From 61726edb9293fe529e6efbe5bb6f1cc953bb3c4e Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Tue, 21 Apr 2020 16:20:10 -0400 Subject: Workaround CWL limit by chunking file list Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- workflows/pangenome-generate/relabel-seqs.py | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) (limited to 'workflows/pangenome-generate/relabel-seqs.py') diff --git a/workflows/pangenome-generate/relabel-seqs.py b/workflows/pangenome-generate/relabel-seqs.py index 970540f..6b022a0 100644 --- a/workflows/pangenome-generate/relabel-seqs.py +++ b/workflows/pangenome-generate/relabel-seqs.py @@ -1,15 +1,17 @@ import os import json -reads = [] -b = 1 -while os.path.exists("block%i" % b): - with open("block%i" % b) as f: - reads.extend(json.load(f)) - b += 1 +def readitems(stem): + items = [] + b = 1 + while os.path.exists("%s%i" % (stem, b)): + with open("%s%i" % (stem, b)) as f: + items.extend(json.load(f)) + b += 1 + return items -with open("subjects") as f: - subjects = json.load(f) +reads = readitems("block") +subjects = readitems("subs") relabeled_fasta = open("relabeledSeqs.fasta", "wt") original_labels = open("originalLabels.ttl", "wt") -- cgit v1.2.3