Gist 776981b42d618f2717fb986bbf501186

100%

Gist 776981b42d618f2717fb986bbf501186

✓ Published0🌍 Public

Last edited Feb 8, 2019

Created on Feb 8, 2019

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.

AI-generated description

Similar vizzes

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

87% match

Loading thumbnail…

Gist fb39aee08b636aec6b8a68d4011241cf

This visualization counts the number of contigs in a genome assembly file. It parses the FASTA-formatted file `gapCloserMinia.break.broken_assembly.fasta` using a Perl script, incrementing a counter each time a line starts with the `>` header character. The final count is printed as a plain integer to the terminal. The script relies solely on Perl's built-in file-handling and regular-expression capabilities, with no external visualization libraries, and does not generate any graphical output.

NNpfn

82% match

Loading thumbnail…

Gist f919aa6a77ff3feb4d8a6d77af5dee85

This example computes the number and length distribution of contiguous sequences from a FASTA file, then writes the results to a tab-delimited text file. It uses Perl’s `Math::Complex` module for mathematical operations, though only basic arithmetic appears. The script reads `gapCloserMinia.break.broken_assembly.fasta`, tracks sequence lengths via regex matching for `[ACTGN]+` lines, and outputs a numbered list of contig sizes, along with the mean and standard deviation. The visualization shows a histogram or table of contig lengths, derived directly from the computed file `tailles_contigues.txt`. There is no graphical rendering; the output is purely textual.

NNpfn

79% 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

77% 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

76% match

Loading thumbnail…

Gist babdf0de5f2b986506f621199e6a642d

This Perl script calculates the total length of a genome assembly by reading a FASTA file named `gapCloserMinia.break.broken_assembly.fasta`. It iterates line by line, summing the number of nucleotide characters (A, C, T, G) found on each line, ignoring headers and other non-sequence content. The script uses a simple regex match to detect sequence lines and accumulates the total count, printing the final genome size in base pairs to standard output. The computation is performed entirely with Perl's built-in file handling and string operators, requiring no external libraries or modules.

NNpfn

74% 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 4127915bd94a1fc0518bb0cceea3b612

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.

NNpfn

68% match