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-rw-r--r--.gitignore1
-rwxr-xr-xclnindexdl.py75
-rwxr-xr-xdownload18
-rwxr-xr-xgiab_clindex14
-rw-r--r--hg002/150/sequence.index.AJtrio_Illumina300X_wgs_07292015.HG002936
-rw-r--r--hg002/250/sequence.index.AJtrio_Illumina_2x250bps_06012016.HG00235
-rw-r--r--hg003/150/sequence.index.AJtrio_Illumina300X_wgs_07292015.HG0031006
-rw-r--r--hg003/250/sequence.index.AJtrio_Illumina_2x250bps_06012016.HG00319
-rw-r--r--hg004/150/sequence.index.AJtrio_Illumina300X_wgs_07292015.HG0041025
-rw-r--r--hg004/250/sequence.index.AJtrio_Illumina_2x250bps_06012016.HG00436
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 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_R2_001.fastq.gz bd37bc5dedb31845361f531803ee03b5 HG002
+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_002.fastq.gz 1bda3ac5c144e0199c132f149db319f7 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_R2_002.fastq.gz b0b82bdb56b23899e26e3393e78eabe7 HG002
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index 0000000..571a911
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index 0000000..fb4859f
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diff --git a/hg004/250/sequence.index.AJtrio_Illumina_2x250bps_06012016.HG004 b/hg004/250/sequence.index.AJtrio_Illumina_2x250bps_06012016.HG004
new file mode 100644
index 0000000..55727db
--- /dev/null
+++ b/hg004/250/sequence.index.AJtrio_Illumina_2x250bps_06012016.HG004
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