/WorkingWithDatabases. The database may be provided in the metadata of an input file.
Optionally specify an input file containing either a list of database features or genomic coordinates for which to collect data. The file should be a tab-delimited text file, one row per feature, with columns representing feature identifiers, attributes, coordinates, and/or data values. The first row should be column headers. Text files generated by other BioToolBox scripts are acceptable. Files may be gzipped compressed.
Optionally provide the window size in bp with which to scan the genome. Option is ignored if an input file is provided. Default is 1000 bp.
Specify the output filename. By default it uses the input file base name if provided. Required if no input file is provided.
Specify whether (or not) the output file should be compressed with gzip.
Specify the number of CPU cores to execute in parallel. This requires the installation of Parallel::ForkManager. With support enabled, the default is 2. Disable multi-threaded execution by setting to 1.
Print the version number.
Display this POD documentation.
This program will calculate percent GC composition, number of CpG dinucleotide pairs, number of expected CpG dinucleotide pairs based on GC content, and the ratio of observed / expected CpG pairs. Calculations are performed on either windows across the entire genome (default behavior using 1000 bp windows) or user-provided regions in an input file (BED, GFF, or custom text file are supported).
Genomic sequence may be provided in two ways. First, a Fasta file or directory of Fasta files may be provided. A small index file will be written to assist in random access using the Bio::DB::Fasta module. Alternatively, a Bio::DB::SeqFeature::Store database with sequence may be provided. Depending on the database driver and implementation, the fasta option is usually faster.
The four additional columns of information are appended to the input or generated file.
Perl Program To Calculate Gc Content Level
This package is free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0.
have been trying for a few weeks not to get this program running. I am newer to programming and it has definitely been a challenge. I think my problem arises with my if statement. I can get it to append the name to the new file, but it simply appends the whole sequence to the file rather than counting it. I am working with a fasta file that contains multiple sequences, the name starting with '>' and the sequence on one line below it. Here is my code. Please help, and thank you so much in advance!!
Perl Program To Calculate Gc Content Analysis
Edit:
Perl Program To Calculate Gc Content Formula
The input file has multiple sequence within it, all with respective titles. they look something like this:The output i would like to contain the name and the percent of Gs an Cs (totaled together)
My idea for the program was to have the user input the file, then the loop either append the line that contains the title to the file GCcontent.txt or to run through the counter i have set up and append it to the file GCcontent.txt
Perl Program To Calculate Gc Content Inventory
Perl Script To Calculate Gc Content
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