Gist 4127915bd94a1fc0518bb0cceea3b612

100%

Gist 4127915bd94a1fc0518bb0cceea3b612

✓ Published0🌍 Public

Last edited Feb 8, 2019

Created on Feb 8, 2019

This example shows a Perl script that filters complete CEGs (Core Eukaryotic Genes) from a CEGMA output FASTA file, extracting only sequences corresponding to KOG identifiers not listed as missing in the completeness report. It reads three input files—the CEGMA FASTA, a completeness cutoff table, and the completeness report—then writes a new FASTA file. The script uses Perl’s built-in file handling and regular expression matching to parse KOG IDs, track a flag for sequence inclusion, and output the selected sequences.

AI-generated description

Similar vizzes

Loading thumbnail…

Gist 431bee0f995b471c4febe9e74accbdea

This example shows a list of KOG identifiers that were missed by the CEGMA completeness report, paired with their corresponding functional descriptions from a separate KOG ID file. The Perl script parses the CEGMA output to detect the section listing missing proteins, then extracts each KOG ID and cross-references it against the KOG ID data file to append the matching description to the output file. The script uses regular expressions to identify KOG IDs and relies on file handles to read and write the text-based data.

NNpfn

84% match

Loading thumbnail…

Gist ccffb77a3cba5716d7a983e6c009de95

This example shows a Perl script that extracts protein IDs and functional information from CEGMA output files by matching KOG identifiers. The code reads two input files, parses each line with regular expressions, and writes matching KOG entries with their descriptions to a new output file. The implementation relies on standard Perl file handling and pattern matching with the `/KOG\d{4}/` and `/^\[.+\]\s(KOG\d{4})\s(.*)$/` regex patterns, without using any external visualization libraries or APIs.

NNpfn

84% match

Loading thumbnail…

Gist e3718d6464d2ba18e5a08233edd0aeb1

This Perl script splits a multi-sequence FASTA file into individual FASTA files, one per sequence. It reads the input file line by line, opens a new output file whenever a header line starting with `>` is encountered, and writes the header and subsequent sequence lines to that file. The code uses the `open`, `close`, and `shift` built-in functions to manage up to 248 output files named `CEG0.fasta` through `CEG247.fasta`. The script demonstrates a simple file-parsing and output-splitting workflow for bioinformatics sequence data.

NNpfn

72% match

Loading thumbnail…

Gist c994b5a229194ab2c98a8580d48f54ef

This example shows a Perl script that corrects FASTA sequence headers by replacing pipe characters with hyphens, making the files compatible with the CEGMA genome analysis tool. The script reads an input FASTA file and writes the corrected output to a second file. It uses the standard Perl file I/O operations `open`, `close`, and the regex substitution operator to modify only the header lines that begin with `>[A-Z]{3}`. The script also checks for an existing output file to prevent accidental overwriting, and it prints a usage message if the correct number of arguments is not provided.

NNpfn

71% match

Loading thumbnail…

Gist 143778d0c50388a317ebc30c0ec5de86

This Perl-based command-line tool calculates GC content and nucleotide percentages from a FASTA file. It reads the input file line by line, skipping headers, and tallies counts of G, C, A, T, and N bases. The output prints GC%, individual base percentages, and the N count, using basic string operations and conditional logic rather than external visualization libraries. The script demonstrates a simple text-based data summary workflow for bioinformatics sequence analysis.

NNpfn

71% match

Loading thumbnail…

Gist 4d45fd0aa5761530e461fa7a84197fe3

This example filters a Perl script that parses a CSV-formatted matrix (`matrice_para.csv`) to extract gene names with no paralogs across 11 species. It writes matching identifiers to a text file (`genes_with_no_para.txt`). The Perl script uses a regular expression to match lines with eleven consecutive zero values, then outputs the first field. The process relies on standard Perl file-handling and pattern-matching operations rather than a visualization library.

NNpfn

69% match

Loading thumbnail…

Gist 4f72b1c54e9f05af3e88d9e0ca702760

This Perl script calculates the total number of nucleotides in a FASTA file. It reads the input file line by line, skipping lines that begin with the ">" character (sequence headers), and sums the length of every remaining line after removing newline characters. The script uses core Perl functionality, including the `-s` flag for optional switch parsing, the `shift` and `@ARGV` array for command-line arguments, and a standard file handle opened with `open`. It prints the final nucleotide count to standard output. The example demonstrates a simple command-line bioinformatics utility for sequence statistics.

NNpfn

68% match

Loading thumbnail…

Gist 776981b42d618f2717fb986bbf501186

This example counts the number of sequences in a FASTA file, displaying the total as a plain numeric output. It reads the file line by line and increments a counter whenever a line begins with the `>` character, which marks a new sequence header. The tool is a Perl script that relies on the standard Perl file-handling and regular-expression capabilities rather than any external visualization library. The output is a single integer representing the number of contigs, scaffolds, or genes, depending on the input file's content. The approach is purely computational, with no graphical rendering involved.

NNpfn

68% match