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| author | Peter Amstutz | 2020-04-21 16:20:10 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-04-21 16:20:10 -0400 |
| commit | 61726edb9293fe529e6efbe5bb6f1cc953bb3c4e (patch) | |
| tree | 49637a78fb9196221d4d6589c2e763b08687aadf /workflows/pangenome-generate/relabel-seqs.py | |
| parent | f4c3da88c1233802fea46cc972a81dc3b5b51185 (diff) | |
| download | bh20-seq-resource-61726edb9293fe529e6efbe5bb6f1cc953bb3c4e.tar.gz bh20-seq-resource-61726edb9293fe529e6efbe5bb6f1cc953bb3c4e.tar.lz bh20-seq-resource-61726edb9293fe529e6efbe5bb6f1cc953bb3c4e.zip | |
Workaround CWL limit by chunking file list
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'workflows/pangenome-generate/relabel-seqs.py')
| -rw-r--r-- | workflows/pangenome-generate/relabel-seqs.py | 18 |
1 files changed, 10 insertions, 8 deletions
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") |