From cc8f99d50236b7d0c365990398785ecc319323ea Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Fri, 28 Aug 2020 10:47:48 +0200
Subject: qc_fasta returns also the seq_type; verified that only one FASTA is
 sent at a time; code cleaning

---
 bh20sequploader/main.py     | 3 +++
 bh20sequploader/qc_fasta.py | 7 +++----
 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")
-- 
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