#2763 - System should ignore spaces before line indexes on GenBank/GenPept sequences import

api/tests/integration/ref/formats/genbank_to_seq.py.out

@@ -1,3 +1,4 @@
 *** GenBank/GenPept to Seq***
 1844-gen_bank.seq.seq:SUCCEED
 1844-gen_pept.seq.seq:SUCCEED
+2763-gen_spaces.seq.seq:SUCCEED

api/tests/integration/tests/formats/genbank_to_seq.py

@@ -25,6 +25,7 @@ def find_diff(a, b):
 files = [
     {"file": "1844-gen_bank", "seq_type": "PEPTIDE"},
     {"file": "1844-gen_pept", "seq_type": "PEPTIDE"},
+    {"file": "2763-gen_spaces", "seq_type": "DNA"},
 ]
 
 lib = indigo.loadMonomerLibraryFromFile(
@@ -36,6 +37,8 @@ def find_diff(a, b):
     mol = indigo.loadSequenceFromFile(
         os.path.join(root, filename), infile["seq_type"], lib
     )
+    # with open(os.path.join(ref_path, filename), "w") as file:
+    #     file.write(mol.sequence(lib))
     with open(os.path.join(ref_path, filename), "r") as file:
         seq_ref = file.read()
     seq = mol.sequence(lib)

api/tests/integration/tests/formats/molecules/2763-gen_spaces.seq

@@ -0,0 +1,20 @@
+        1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg
+       61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct
+      121 ctgcatctga agccgctgaa gttctactaa gggtggataa catcatccgt gcaagaccaa
+      181 gaaccgccaa tagacaacat atgtaacata tttaggatat acctcgaaaa taataaaccg
+      241 ccacactgtc attattataa ttagaaacag aacgcaaaaa ttatccacta tataattcaa
+      301 agacgcgaaa aaaaaagaac aacgcgtcat agaacttttg gcaattcgcg tcacaaataa
+      361 attttggcaa cttatgtttc ctcttcgagc agtactcgag ccctgtctca agaatgtaat
+      421 aatacccatc gtaggtatgg ttaaagatag catctccaca acctcaaagc tccttgccga
+      481 gagtcgccct cctttgtcga gtaattttca cttttcatat gagaacttat tttcttattc
+      541 tttactctca catcctgtag tgattgacac tgcaacagcc accatcacta gaagaacaga
+      601 acaattactt aatagaaaaa ttatatcttc ctcgaaacga tttcctgctt ccaacatcta
+      661 cgtatatcaa gaagcattca cttaccatga cacagcttca gatttcatta ttgctgacag
+      721 ctactatatc actactccat ctagtagtgg ccacgcccta tgaggcatat cctatcggaa
+      781 aacaataccc cccagtggca agagtcaatg aatcgtttac atttcaaatt tccaatgata
+      841 cctataaatc gtctgtagac aagacagctc aaataacata caattgcttc gacttaccga
+      901 gctggctttc gtttgactct agttctagaa cgttctcagg tgaaccttct tctgacttac
+      961 tatctgatgc gaacaccacg ttgtatttca atgtaatact cgagggtacg gactctgccg
+     1021 acagcacgtc tttgaacaat acataccaat ttgttgttac aaaccgtcca tccatctcgc
+     1081 tatcgtcaga tttcaatcta ttggcgttgt taaaaaacta tggttatact aacggcaaaa
+     1141 acgctctgaa actagatcct aatgaagtct tcaacgtgac ttttgaccgt tcaatgttca

api/tests/integration/tests/formats/ref/2763-gen_spaces.seq

@@ -0,0 +1,15 @@
+GATCCTCCATATACAACGGTATCTCCACCTCAGGTTTAGATCTCAACAACGGAACCATTGCCGACATGAGACAGTTAGGT
+ATCGTCGAGAGTTACAAGCTAAAACGAGCAGTAGTCAGCTCTGCATCTGAAGCCGCTGAAGTTCTACTAAGGGTGGATAA
+CATCATCCGTGCAAGACCAAGAACCGCCAATAGACAACATATGTAACATATTTAGGATATACCTCGAAAATAATAAACCG
+CCACACTGTCATTATTATAATTAGAAACAGAACGCAAAAATTATCCACTATATAATTCAAAGACGCGAAAAAAAAAGAAC
+AACGCGTCATAGAACTTTTGGCAATTCGCGTCACAAATAAATTTTGGCAACTTATGTTTCCTCTTCGAGCAGTACTCGAG
+CCCTGTCTCAAGAATGTAATAATACCCATCGTAGGTATGGTTAAAGATAGCATCTCCACAACCTCAAAGCTCCTTGCCGA
+GAGTCGCCCTCCTTTGTCGAGTAATTTTCACTTTTCATATGAGAACTTATTTTCTTATTCTTTACTCTCACATCCTGTAG
+TGATTGACACTGCAACAGCCACCATCACTAGAAGAACAGAACAATTACTTAATAGAAAAATTATATCTTCCTCGAAACGA
+TTTCCTGCTTCCAACATCTACGTATATCAAGAAGCATTCACTTACCATGACACAGCTTCAGATTTCATTATTGCTGACAG
+CTACTATATCACTACTCCATCTAGTAGTGGCCACGCCCTATGAGGCATATCCTATCGGAAAACAATACCCCCCAGTGGCA
+AGAGTCAATGAATCGTTTACATTTCAAATTTCCAATGATACCTATAAATCGTCTGTAGACAAGACAGCTCAAATAACATA
+CAATTGCTTCGACTTACCGAGCTGGCTTTCGTTTGACTCTAGTTCTAGAACGTTCTCAGGTGAACCTTCTTCTGACTTAC
+TATCTGATGCGAACACCACGTTGTATTTCAATGTAATACTCGAGGGTACGGACTCTGCCGACAGCACGTCTTTGAACAAT
+ACATACCAATTTGTTGTTACAAACCGTCCATCCATCTCGCTATCGTCAGATTTCAATCTATTGGCGTTGTTAAAAAACTA
+TGGTTATACTAACGGCAAAAACGCTCTGAAACTAGATCCTAATGAAGTCTTCAACGTGACTTTTGACCGTTCAATGTTCA

core/indigo-core/molecule/src/sequence_loader.cpp

@@ -169,6 +169,8 @@ void SequenceLoader::loadSequence(BaseMolecule& mol, SeqType seq_type)
 
         if (start_char)
         {
+            if (ch == ' ' || ch == '\t')
+                continue; // skip leading whitespaces
             if (ch >= NUM_BEGIN && ch < NUM_END)
             {
                 isGenBankPept = true;
@@ -2015,6 +2017,8 @@ void SequenceLoader::loadSequence(KetDocument& document, SeqType seq_type)
 
         if (start_char)
         {
+            if (ch == ' ' || ch == '\t')
+                continue; // skip leading whitespaces
             if (isdigit(ch))
                 isGenBankPept = true;
             start_char = false;