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| author | flu0r1ne <flu0r1ne@flu0r1ne.net> | 2022-09-26 01:32:10 -0500 |
|---|---|---|
| committer | flu0r1ne <flu0r1ne@flu0r1ne.net> | 2022-09-26 01:32:10 -0500 |
| commit | 2f1781ada00bdd5d4a0181d669f8f4b8d74fccc7 (patch) | |
| tree | 8e05cc52e062cb4d14382d7bd83681943e6bc02e | |
| download | giab_index_autodl-2f1781ada00bdd5d4a0181d669f8f4b8d74fccc7.tar.xz giab_index_autodl-2f1781ada00bdd5d4a0181d669f8f4b8d74fccc7.zip | |
Add basic indexes
| -rw-r--r-- | .gitignore | 1 | ||||
| -rwxr-xr-x | clnindexdl.py | 75 | ||||
| -rwxr-xr-x | download | 18 | ||||
| -rwxr-xr-x | giab_clindex | 14 | ||||
| -rw-r--r-- | hg002/150/sequence.index.AJtrio_Illumina300X_wgs_07292015.HG002 | 936 | ||||
| -rw-r--r-- | hg002/250/sequence.index.AJtrio_Illumina_2x250bps_06012016.HG002 | 35 | ||||
| -rw-r--r-- | hg003/150/sequence.index.AJtrio_Illumina300X_wgs_07292015.HG003 | 1006 | ||||
| -rw-r--r-- | hg003/250/sequence.index.AJtrio_Illumina_2x250bps_06012016.HG003 | 19 | ||||
| -rw-r--r-- | hg004/150/sequence.index.AJtrio_Illumina300X_wgs_07292015.HG004 | 1025 | ||||
| -rw-r--r-- | hg004/250/sequence.index.AJtrio_Illumina_2x250bps_06012016.HG004 | 36 |
10 files changed, 3165 insertions, 0 deletions
diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..6dd8c90 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +**/*.fastq.gz diff --git a/clnindexdl.py b/clnindexdl.py new file mode 100755 index 0000000..5b1f537 --- /dev/null +++ b/clnindexdl.py @@ -0,0 +1,75 @@ +#!/bin/env python3 + +import csv +import subprocess +import sys +from pathlib import Path +from multiprocessing import Pool +import time + +def md5sum(path): + ''' + Compute MD5 message digest and return hex digest + ''' + res = subprocess.run(['md5sum', path], capture_output=True, check=True) + sums = str(res.stdout, encoding='ascii') + + if sums != '': + return sums.split()[0] + +def flatten_filename(ftp_url): + ''' + Transform URL into a unique filename: + + ftp://domain.ext/some/path/read_file.gz -> some__path__read_file.gz + ''' + _, ext = ftp_url.split('//') + _, *path = ext.split('/') + return '__'.join(path) + +def wget_and_verify( ftp_url, md5, output_dir ): + basename = flatten_filename(ftp_url) + + filename = output_dir / basename + + sums = md5sum(filename) + + if sums == md5: + print(f'[{filename}] skipping already exists') + return + + print(f'[{filename}] : starting download') + + retry = 0 + while retry < 3: + out = subprocess.run(['curl', ftp_url, '--output', filename], capture_output=True) + + if out.returncode != 0: + print(f'[{filename}] ERR: curl failed') + + sums = md5sum(filename) + + if sums != md5: + retry += 1 + print(f'RETRY {retry}: ERR: checksum mismatch {sums} != {md5}', file=sys.stderr) + else: + print(f'[{filepath}] : completed download') + return + + print(f'ERR: MAXIMUM RETRIES EXCEEDED', file=sys.stderr) + +def download_all_from_index( index, output_dir, threads ): + + reader = csv.DictReader( index, delimiter='\t' ) + + with Pool(threads) as pool: + res = [] + + for files in reader: + r = pool.apply_async(wget_and_verify, (files['FASTQ'], files['FASTQ_MD5'], output_dir)) + res.append(r) + r = pool.apply_async(wget_and_verify, (files['PAIRED_FASTQ'], files['PAIRED_FASTQ_MD5'], output_dir)) + res.append(r) + + for r in res: + r.get() diff --git a/download b/download new file mode 100755 index 0000000..ce20123 --- /dev/null +++ b/download @@ -0,0 +1,18 @@ +#!/bin/env python3 + +import argparse +from clnindexdl import download_all_from_index +from pathlib import Path +import os + +parser = argparse.ArgumentParser() +parser.add_argument('indexes', metavar='indexes', type=str, nargs='+') +parser.add_argument('--threads', '-t', type=int, default=6) + +args = parser.parse_args() + +for index in args.indexes: + with open(index) as file: + basedir = Path( index ).resolve().parent + + download_all_from_index( file, Path(basedir), args.threads ) diff --git a/giab_clindex b/giab_clindex new file mode 100755 index 0000000..e537b81 --- /dev/null +++ b/giab_clindex @@ -0,0 +1,14 @@ +#!/bin/env python3 + +import argparse +from clnindexdl import download_all_from_index +from pathlib import Path + +parser = argparse.ArgumentParser() +parser.add_argument('index', type=argparse.FileType('r')) +parser.add_argument('--threads', '-t', type=int, default=6) +parser.add_argument('--output_dir', '-o', type=str, default='.') +args = parser.parse_args() + +if __name__ == "__main__": + download_all_from_index( args.index, Path( args.output_dir ), args.threads ) diff --git a/hg002/150/sequence.index.AJtrio_Illumina300X_wgs_07292015.HG002 b/hg002/150/sequence.index.AJtrio_Illumina300X_wgs_07292015.HG002 new file mode 100644 index 0000000..cd04688 --- /dev/null +++ b/hg002/150/sequence.index.AJtrio_Illumina300X_wgs_07292015.HG002 @@ -0,0 +1,936 @@ +FASTQ FASTQ_MD5 PAIRED_FASTQ PAIRED_FASTQ_MD5 NIST_SAMPLE_NAME +ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/NIST_HiSeq_HG002_Homogeneity-10953946/HG002_HiSeq300x_fastq/140528_D00360_0018_AH8VC6ADXX/Project_RM8391_RM8392/Sample_2A1/2A1_CGATGT_L001_R1_001.fastq.gz 48e52acfce7548bddad2b3f89e8e0348 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