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Merge pull request #32 from sanger-tol/cov
add vecscreen test set on ci, checkin coverage related scripts, updat…
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,66 @@ | ||
| #!/usr/bin/env python3 | ||
| """ | ||
| Script conversion of .sam file with mapped reads to sorted and indexed .bam file | ||
| """ | ||
| # MIT License | ||
| # | ||
| # Copyright (c) 2020-2021 Genome Research Ltd. | ||
| # | ||
| # Author: Eerik Aunin ([email protected]) | ||
| # | ||
| # This file is a part of the Genome Decomposition Analysis (GDA) pipeline. | ||
| # | ||
| # Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| # of this software and associated documentation files (the "Software"), to deal | ||
| # in the Software without restriction, including without limitation the rights | ||
| # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| # copies of the Software, and to permit persons to whom the Software is | ||
| # furnished to do so, subject to the following conditions: | ||
| # | ||
| # The above copyright notice and this permission notice shall be included in all | ||
| # copies or substantial portions of the Software. | ||
| # | ||
| # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE | ||
| # SOFTWARE. | ||
|
|
||
| import general_purpose_functions as gpf | ||
| import argparse | ||
|
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| def main(sam_file, threads, fasta_path): | ||
| sam_file_extensionless_path = sam_file.split(".sam")[0] | ||
| bam_file = sam_file_extensionless_path + ".bam" | ||
| sorted_bam_file = sam_file_extensionless_path + "_sorted.bam" | ||
| sam_to_bam_command = None | ||
| if fasta_path == "": | ||
| sam_to_bam_command = "samtools view -Sb -@ {} {} > {}".format(threads, sam_file, bam_file) | ||
| else: | ||
| sam_to_bam_command = "samtools view -T {} -Sb -@ {} {} > {}".format(fasta_path, threads, sam_file, bam_file) | ||
| gpf.run_system_command(sam_to_bam_command) | ||
| sort_bam_command = "samtools sort -@ {} {} -o {}".format(threads, bam_file, sorted_bam_file) | ||
| gpf.run_system_command(sort_bam_command) | ||
| index_bam_command = "samtools index " + sorted_bam_file | ||
| gpf.run_system_command(index_bam_command) | ||
| remove_sam_command = "rm " + sam_file | ||
| gpf.run_system_command(remove_sam_command) | ||
| remove_unsorted_bam_command = "rm " + bam_file | ||
| gpf.run_system_command(remove_unsorted_bam_command) | ||
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| if __name__ == "__main__": | ||
| parser = argparse.ArgumentParser(description=__doc__) | ||
| parser.add_argument("sam_file", type=str, help="Path to input SAM file") | ||
| parser.add_argument("--threads", type=int, help="Number of threads (default: 1)", default=1) | ||
| parser.add_argument( | ||
| "--fasta_path", | ||
| type=str, | ||
| help="Optional (needed when the reads have been mapped to a genome larger than 4Gb with minimap2): path the FASTA file to which the reads were mapped", | ||
| default="", | ||
| ) | ||
| args = parser.parse_args() | ||
| main(args.sam_file, args.threads, args.fasta_path) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,27 @@ | ||
| #!/usr/bin/env python3 | ||
| """ | ||
| Script for finding the average coverage of each scaffold in a SAMtools depth output file | ||
| """ | ||
|
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||
| import sys | ||
| import general_purpose_functions as gpf | ||
|
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| in_path = sys.argv[1] | ||
| in_data = gpf.ll(in_path) | ||
| scaffs_dict = dict() | ||
|
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| for line in in_data: | ||
| split_line = line.split() | ||
| scaff_name = split_line[0] | ||
| coverage = int(split_line[2]) | ||
| if scaff_name in scaffs_dict: | ||
| scaffs_dict[scaff_name]["coverage_sum"] += coverage | ||
| scaffs_dict[scaff_name]["scaff_len"] += 1 | ||
| else: | ||
| scaffs_dict[scaff_name] = dict() | ||
| scaffs_dict[scaff_name]["coverage_sum"] = coverage | ||
| scaffs_dict[scaff_name]["scaff_len"] = 1 | ||
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| for scaff_name in scaffs_dict: | ||
| average_coverage = scaffs_dict[scaff_name]["coverage_sum"] / scaffs_dict[scaff_name]["scaff_len"] | ||
| print(scaff_name + "," + str(average_coverage)) |
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