GitHub - enormandeau/Scripts: Collection of various scripts

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 315 Commits
00_deprecated		00_deprecated
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
argparse_example.py		argparse_example.py
avg		avg
beagle_extract_wanted_snps.py		beagle_extract_wanted_snps.py
beagle_remove_unwanted.py		beagle_remove_unwanted.py
beagle_sliding_window.py		beagle_sliding_window.py
beagle_split_by_n_samples.py		beagle_split_by_n_samples.py
body.sh		body.sh
complexity_by_sliding_windows.py		complexity_by_sliding_windows.py
compress_directories		compress_directories
datify.sh		datify.sh
estimate_numreads_per_sample.sh		estimate_numreads_per_sample.sh
fasta_GC_disctibution_graph.py		fasta_GC_disctibution_graph.py
fasta_complexity_by_sliding_windows.py		fasta_complexity_by_sliding_windows.py
fasta_count_kmers.py		fasta_count_kmers.py
fasta_deinterleave.sh		fasta_deinterleave.sh
fasta_digest.py		fasta_digest.py
fasta_extract.py		fasta_extract.py
fasta_extract_first_only.py		fasta_extract_first_only.py
fasta_extract_flanking_regions.py		fasta_extract_flanking_regions.py
fasta_extract_group.py		fasta_extract_group.py
fasta_extract_max_length.py		fasta_extract_max_length.py
fasta_extract_min_coverage.py		fasta_extract_min_coverage.py
fasta_extract_min_length.py		fasta_extract_min_length.py
fasta_extract_n_sequences.py		fasta_extract_n_sequences.py
fasta_extract_name.py		fasta_extract_name.py
fasta_extract_random_sequences.py		fasta_extract_random_sequences.py
fasta_extract_scaffold_regions.py		fasta_extract_scaffold_regions.py
fasta_extract_wo_indel.py		fasta_extract_wo_indel.py
fasta_keep_first.py		fasta_keep_first.py
fasta_lengths.py		fasta_lengths.py
fasta_longer_nb.py		fasta_longer_nb.py
fasta_max_len.py		fasta_max_len.py
fasta_mean_len.py		fasta_mean_len.py
fasta_min_len.py		fasta_min_len.py
fasta_n50.py		fasta_n50.py
fasta_nstats.py		fasta_nstats.py
fasta_number_sequences.py		fasta_number_sequences.py
fasta_random.py		fasta_random.py
fasta_random_length.py		fasta_random_length.py
fasta_remove.py		fasta_remove.py
fasta_remove_duplicates.py		fasta_remove_duplicates.py
fasta_remove_regions.py		fasta_remove_regions.py
fasta_remove_sequences_with_N.py		fasta_remove_sequences_with_N.py
fasta_remove_start.py		fasta_remove_start.py
fasta_rename_matepair.py		fasta_rename_matepair.py
fasta_rename_sequences.py		fasta_rename_sequences.py
fasta_replace_short_reads.py		fasta_replace_short_reads.py
fasta_reservoir_sampling.py		fasta_reservoir_sampling.py
fasta_reverse_comp.py		fasta_reverse_comp.py
fasta_separate_tags.py		fasta_separate_tags.py
fasta_sort_sequences_by_name.py		fasta_sort_sequences_by_name.py
fasta_split.py		fasta_split.py
fasta_split_long_sequences.py		fasta_split_long_sequences.py
fasta_split_n_nucleotides.py		fasta_split_n_nucleotides.py
fasta_split_scaffolds.py		fasta_split_scaffolds.py
fasta_split_sliding_window.py		fasta_split_sliding_window.py
fasta_to_fake_fastq.py		fasta_to_fake_fastq.py
fasta_to_simple_agp.py		fasta_to_simple_agp.py
fasta_total_length.py		fasta_total_length.py
fasta_total_length.sh		fasta_total_length.sh
fasta_unwrap.py		fasta_unwrap.py
fasta_wrap.py		fasta_wrap.py
fastqCombinePairedEnd.py		fastqCombinePairedEnd.py
fastq_deinterleave.sh		fastq_deinterleave.sh
fastq_extract.py		fastq_extract.py
fastq_min_length.py		fastq_min_length.py
fastq_min_max_length.py		fastq_min_max_length.py
fastq_remove.py		fastq_remove.py
fastq_reservoir_sampling.py		fastq_reservoir_sampling.py
fastq_split.py		fastq_split.py
fastq_split_to_4_files.py		fastq_split_to_4_files.py
fastq_to_fasta.py		fastq_to_fasta.py
fastq_to_trimmed_fasta.py		fastq_to_trimmed_fasta.py
fastq_trim.py		fastq_trim.py
fastqgz_subsampling.py		fastqgz_subsampling.py
fastqslim.py		fastqslim.py
gmailsend.py		gmailsend.py
line_extract.py		line_extract.py
line_remove.py		line_remove.py
markers_extract_to_file.py		markers_extract_to_file.py
markers_extract_to_screen.py		markers_extract_to_screen.py
merge_alternate_columns.py		merge_alternate_columns.py
number_add_zeros.py		number_add_zeros.py
number_pad_spaces.py		number_pad_spaces.py
parse_dupes.py		parse_dupes.py
plot		plot
plot2		plot2
plot2lines		plot2lines
plotlines		plotlines
progress_bar.py		progress_bar.py
reduce_photos.sh		reduce_photos.sh
reduce_png.sh		reduce_png.sh
rename_scaffolds.py		rename_scaffolds.py
rename_scaffolds_shortname.py		rename_scaffolds_shortname.py
resize_term.sh		resize_term.sh
script_autobackup_example.sh		script_autobackup_example.sh

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About these scripts

This is a collection of scripts written over the years to solve specific problems. Some of them are well tested, others not so well. As they have been written over a long period of time, the style and quality vary.

Use at your own risk

These programs are provided as is, without any implied garanty of usefulness.

Licensing

Read the LICENSE file for information about the license affecting these files

License

enormandeau/Scripts

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