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| author | Peter Amstutz | 2020-04-20 13:41:56 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-04-20 13:41:56 -0400 |
| commit | d29dfd593233541b85c1cefb239650279d57d59f (patch) | |
| tree | 51fa615a05a2606021bdf8c537ad8b36ae4e0a8c /workflows/pangenome-generate/relabel-seqs.py | |
| parent | d781e42c9adac07253cb928ae66e9b7314710267 (diff) | |
| download | bh20-seq-resource-d29dfd593233541b85c1cefb239650279d57d59f.tar.gz bh20-seq-resource-d29dfd593233541b85c1cefb239650279d57d59f.tar.lz bh20-seq-resource-d29dfd593233541b85c1cefb239650279d57d59f.zip | |
Relabel sequences to match metadata subjects.
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 | 13 |
1 files changed, 13 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/relabel-seqs.py b/workflows/pangenome-generate/relabel-seqs.py new file mode 100644 index 0000000..32f2386 --- /dev/null +++ b/workflows/pangenome-generate/relabel-seqs.py @@ -0,0 +1,13 @@ +import sys + +reads = $(inputs.readsFA) +subjects = $(inputs.subjects) + +for i, r in enumerate(reads): + with open(r["path"], "rt") as fa: + fa.readline() + print(">"+subjects[i]) + data = fa.read(8096) + while data: + sys.stdout.write(data) + data = fa.read(8096) |