Change alignment processing by BlastHit and add test datasets

.gitignore

@@ -57,4 +57,4 @@ docs/_build/
 target/
 
 # Custom exceptions
-*test/
+

BlastHit.py

@@ -66,6 +66,7 @@ class BlastHit(object):
         @param  qseq Sequence of the query aligned on the reference
         """
 
+        # Store parameters in self variables
         self.id = self.next_id()
         self.q_id = q_id
         self.s_id = s_id
@@ -73,6 +74,10 @@ class BlastHit(object):
         self.length = int(length)
         self.mis = int(mis)
         self.gap = int(gap)
+        self.q_start =  int(q_start)
+        self.q_end =  int(q_end)
+        self.s_start =  int(s_start)
+        self.s_end =  int(s_end)
         self.evalue = float(evalue)
         self.bscore = float(bscore)
         self.qseq = qseq
@@ -81,17 +86,6 @@ class BlastHit(object):
         self.q_orient = int(q_start) < int(q_end)
         self.s_orient = int(s_start) < int(s_end)
 
-        # Autoadapt start and end so that start is always smaller than end
-        if self.q_orient:
-            self.q_start, self.q_end = q_start, q_end
-        else:
-            self.q_start, self.q_end = q_end, q_start
-
-        if self.s_orient:
-            self.s_start, self.s_end = s_start, s_end
-        else:
-            self.s_start, self.s_end = s_end, s_start
-
     def __repr__(self):
         msg = "HIT {}".format(self.id)
         msg += "\tQuery\t{}:{}-{}({})\n".format(self.q_id, self.q_start, self.q_end, "+" if self.q_orient else "-")

test/query_sample.fa

+>query_001%_mutation_forward
+ATTTATCTAGGAACAGGAATGCACTTTTGGGGAAAGGTTTTCCATACCAAGGAAGGGGCAGTGGCTGGACTGATAGgACATTATTCTGtAAAAACTTATG
+>query_002%_mutation_forward
+ACAAGTTGCCAACCAAGCGTCAGAAATTGGTGGTCATGGTGGGAGAAAAGCCCATTACCATAACTCAGCACTCGGTAGAAACCGAAGGCTGCATTCACaC
+>query_003%_mutation_forward
+CGCTCTAGACCGTGCAAcAGGAGAGCCTGTAAGCGGGCACgCTTCCGTGGTCTGGTGGATAAATTCGCAAGGGTATCATGGCGGACGACCGGGGTTCGAG
+>query_004%_mutation_forward
+TCGGCTAAgATGGCCTGCTGCACCTGCGTGAGGGTAGACTGGAAGTCATCCATGTCCACAAAGCaGTGGTATGCGCCCGTGTTGgTGcTGTAAGTGgAGT
+>query_005%_mutation_forward
+TTgTaCTCTCGTGTGTaTGTGTCTGTTCGCCATCCCcTCTCCGCTCGTCACTTATCCTTaACTTTTCAGAGGGTCCCCCCGtAGAgCCCGGTCACCCTCA
+>query_006%_mutation_forward
+GGGCTCCAGTGAGCAGGAACTGAAAGCCATTGTCAgAGATCTTGGTTGTGtGCCATATTTTTTGGGCcCCTATGACAAtCGCTTaCCtGGCTTTGTTTCT
+>query_007%_mutation_forward
+GAATCTaATTGAGCAGGCACCCCTaACtGTGGCCGAGtAGgTGCAGCGCGACTTTCTGACGGtATGGCGCCGatTGAGTAAGGCCCgGGAGGCCCTTTgC
+>query_008%_mutation_forward
+AAACAACAGGcACATGAcTATATTTATCgAGGAACAGGAATGCACTTTTGGGGAAAGGTTTTCCATACCAAGGAAGGaGCAGTGGCTGGACTGATcGAAC
+>query_009%_mutation_forward
+GTCATACCTGATATCGCCTCcCTCAACGAAGTcCCggAAATCTTTGAGGGcCTTGGACGCGACGtGAAcCaCGCGGCAAACGCTCTGCAACAGGAAAACA
+>query_010%_mutation_forward
+AACTACGTCgTCTCCcGCcGCCACACaCccCGCCAGCACCTGTCGTCAGCGCCATTATGAGCAgcGAAATTCaCACGCCCTACATGTGGAGTTACCAGaC
+>query_011%_mutation_forward
+AAcGGCGtGGCaCGCCGCGcCTACGTCCGaGACTGCGTTaACcTATTTCTATGCTACACCaGtgAGcCGGCCATGccCaTTTGGCAGCAGTGCTTGGAGG
+>query_012%_mutation_forward
+cTCGCtTaGgGCGAGCtCcTACTCcGATGGtAGaCGGTCgTGTgGATtAGGATGATCTGGACaAAtAGCATCAGGGGCTCGCGCCAcCCcgAacaTTCcC
+>query_013%_mutation_forward
+CGatAGaCAATCCTAcCTCTGCAGACCTCGTCCTtTGAaCCGCGCTgTtGtGGCATTGGgAtTCTGCAATTTgTTGAGcAGccTGgGCCATCGGTCaACT
+>query_014%_mutation_forward
+CCCCATAGGAGGTATAACAAAATTgATAtGAGAGAAAAtCACATAAACACgTGAAAAACCCTCCTGgCTgGGCAAAtTcGCgCCCTCCCGCTtCAGAcCA
+>query_015%_mutation_forward
+AGACtCTGcGCGGTCTggAAGATCTTtTTCCCTTcAACTAtTAAAAcAAAAgAATcAAGCATCACTTACgcAcAATaAGTTAGtAAATTTCTGTCCAGcT
+>query_016%_mutation_forward
+TTGATGcTGTgAGTGCAGcTGGCCATAACGcAgCAGTTAACGGTCaGGTGACCCGtCTGCGAGAGCgCGGcGTACCTGAGACGCGAGTAAGCCCTCGAGT
+>query_017%_mutation_forward
+CGACCACCTgCAACCgGTCAAAGtTcAAgTtaTTgATCACGCcATACAGCAaCGaACAGGTCAGCGTGGAAATTGAATGGGAGCTGCgGAAGGAAAACct
+>query_018%_mutation_forward
+tTTtCCTGTTgATCAATcAcCCGGTTGAcTCGTaTtAGTTGAAtcTTGGTaTCTGCattGGGCGcATTCGcTcCGATGCgTaTCCTgGGGaCCGGCCTGa
+>query_019%_mutation_forward
+CaGCGCGCaCACACGTGGCGGCCGCCGACCTGGTAcCCGCATcacAGgAGAtGGTGAgCCcGGGCGATCtCACCCTTTGGCGgAcCCCATTCTCtAGTcA
+>query_020%_mutation_forward
+GaTGCCTGAacCCCCGcgGTGTAGcTAACaACGATACGGGAGGGgccAgCATCTtGCCCgAGTGCTtCAAcGATAaCGCGAGAaCtACGCTCACCGGCTC
+>query_021%_mutation_forward
+CAtTGtAACACTATgAGCGCCGGGTGGTGCACtCTGcCgAGgACGCTCgaGTCGGAGtTCAGATtCaCGcCCAGGTgCTCaGCGcTcCTCAGtGCGtACG
+>query_022%_mutation_forward
+TCTatGtCCGGCaGGACTGCGGCGtACGGcGaggTtagTaCtCGTCtTGCgAGAgCCCGCTaGCAAAcTCCTCCGGAAACAGGGtgGAGCCtCTTTaTTG
+>query_023%_mutation_forward
+CGCCCcCCGCTTgaTTCTCTACCATCACaGCGTGGCaTcCaCCtGTAACAcCCTtgtTgAgTACCtTCATCTCTACAtgCtAaAgTaacCCGGCGGCAct
+>query_024%_mutation_forward
+GcgGATgGCTAatCTGaGCGcTTTTAgGGtCAGCAAGCGAACtGGgtTTGCCAGCaGGaGCGCCCTCTcGTAAGGTcGGGAAGgCCTGCAAAGTAAACTG
+>query_025%_mutation_forward
+CGGGGgcCgCAACTCCATGCcCAcCgGaCCCCAaGTAtAGCtCAaCCTGCaTtGCcgCggGGActAtgTCTtCtGCTTCCcGGAGCGCCACTgGtCtgAC
+>query_026%_mutation_forward
+cGCAAcaaGAGAAGatAGAGAGCcACTTCCAgcTGCACtTGCgCcTGGAAAgCAgCGGaGTGAAAaCCATGtTTaTccagCcTTTCCTtAtgCAGATTCG
+>query_027%_mutation_forward
+aCCaGTTCCGAgtCataCtacTgCgcGAaACCTGTCCGCCTTTCTCCCTTaGGGAAGCGTcGCcacaTCTCtcAaCTCACGCTGTAatTcTaTCAGgTCG
+>query_028%_mutation_forward
+AaAtaCacTcgTaCAagcGCGcCAGCGtCAGCtGCtGgAACAGCAtCGaaCtaACtGAAGCAAAGGCGtCCcGATAGCtAGAaTCcGACAtAGCCCAgGA
+>query_029%_mutation_forward
+gGTCCctTGAGCCGCtaTCTGGAGGCcTTGGAACTaTGCAATcaATTGgcGAaTaTGTGCCAgtcGTCcAtTcgAACCCCTTCTacaGAaCTCaCGGCCt
+>query_030%_mutation_forward
+gGTTCGCTCaAgGCcGtGaTGTagcCACGAACCCgCCGgTCAGgCatACCGCTGacCgTaAcCCtGTAACTtTaGTCaTaAGTCCAACCCtccAAtgCAC
+>query_031%_mutation_forward
+TTtCCtcaGCTcAgaaAGaGAtGCtCCTATCggttCGAgCaGTCgtTTgCGcTCtTCCgTAcTTGCCcGACcCCgCGTCcTGaAGATgAtTAtGATAtGG
+>query_032%_mutation_forward
+agCcAgACCTgCaTgGGgTAgAGCACaCCtTGGcGGTATTTctACTcgAtgAGATcCtACTcCCACTTTTttagtCGTcgCTGGCAGCcAgaCATCAgtA
+>query_033%_mutation_forward
+CTGACAGTTcCCAATGgggAAgCgGTGAGGgACCaATCggAGCGATCgGTCTATTTCGTTCgTCCAgAaTgGCCTGAgTCCCCGTgcctTgGccgttaAC
+>query_034%_mutation_forward
+CTctAtCGTGtTACGCGTGgaGaGgAacccCCGCGatAttctgTGTggCGaGtCCctGAaGGAGAcGcGCtCGtGagGATGaGGtATtGAAtGTTtCACG
+>query_035%_mutation_forward
+TaAGGGCAcTCGCGAGcGGTacaCtCTGAgAgCTcGAtCCCCGAAtCCCAAAGCCAACCAcacAActCAGGACcACGtCCGaGtTCTGGgGCTTCgTGGC
+>query_036%_mutation_forward
+GCAgCaGgCCcAACCCTGaAaggCAcCcAGATCgTcGTctCCgTtTagGTGCaGAGTAcAcTAAAccCAGAtATTcAAAagggCatGaGCTtCTATCGCC
+>query_037%_mutation_forward
+CAgGaCAAAgcGcACGCCctACaTAGaCgTAaTTatTcggGCgtAtgCcGGgGCGcGCGTGACAAcCccATCTGCGaCTCCaGcCTCGgCGCTTAGtTCG
+>query_038%_mutation_forward
+TgTGtCAtGtATcCTCcGAGaTccGCTtACCAttaTAGgCCCaATGTAAGgTgGTaGCtaaGtCGGtcATATAgAATGatAGaTGCaaCTatAAAAATCc
+>query_039%_mutation_forward
+ACcGaaCAttCTGCtctcCtACagccAACAGgTCTACAatgTCCTaGAGtGtCAtTtGaCaTtgggaCGgAGCCACAaatCGgAGATTAGGAcCGCCACa
+>query_040%_mutation_forward
+ATTACAGgCtCatTtctAGGTcTAttAAAAaTAATAaGcaccAgctgCgCtTAgAtACtaGAAcAACCtTCtaGCaagGGCAgAATAGtACCgcCCCaCa
+>query_041%_mutation_forward
+acGCAACgGCGttTGctgtAtCTttTggACTcTgGCCGatACAAtTGCTcaaCCCGCagCaCtGaTcAtTcgTagaACaTTtgAaTGtataAGGgcggag
+>query_042%_mutation_forward
+tAAAtCtAGTCAgACATgAACtTGGcAccATCTaCACCtCTactAGgTACCTCAGAAGCCgTtACTGaGcCaGtCatgGCctaaaTAgTGagttCGtGCA
+>query_043%_mutation_forward
+aCAtAtaaAAAtCctcaCaTGCAAAatTgAGGtCgCCTaACttgCcCCGtcgtCAaTACCgcTgCcAagAaaGCtatggCCgCcggAACTgtTctCAtTG
+>query_044%_mutation_forward
+CGTTTctaTAaTagTgTcgaACACCacGCAacaGGgtAaGatgaTTTcGtAaCAGTGCcTGGgGGAGgGCAAgCTCtctGcGCTtCcaAAgCTGCTAccG
+>query_045%_mutation_forward
+CtAGttAAAACtCAAagGCttttgtgAgcCAGcgAGCTTcCttTcGtgcTctATGaCGATtGCgAaACTGcGCctTcTTAgGtACAtCAActtAAaCGGc
+>query_046%_mutation_forward
+tCTCGtTCACTaAaaCcgTGCGgcCGGTgtcaCGGCgGgGtCGcaCGGagaCgctTCAgcCttgGcCGGTAAccgGGTcATCCttAacgTCcGGGGAatt
+>query_047%_mutation_forward
+GCGCCTTATCCGaTAttTgTCcTgcTttcTgaAAggtaGaAttctAgGggTTAggGtgAgTGGCAtCtGCCAaTGGcgcgAaGAgcgaCAtAttGctcTA
+>query_048%_mutation_forward
+CAgTtGcgtACTAcaAGCaCCaaGgttacCAtGgcGcCCcGtACtCTCTTGTgGcctATgAGcTCCGCGctgcGacCCTCCagtTTctcCcGGGgatAac
+>query_049%_mutation_forward
+aAtGTtaGtAgCgctccgAcctaaCtGAtcGgGttgcttGGacCTtgAcTTaGAgcCGGcAcGgTTGAggatcCAGtacCCATaCCatGaTaaaAtGttt
+>query_050%_mutation_forward
+TtaACtCTtAtGGGCtgGaCGCGCCGgatCcAgtgCCGaGcCaGCtTaTACTTcgTTaTtTcCTgCgCCatGtccgttctagTaGGaGTgatGCcGgAGT
+>query_001%_mutation_reverse
+CCAACCTTACCAGAGGGCGCCCCAGCTGGCAATTCCGGTTCGCTTGCTGTCCATAAAACCGCCCAGTCTAGCTATCGCCATGTAAGCCCACTGCAAGCTA
+>query_002%_mutation_reverse
+TAAATTCTCTGAATCAGTTTTTCGCGAATCTGACTCAGcAAACGTCCCAAAACCATGGATTTCACCCCGGTGGTTTCCACGAGCACGTGCATGTGGAAGT
+>query_003%_mutation_reverse
+TACCCACTCCGTCGGCGCCTTCGTTAaTGTCTGCCATTGGTGCGCCACCGCCTGCAGCCATTGTATTAGGTCCCACACCAGAGGGCGCTGCTGGAGGTTC
+>query_004%_mutation_reverse
+AACCATCGGCAGCCATACCTGATTaAAATCATTTATTcTTgAAAGATGCAGTCATCCAAATCCACtTTGACCtGATCGCAGGCAGTGCAAGCGTCTGGCA
+>query_005%_mutation_reverse
+GTGCACGACGCGGtaTGTCCGGCCAATCgGTTTTCCGGCAAGTCTTGCcGtATGTTCTTCTCTGAAGGCGCAAAGGCTCAGGTGGCTcTTAAGCAGATCA
+>query_006%_mutation_reverse
+CCGTACAGTAGGGgTCGTCTACCTCCTTTTGAaACAGAAACCtGCGCTgCCATACTGGAGGATCATCCGCTGCTGCCCGAATGTAACACTTaGACAAaGC
+>query_007%_mutation_reverse
+GTAACTTGTATGTGTTGGcAATcGTAGTTTTCTcAAAATGGGAAGTGACGTAACGTGGGAgAACGGAAGTtACGATTTGAaGAAGTTGTatGTTTTTTGG
+>query_008%_mutation_reverse
+TTTTGCgTAGGCAGGAGGGTTTTTCAGGTGTTTATGTGTTTTTCTCTCCTATTAATTTTGgTATACCTCCTAgGGGGGCTGTcATaTTGTaTCTACGCCT
+>query_009%_mutation_reverse
+GGCCGAAAaGTGaTGCcGATCTCCAACACCGgCGCAAGGTGCTGCGTGCACGACtCGGCCTGTCCGGCCgcTCAGTTTTCCGGCAAcgCaTGCGGCATaT
+>query_010%_mutation_reverse
+TTAcACtGGTCTGTGAGGtgCCTGAcTTTacGCAATtATGATTCGCTGCTTGAcGCTGAAGGTGGAGGGCGCTacGGAGCAGATTTcTgCAATGGCCGGA
+>query_011%_mutation_reverse
+ACaAAGCCTGGGGCgTGGCCGACCGtCTGCGCATTCAGCcGaCCGGACCCAAGGACATGCATCGgAACGAATTCGCCCTTCGCAGAGACCAAAGTTtgAg
+>query_012%_mutation_reverse
+GgtGCCCTAGACcAATATTACGCGCTATGAaTAACACAAAATTAaaCAGATTTCAgTTCCTCTTcTTCAGTTTTCCCGCGAAAATGGCCAAATCTTAtTC
+>query_013%_mutation_reverse
+TTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTgTTTCCTGCGTTATCCtCaGAcTCTGTGGgTAACtGTATTACCGCCTTTGtGTtAGCT
+>query_014%_mutation_reverse
+CCTCACaGAgTAAGCATTGGTAACTGTCAGACCAAGTTTACTCgTgTATAtTTTAGAcTGAcTTAAAACTTCATTTTTAATTgAAAAGcATCTAGcTGAA
+>query_015%_mutation_reverse
+ATCTGGAaCaGGTGAtCGTGGGTCTCGCGGcATCcTTGCAGCACcGGGGCCAGcTGGTAAGCCCTCCCGgATCGTAGTTATCTAaACGAgGGGGAGTCAG
+>query_016%_mutation_reverse
+TATTAcGTaCCACACCAGAGtGtGCTGCcGccGGTTCTCCtAGAGGTTGAGGGTCTGGtACTGACTCTGAGTtGCCAcTCTGACCAcAATTGAGTCTTTT
+>query_017%_mutation_reverse
+CATaGCTGCAGCAATGGCccCAACGTTGCGCAAACTATTAACTcaCGAACTACgTAgTCTgcCTTCCCGGCAACtATTAATAGACTGGAcaattGCGGcT
+>query_018%_mutation_reverse
+AATAAaAAAgCGCCAtaTTTGACCCGGcACGCGGtAAACcCCgcAGAAAAACACCTGGGtcAGctTCCctGggAAacGTCtAAGTtCCtGCGGgCCTAGA
+>query_019%_mutation_reverse
+TTttGCATAAATCCAACAGCGcTTGTATAGGCTtTGCCcTCAGaAAtATCTCaATTTCTAAAGTTCCAATATTtTGGcTCCAtGtAaGAATTGTTTAGTA
+>query_020%_mutation_reverse
+GGtCCGCGGCTGCcGCTGATAGGGCTGCGttGcCGGGGGGATTGGGTTGAGaTtCatagtGGACTtGGGGTCCAAGTcgACCCtCCGTCCCTTgCaTAcC
+>query_021%_mutation_reverse
+CAtGTTTATGTTTcACTaGGTcTTTaTGAacGtTGGGCaCACAGTGGTTgCATTTTGGGAGGTtAGaaTGCCccCgcCaaCCAGtGAcgaGCCGgTGCCC
+>query_022%_mutation_reverse
+tAcAacCCAACTaTGACCCGcgACGCGGcAAACgCaTGAaAAAAcCACCTGGGCGAcTCTCCACcaAAACGGTatAccTtCagGCGGCCCcAGACgcAcA
+>query_023%_mutation_reverse
+ATTgAcAGcttCAAAACcCAaCaaAGcCGCtaGCAAAGaACTTGTGGCtaCttCAaTttAaCAtGgGTTaCAGGattAGcTGCTtTaagTCTCCtaTaAA
+>query_024%_mutation_reverse
+aGtaACtCgTTgTTGACtACAGAAAgGGtTTGcGATTCTGAaAaGGGtAAGCcCTCTAAACAGcCTTTCTcTaCGTGAGaGAAGCAGATATTTtAtTTaT
+>query_025%_mutation_reverse
+CTCCGCGcCgTCCAGCaTGCGtgGAtGCgGATCTTCGCTTTTGTGcTACAcGgtGaTGCGGcTGAGGttTCGCAGAGACCTacTTTTTATTTTtAGCTCT
+>query_026%_mutation_reverse
+AaaCTtggCTGTgCGGTGCTGTATTGgaTGcTGAAAGAGTTCcGCTTaGtCTGaTgGAAcGaGtTCacAGGcTCCGCAGGTgCAaGCGTaTcacTGcTCA
+>query_027%_mutation_reverse
+AcagTCCaGtcCcACtAtACCGGCTTCCcTCCGAtTtCtTGCcCGCaCGAccCGATGaTgCGCTTGaTccTgGAATGGaCAGGaAtCCGGAgCAAtCGaA
+>query_028%_mutation_reverse
+gaTTGcaCTGgAGATGgAtGGTCCCCgtgtAGTCCgTGGTcGaCctCcaCTGTCTtgTgTTTTGACtAACggtCTCTTTaTgCCCTaTgTctaTTaTAGc
+>query_029%_mutation_reverse
+ActTAgTaaCCcTCaAGTGaAcCCGTccTTAaGCCACCACgTtAccAACTaccaAGgACCGCaTAatacCCTCGCcCTcCTAATCgTGTTACCAGgGaaT
+>query_030%_mutation_reverse
+TCCAAcCTGGAACAAttCTCAAaCCTAgtTCGGTCTATTaaaTgGAaTccTtAGcatTTaTGtCGATTTCGagaTtTTtGTTAAAAAATGgGCaGAaTTc
+>query_031%_mutation_reverse
+GAtTCTGGgaGCAACTCCCATgCCTgCcgaGaCcCCCtccTCAgAAAGgTtTCAcAAAcGtCGaGgAGATaCgCGaacAcagCGCTtcGGgCCTTAATCA
+>query_032%_mutation_reverse
+AAaATCgaGGcTcGtCtgCGgTATtTCCTtATAGCccTCCGCCAgACaCAtCCGtCCACAaTtGAcGAtatCAGAAAAttGtCgcTTTTgCACCtgtATA
+>query_033%_mutation_reverse
+AgcGGTTCTGCgcCatCAtaagCGggTCACGCGaATCcacCagCtGtaGCACCCTTGGGgACttaTCAGGAttGGcCtgTttTAtCCGCGCtgGGgtgTt
+>query_034%_mutation_reverse
+ATTACAtATTACGtGTGtGGTAACGGGTGgtAgTGGtGCtGGGcTttagtTACctGCaTTCaGTATTAtCAtCAggGTCCAagtTTGTAagTcgGTtcTt
+>query_035%_mutation_reverse
+gCTCAGTgAGCATggACCctGGAttaCcAGgTaTtaCGAGTCTTcCAacAAcGGGGgGcaGgaGGcgaTGTtTAAtACTgTATcGCCGcTGtaTGaGACC
+>query_036%_mutation_reverse
+GtCCAGtTGCcatTCCGtaaGGCTGgGGTcGGCAaGtCAtGATAtGGGgAgCTacCAGTcaTGGAAAAAaATtTGAgAaGccaCAAGCACgaCTaGCACG
+>query_037%_mutation_reverse
+gATCTctGaCaAtATaGGgCCtTcgAGGgAaAgGTaCCGGaTgTGCCAGACCgTtCCacGTgAGGCCtCCTGGCTGaTaAtAGTTCCAAccTGAatAcaC
+>query_038%_mutation_reverse
+tTgGcAgGGGtAGcggatCGGgTaAAGCtTAaGCcatCGtCGCATaGgATCtcCCgcGAcGcATgtTTTaTCGttgtGtGtgAaGTaAacTGtCcGGAGA
+>query_039%_mutation_reverse
+AAgCAcGTtgCaGcTtTcTgAcGTatTCaTTCgtTcgTCAGTagGgAcAacCCAgGcAGcTgTAtCTCccaCGAtcCTcTggCGAAgttGcAGtGcAGcG
+>query_040%_mutation_reverse
+GAtAAaAagGGtccCCATCCGAGTACtgGaTCttcCcATaCGtgGTTggtgccGtcGcTCGAAaGGGCAGGaAGCgatcTCAgGCtTATGaAGCCaCCGC
+>query_041%_mutation_reverse
+gTTGctACacCtTGTcaACACCccCGaACAaCtAcAACtaCAtgTcccCCcCAgCCcaCGCTTAacTGTaaagCaCCcatCTTGtAcaccgtgAtTcaCc
+>query_042%_mutation_reverse
+CcaTgGCCcAAGaAGGTccTtTCGgaGcTGGtaCtcCCCcgTGTaCgGggGaAGAgggaaTgcTcGAGGgGaaTGTgGccaGTGGaacGGGCCCgatTcC
+>query_043%_mutation_reverse
+CatGCgaaGaGACCctTACAtgatCCAcCGgaCcctCGaCCGaTaCaaatGCggTCTTtCtTTCCgcTggCGaCctGTTCGtCGaCTTTgaCtGTCcAGg
+>query_044%_mutation_reverse
+ACtTCgaGTggaaGTggACAcAGcTcTccAGGcCcacCCGGActAcaTagGGaTggttaTCgGGgGGTcGGTGcGGTcCAaCttgtGGgGAgGCACTgcc
+>query_045%_mutation_reverse
+CTGttTGCACggAAcCTCCcCGGcAgttAGCgCTttaGatAaCcTTcGTTTaCtTaGCTgCaCCAAcTgaGacGGaaCGCaCGcaTtggGgCAGCcCGCc
+>query_046%_mutation_reverse
+tGaggaaTCgcTagGggccCTgCCCccCaaTaaTaaCCcCGTTCaaCaGCgTTCgCtaTCAtcgaCTtAcaacttttCgCCaTaTAGGGTcCCacaTTAt
+>query_047%_mutation_reverse
+CATcTtcTagagAAACCctcTCcGGAtgggACTTGcCgtAgATCgagcTgTccgGtgtgtcTaGcAcgaATgtcggaATTcgcACCCcGtGgcCCcgAAG
+>query_048%_mutation_reverse
+CgCAcCAGgCCAGcgAAcGTTtagATTtTTGaTaatCCCGGTTGcCaTTagGACGCtTgGTTaGtccagtCtGGcTCCctGCAGttAcTgggggGCCTGg
+>query_049%_mutation_reverse
+gcgCaacaTCcgAgaGtACctgGAAAAGaGtCTCCcGttgCgTAtcCAgACtattCCAaTtCGaCgcAtgGTtGCtgatagGCTTtTacGCCcgccaCAG
+>query_050%_mutation_reverse
+aACggcTGCTGTaAgctaTAAGctaAGggCCcAGTTTAtatAttATAGCgcTcaaTtAAaatgAgTtgActCCATtcaCAATTTagGTggTGAGcGtAag

test/query_small.fa

+>query_001%_mutation_forward
+CTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGAT
+>query_025%_mutation_forward
+CGTccGCTCGTGATGCTTGgAGGTCAtCTCgGCAAACGACTGCAGGaACGCCTGaAcGtATCGtCCCtTCAcCtcCgttAcGtTCTTGTgaCTGGTGAAt
+>query_006%_mutation_reverse
+ACGTGAAAAGGATgTAGGTGAAGATCCTTTTTGATAATCTCATaGCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCT
+>query_026%_mutation_reverse
+GtCGTgtcGAtGGggTcGGCaCAaGTCTGTGAGTGCGCCCATaGAaATAAAGTTACcGtAGtAaGGGATGgGCCAcAGtGTGCaAgCGCCCTGGTaCACC