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-rw-r--r--bh20sequploader/main.py3
-rw-r--r--bh20sequploader/qc_fasta.py7
2 files changed, 6 insertions, 4 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index d5de63e..80c33c8 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -40,7 +40,10 @@ def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True):
log.debug("FASTA/FASTQ QC" if do_qc else "Limited FASTA/FASTQ QC")
target.append(qc_fasta(sequence_p1, check_with_mimimap2=do_qc))
if sequence_p2:
+ if target[0][2] == 'text/fasta':
+ raise ValueError("It is possible to upload just one FASTA file at a time")
target.append(qc_fasta(sequence_p2))
+
target[0] = ("reads_1."+target[0][0][6:], target[0][1])
target[1] = ("reads_2."+target[1][0][6:], target[0][1])
except Exception as e:
diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py
index e5c039e..215d6fd 100644
--- a/bh20sequploader/qc_fasta.py
+++ b/bh20sequploader/qc_fasta.py
@@ -63,8 +63,7 @@ def qc_fasta(arg_sequence, check_with_mimimap2=True):
tmp2.write(submitlabel.encode("utf8"))
tmp2.write(("".join(submitseq)).encode("utf8"))
tmp2.flush()
- subbp = 0
- refbp = 0
+
similarity = 0
try:
cmd = ["minimap2", "-c", tmp1.name, tmp2.name]
@@ -85,10 +84,10 @@ def qc_fasta(arg_sequence, check_with_mimimap2=True):
if similarity < 70.0:
raise ValueError("QC fail: alignment to reference was less than 70%% (was %2.2f%%)" % (similarity))
- return ("sequence.fasta"+gz, seqlabel)
+ return ("sequence.fasta"+gz, seqlabel, seq_type)
elif seq_type == "text/fastq":
sequence.seek(0)
sequence.detach()
- return ("reads.fastq"+gz, seqlabel)
+ return ("reads.fastq"+gz, seqlabel, seq_type)
else:
raise ValueError("Sequence file does not look like a DNA FASTA or FASTQ")