faster tests

.travis.yml

@@ -109,7 +109,7 @@ install:
 # command to run tests
 script:
   - ls
-  - travis_wait 40 coverage run -m pytest tests/
+  - travis_wait 60 coverage run -m pytest tests/
   #- coverage run -m pytest tests/
   - coverage report --show-missing  
 after_success:

tests/test_files/athaliana/genome/Arabidopsis_thaliana.TAIR10.cdna.5.fa

@@ -0,0 +1,175 @@
+>AT1G19090.1 cdna chromosome:TAIR10:1:6589835:6592762:1 gene:AT1G19090 gene_biotype:nontranslating_CDS transcript_biotype:nontranslating_CDS gene_symbol:RKF2 description:receptor-like serine/threonine kinase 2 [Source:TAIR;Acc:AT1G19090]
+GAAAAAGGAAGCGGGAGAGGGGAGCCCAGTACTTGAGGACAGGAGAAGGATTGATTGTAC
+ATAAATCTCTTTCTTTTTTGATTGCCTACAAAATCGGCTTCGGGACTAAAATTAGAACTC
+CATTGGAGAATGAGTTAGTCAAAAAAAAATTCCCTAAATTAAGACAAATGCAAGCACAAG
+AGAAGCAAAATCTCTCTGTCTCTTCTCTGAATTCAAAACAAAGGTTTTTCAATCTGTCAA
+AGCTCACAATGAACCGAAATTACAGAGAGATTGACTCGTCTTCTTCGATTTTTCTTATCT
+CCTTTTACGACAAAGTACCTAATCCACCTTCTCCACCCACTCGCCGTTGTGGAGAGGGAG
+AGACACCCGGCGGAGTTGGAGTGGGTGGAGGAAGAAGAAGAAGACGAGAGCAGAAACAGA
+GGATTCATCGATGTTATACTCTATCAAAAATTGCAGATTTGCATATGGAAAGACTTCTTC
+TTCACGATTCATGATCACACGTCGTCCGATTTCTGATGCAAATTTGTGCTTCGATCGCTC
+AATTCCTCGCTTGGGTTTCATTCCTTGTACTATTAGCGACGGTGGGCTCTTCTTCTTCTT
+CGGAATCTCTCCTAAATTGTCAACCTTTAGATCACCACCTTGTAAACCCTAGTCGTCTGC
+TTGGTTTCCTCAGAGCAATGTCTTCCGTCAATGATTTCATAACCAACGACAAGCTTTGGG
+TCGTTTCTTCCATCACCGATGTATCTCCACCTATCTATGTGTTTCTACAGTGCAGAGAAG
+ATCTCTCTGTTTCCGATTGTCGACATTGCTTCAACGAGAGCAGATTGGAGCTCGAGAGAA
+AATGTTCGGGTTCCGGTGGTCGAATCCATAGTGATAGATGCTTCTTACGGTTTGATGATC
+GAGATTTCTCTGAGGAATTTGTTGATCCTACATTTGATAAAGCTAACTGTGAGGAAACAG
+GGACAGGGTTTGGAGAATTTTGGAGATTTCTTGATGAGGCTTTGGTGAATGTAACTTTAA
+AGGCTGTTAAAAATGGAGGGTTTGGTGCAGCTTCAGTGATTAAAACCGAGGCCGTGTATG
+CATTGGCTCAGTGTTGGCAAACACTTGATGAGAACACGTGTCGAGAGTGTTTGGTTAATG
+CTAGATCGAGCTTGAGAGCTTGTGATGGACATGAAGCTAGAGCTTTTTTTACTGGGTGTT
+ACTTGAAGTATTCTACACACAAGTTCTTTGATGATGCTGCAGAACATAAACCTGACGCTG
+ATCAGAGAAACTTTATAAGGTCATCGTTTTTTCCACATTTGAGTGATCGTGATGTTACGA
+GATTAGCAATTGCTGCGATTTCGTTGTCGATTCTTACTTCTCTTGGAGCCTTTATCAGTT
+ACAGACGGGTTTCAAGGAAAAGAAAAGCTCAAGTTCCATCGTGTGTAAATTTCAAATACG
+AGATGCTTGAGAAAGCGACCGAGTCTTTCCATGACTCTATGAAACTAGGCCAAGGAGGGG
+CCGGTTCTGTATACAAAGGGATTCTTCCAGTGGCAGAATCGTTGCAGTCAAAAAGCTCTT
+CTTTAACACACGTGAATGGGCAGATCAATTCTTCAACGAAGTGAATCTGATCAGCGGAGT
+TCAACACAAGAACCTTGTGAGACTACTTGGTTGCAGCATTGAAGGTCCCAAAAGTCTTCT
+TGTCTATGAATATGTTCATAACAGAAGCCTTGATCAAATCCTTTTCATGAAGAACACAGT
+CCATATTTTGAGCTGGAAGCAACGGTTTAACATCATTATAGGAATATCAGAAGGTCTAGA
+ATACCTTCACAGAGGATCTGAAGTAAAAATCATCCATAGAGACATCAAAACCAGCAATAT
+TCTCCTTGATCGAAACCTAAGTCCCAAAATAGCTGATTTTGGACTCATACGTTCCATGGG
+CACTGACAAAACGCAAACCAATACTGGAATTGCTGGAACACTTGGTTATCTGGCTCCTGA
+ATATCTGATCAAAGGCCAATTAACAGAGAAAGCTGACGTTTACGCATTTGGAGTTCTTAT
+CATCGAGATAGTAACTGGCAAGAAAAATAACGCATTCACGCAAGGAACTAGCTCGGTTTT
+ATACTCTGTATGGGAACATTTTAAAGCAAACACTTTAGATCGCTCTATCGATCCTCGGTT
+GAAAGGGAGTTTCGTAGAGGAAGAGGCCTTGAAGGTTCTTCAAATCGGATTGTTGTGTGT
+TCAATCTTCTGTAGAGTTGAGACCGTCAATGTCTGAGATAGTCTTCATGTTACAGAACAA
+AGATAGTAAATTTGAATATCCGAAACAGCCTCCGTTCTTGAGTGCCAGTGTTCTAATGCC
+AGATGAGGAGACTAGAGTCTGATATTATCAGTTTCTTAGGATTGTTAATGTTCTTCTGTA
+AATGCTCAAAAATGGATTTTACACCATTTCTTTCTCCTTTTCAAATCTTTTATCGTTCAT
+ATTTTATTATGAAGGTCAACAAAAATGGAACCAAGGCTAGATTCTAAAA
+>AT1G18320.1 cdna chromosome:TAIR10:1:6304360:6305689:1 gene:AT1G18320 gene_biotype:nontranslating_CDS transcript_biotype:nontranslating_CDS description:Mitochondrial import inner membrane translocase subunit Tim17/Tim22/Tim23 family protein [Source:TAIR;Acc:AT1G18320]
+CTACTCTCTTAACCTTTGAAATGGCTGATTCGAGTGCTGCTGAAACAACAACCGGTGCTT
+CTTCTCCCCCCGCGGCTTCTGATGAGAACTCTACCAGATTCAACCGATCCGGATGCCAAC
+CATCGAGGAGATCCGAGCTCAAGAGGTTTGGAACAACTGCGCCGTTCGTGCTGTAACTAG
+TGGAGTCATGGGAGGAGGACTCGGGTTGATGATGGGTTTGTTCCTGGGGGCATTAGATAA
+TCCTATTACGCATGATACTATGACGGCTAGGTAGCAGTTTGTGTTCACGGCAAAACAAAT
+GGGGCAAAGGAGTTGGAATTCCTGTAAGACATTTGCAGTTATGGGTTTGGTTTTCTCTGC
+TGCAGAATGCATTGTCGAAAAGGCAAGAGCTAAGCATGACACTGTAAACACCGCTATAGC
+TGGATGTGTTACCGGTGGTTCAATGTCCGCCCGAGGTGGGCCAAAAGCTGCGTGTATAGG
+TTGCGCTGGATTTGCAATTTTCTCTGTACTCATAGAGAAGTTCTTTGATAGGCATACATA
+AACCAGTGAGATATCTAACAGACGCCATTGCTGAGATTTTTTTGCTGCTTCTTTTCTGTG
+ATAGTGATACAGTTCATCACCTGAACCCAGGGAGATAGAAGCTAGAATTACACTTTTCAA
+TATAGAATAAGCAAGGCTTGTGTTGATTGCATATACTTC
+>AT5G11100.1 cdna chromosome:TAIR10:5:3532402:3535221:1 gene:AT5G11100 gene_biotype:nontranslating_CDS transcript_biotype:nontranslating_CDS gene_symbol:SYTD description:Calcium-dependent lipid-binding (CaLB domain) family protein [Source:TAIR;Acc:AT5G11100]
+ATGGGTTTTCTCTTTGGTTTGTTCATAGGAATCGCGGTTTCTTTCGGTTTGGTCGTCGCA
+TTTGCTCGCTACTCTAGTGTCAGATCCACTCGTCGAGCTGATTTGGCAAAGACCATTGCT
+GCATTTGCAAGAATGACAGTTCAAGATTCGAGAAAACTTCTCCCGGGAGATTTTTATCCT
+TCTTGGGTTGTGTTTTCTCAGAGACAAAATTAAATTGGCTTAATCTTGAACTTGAAAAGA
+TCTGGCCTTATGTAAATGAGGCAGCTTCTGAGCTGATTAAAAGCAGTGTGGAACCAGTAC
+TTGAACAGTATACACCAGCTATGTTAGCATCTCTCAAGTTCTCTAAATTCACACTTGGGA
+CTGTGGCTCCTCAGTTCACAGGAGTTTCTATCTTAGAAAGTGAAAGTGGACCTAATGGAA
+TCACAATGGAACTTGAAATGCAATGGGATGGTAATCCAAAAATCGTGTTGGATGTCAAAA
+CCTTACTTGGCGTGTCTCTACCTATTGAGGTCAAAAACATAGGATTCACAGGTGTTTTCA
+GGCTGATTTTCAAACCTCTTGTTGATGAATTCCCTTGCTTTGGGGCACTTTCTTATTCAC
+TCCGCGAGAAGAAAGGGCTTGATTTTACCCTCAAAGTTATAGGTGGTGAATTAACATCAA
+TTCCAGGGATTTCAGATGCAATCGAAGAAACTATTCGTGACGCCATTGAAGACAGTATAA
+CATGGCCAGTTAGGAAAATTATACCTATTTTACCAGGAGATTACAGTGATCTGGAGTTGA
+AACCTGTTGGAAAATTGGATGTGAAGGTTGTGCAAGCAAAGGACTTAGCTAACAAAGACA
+TGATTGGAAAATCTGATCCTTACGCTATTGTATTCATTCGCCCTTTGCCTGACAGAACCA
+AAAAGACCAAAACTATTAGTAACTCGTTGAATCCGATTTGGAATGAACATTTTGAGTTCA
+TTGTGGAAGATGTCTCAACTCAACATTTGACAGTAAGAGTCTTTGACGACGAAGGAGTTG
+GATCTTCTCAGCTTATTGGGGCTGCTCAAGTACCGTTAAATGAACTCGTACCCGGGAAAG
+TTAAAGATATTTGGTTGAAGTTAGTCAAGGATTTAGAGATCCAAAGGGATACAAAAAATA
+GGGGTCAGGTGCAGTTGGAGCTCTTATATTGTCCCTTAGGCAAAGAAGGCGGATTGAAGA
+ACCCGTTTAACCCGGACTACTCATTGACCATTTTAGAGAAGGTACTGAAGCCGGAAAGCG
+AGGATTCGGATGCCACGGATATGAAAAAACTGGTGACCTCGAAGAAAAAAGATGTGATAG
+TGAGAGGAGTGTTGTCTGTGACAGTGGTGGCAGCTGAAGACTTACCAGCTGTAGATTTTA
+TGGGAAAAGCAGATGCATTTGTGGTAATCACATTGAAGAAATCAGAAACGAAATCCAAGA
+CAAGGGTAGTACCGGATAGCTTGAATCCGGTTTGGAACCAGACGTTTGATTTTGTAGTGG
+AAGATGCTTTGCATGATCTATTGACGCTTGAAGTATGGGACCATGACAAATTTGGCAAGG
+ACAAGATAGGGAGAGTGATAATGACATTGACGCGAGTGATGTTAGAAGGAGAGTTTCAAG
+AGTGGTTTGAGTTAGATGGAGCTAAATCAGGGAAGCTTTGTGTCCATCTTAAATGGACTC
+CTAGGCTTAAGCTCAGAGACGCCTCTTGA
+>AT4G35335.1 cdna chromosome:TAIR10:4:16807265:16810216:1 gene:AT4G35335 gene_biotype:nontranslating_CDS transcript_biotype:nontranslating_CDS description:Nucleotide-sugar transporter family protein [Source:TAIR;Acc:AT4G35335]
+GAGATCTGAGAGCTTGAAACAATGGAGTACCGGAAAATCAAAGATGAGGACGATCATGAC
+GTTGCTTCTGATATCGAGAGTGTGAAAGGAAAATCTCATACCGTTGCTTCGAGTAACATT
+GCAATGGCTACTCTGGGTGTTGGATCCAGTGAACGGATCAACTGGAAACGAAAGGGTGTA
+GTAACATGTGCACTGACGATTCTGACGAGTTCTCAAGCGATACTTATCGTGTGGTCGAAA
+CGAGCTGGGAAGTATGAGTATAGTGTTACAACCGCCAACTTTTTGGTTGAACTCTGAAAT
+GTGCGTTATCTCTTCTTGCTTTGACAAGGATATGGAAAAATGAAGGTGTTACTGACGACA
+ACAGGTTAAGCACAACATTTGATGAAGTTAAAGTCTTTCCAATTCCCGCAGCATTGTATC
+TTTTTAAGAATTTGTTACAGTATTATATTTTTGCATATGTAGACGCCCCAGGCTATCAGA
+TATTGAAGAACTTGAACATCATAAGTACCGGTGTCTTGTACAGAATTATACTGAAGAGAA
+AATTGAGCGAGATTCAGTGGGCGGGTTTCATTCTATTGTGTTGCGGATGCACCACTGCTC
+AGTTGAATTCAAATTCTGATCGTGTTCTTCAGACATCTCTTCCTGGCTGGACTATGGCAA
+TTGTCATGGCTCTTTTAAGTGGTTTCGCCGGAGTGTACACAGAGGCCATTATTAAAAAGC
+GACCTTCAAGGAATATAAATGTACAGAACTTCTGGCTATATGTCTTTGGGATGGCTTTCA
+ATGCTGTTGCTATAGTGATCCAAGATTTTGATGCCGTTGCAAATAAGGGATTCTTCCATG
+GTTACTCCTTCATCACATTACTCATGATTCTTAACCATGCTCTCAGTGGCATTGCTGTGT
+CGATGGTGATGAAATATGCAGACAATATCGTGAAGGTTTATTCGACATCAGTGGCGATGC
+TTCTCACCGCAGTTGTCTCTGTATTCCTCTTCAATTTTCATCTTTCCTTAGCCTTCTTCT
+TGGGTTCAACGGTCGTCTCTGTTTCAGTATATTTACATTCCGCAGGGAAGCTACGATAGT
+AAAGATCTTCACACTTACATCTACCAAGAAAACACCATTATTCTAGTACAGAGATAAAGC
+TTTTGAACGATTACGATTTTGTTTTTCGTGTAGGTATATTCACATTTGTGCTTCTGTATT
+GATTTTTTTTTCCGTCTCATGAAACCTTCTATTCTCATTTGTACGATACCAAAACTTATC
+AAGAATAGTTACAATTTCAG
+>AT1G60930.1 cdna chromosome:TAIR10:1:22430847:22438877:-1 gene:AT1G60930 gene_biotype:nontranslating_CDS transcript_biotype:nontranslating_CDS gene_symbol:RECQL4B description:RECQ helicase L4B [Source:TAIR;Acc:AT1G60930]
+GAGGGAGAGAGAGAGTGAACCTTTTTAACTATCCCGCCATACGAAAATCGCAGAAAGCTG
+TAATTGGAGACGCGCTCTTTCTTCTCTCTCGCCTCGTGATCTTACCGGAAAAGTTTCGTC
+GCCGGAGTTTCACTATTTCGCCGCAGAAGCACTAGAGTTTCATCTGTTTGAAAATTAAAT
+GGTGGTGACAAGAGGAGATAAATTTGCTGGAAGCTCTTTGGCATGTAAATCTATGATCGG
+TGCTAATAAAATGAGTGGGAGTCATCTCCATGAAGTTAATAATTCCAGAAGTCACTTTCC
+TCAAACAAATTGGTTGAAAGTTGCCAAGGCGTTTGAGTGTATACCATCCTTAAATAAGTT
+TATGGGCTCCAATTTCCTTTACTCTCTAGAAAGTCAAAAGCTGGGAAGAGATAGAGAAAT
+GGCTGCAAGGTCAATTGAAAACATCGCTCCTGTAACTGTACAAACTTTGGCACGACCACA
+AATTGAGAAGGCTTGGTGTACTCTTATAAATCTATCAATAAATAATACCTACCTGAGACC
+TGGCATTACTCCTGCAATTGATAATGACAGCACTAGTCGTACATCTTCTACGAAAGGATC
+CACTTTTAAAGTTACATCCAATGCTGATGGATCTTTCTGCGCACACAATCATCCAGAGCA
+TAGTCAAAGGAGTGTAAGAGGCACTGCAAAATCAATTGACAGTTTCTCCTCCTCTTCCGT
+AGGTGATAATAAAATAATTATTGACAAGGTTCCACGGGTCAACTATGAGGTTAGAGATTC
+AGTAACTGTTACAAATGGTATGGAGATGCCACCAATCAAAAATTCTGCACAACTAGCCAG
+ACCGGTGGAGCCTAGGGAAGTTAGTCTTGGTGAGATTGATTATGATGACATAATGGAGAT
+TATTGACGTAGACCAGATTGCGATGGAACACTGCCCTTCAACGTGTACGAAGCAACCATC
+AGTATCTAAGTTTGTGGATATATTTACTTCCAGAAGAGAAGAAGAGCAAGGTTTGCCTCC
+TGAAATATGTTCCAACTGTAGTCATGGAATAAAGCTAGGGCTTTGTCCTGAAGCTTCTAC
+CCATGTGGAACAAATGAAGGATACGCTGCTTGCAATATCAAATGAAATCCTCGACAATAC
+TTATGACCTGGGCCCTGATCATGTTGAACAGCTTCATCAAAAGAGATTACTGTTGAAAAA
+GCAAATCCAGCAGCTCGAGATCCTTATCCATAATAAAGAAAGGAAAAAATCTCAGTGTTT
+GGTATCTATACCTTCTCATAATACTCAGTATGAAACACCTCAAACAACAAATCTTGAGGT
+GGTTTATGGGCAGACAGATTCTCCAACTCATGTAAAAGAGCAAGGCAGATGTGTAACTGA
+TAACTGGAATATGCCAAGAGACTATTTAGTTTCTAAAGAGAGGTATGATATTTCATCTGG
+TTCTGAAGAGAGGGAACAATCTGTTTCCGAGGTTATAGATGTCACTGATACCGAGAGTTC
+AAATGACAAAAAGTGGACCAGTAGTGATTTTCCTTGGACGAAAAATCTGGAGGTCTATAA
+CAAATTAGTGTTTGGAAACCACTCATTTCGACCCAACCAAAGAGAGATCATTAATGCTAC
+AATGAGTGGTTGTGATGTTTTTGTTTTGATGCCAACCGGAGGGGGGAAAAGCTTAACATA
+TCGCTCCCTGCTCTACTCTGTGCAGGAATAACATTAGTCATTTCTCCACTTGTTTCACTC
+ATTCAAGACCAGATAATGAACTTATTGCAGACCAATATATCTGCTGCTTCCTTAAGTGCC
+GGAATGGAATGGGCTGAACAACTAGAGATACTTCAGGAGCTGAGCTCTGAGAAGTCTAAA
+TACAAGTTACTGTATGTAACACCAGAAAAAGTGGCAAAAAGTGAATCCCTTTTAAGGCAC
+CTCGAAATCTTAAACTCCCGTAGTTTGCTTGCTCGATTTGTTATTGATGAAGCTCATTGT
+GTGAGTCAGTGGGGGCATGACTTTCGACCTGACTACCAGGGTCTTGGTGTTCTGAAGCAG
+AAGTTTCCAAACATTCCCATGTTAGCTTTGACAGCTACTGCAACAACCAGCGTGAAAGAA
+GATGTTGTACAAGCTCTCGGGCTGGTAAACTGTGTTGTTTTCCGGCAAAGTTTTAATCGC
+CCTAATCTATGGTATTCTGTTGTTCCCAAGACAAATAAGTGTTTGGAAGATATTGACAAG
+TTTATCCGGGAAAACCATTTTGATGAATGTGGCATCATTTATTGTCTTTCAAGAATGGAC
+TGCGAAAAAGTCACGGAAGCATTGCGGGTGTTTGGCCATAAAGCGGCCTTCTACCATGGC
+AGTATGGATCCTGGTAAACGTGCCTTTGTACAGAAACAATGGAGCAAGGATGAAATCAAT
+ATAATATGTGCTACAGTGGCATTTGGAATGGGAATCAATAAGCCTGATGTTCGTTTTGTA
+ATTCATCATTCTCTACCAAAGTCCATAGAAGGCTATCATCAGGAATGTGGTCGTGCTGGT
+AGAGACGGCCAGAGGTCATCATGTGTTTTGTATTACAGTTACACTGATTATATTCGAGTG
+AAGCATATGATTAGCCAAGGAGGACTTGGCCAAGGCCAGATGAAAATGGGATATAATTGC
+AAAGCAAGTTCAGGGAGGATGCTCGAAACGAACACGGAAAACCTTCTCCGCATGGTTAGT
+TACTGTGAAAATGAGGTGGATTGTCGACGTTTCTTACAGCTAGTTCATTTGGGAGAAAAA
+TTTGATTCGACAAACTGCAAAAACACATGTGATAATTGTTCCAGCAGCAAAATTTTGATT
+GACAAAGATGTAACTGTGATTGCAAGGCAACTGGTGGCACTGGTTAAGCTAACAGGAGAA
+AGATTTTCGTCAGCTCATATTGTAGAAATCTACAGGGGATCCTTAAACCAGTCGGTCAAG
+AGAAACAGACAAGACACTTTGCACCTCCACGGAGCAGGAAAGCATTTAACTAAAAGTGAA
+GCCTCTCGTATTTTGCACTACCTTGTGACAGAGGATATTCTCGCAGAGGGTGTTAAAAAA
+AGTGAACTGTATGGATCTGTATCGTCATTGCTGAAGGTGAACAGATCAAAGGCCGCCTCG
+CTCTTATCTGGAGGCCAGAGTATAACAATGAGATTTCCTTCGACCATAAAAGTGTCAAAG
+CAGAGCAAATCCACAGCAAATCCAGCAAAAGTTCCACTTAAGCAAACTACCCTTCCAATG
+GCAAAAGCTGCCCCACAAGATTCGAATCTCTCCGGCATTTTGTTGACAGCCTTGAAAAAT
+CTTCGGACTGATATTGTCAAAGAATCGCCAGATTTAGTCATGGCATATCATATATTCGGC
+AATGCGACGCTTAAAGAGATAAGTAAACGACTTCCCAGAACCAAAGAGGAACTCCTTGAT
+ATCAATGGTCTAGGAAAAGCCAAGGTGAGCAAATACGGAGATCGGTTATTGGAAACCATA
+GATTCAACCATCAACGACCACTACAAAACCCGTCCCGGTTCAGGGAAGAGGAGAAGAGAC
+GAGAACGTTAATCCGAATGTAGCAGAAGATGATGATCCCGATTGGAGTGCGAGTCAGTCT
+CACAAAAAGGTAGTGAAGAACAAAAAATAACACGTTCATAAACTTTAAAGGACCCAAACA
+AACTAAAAAATTAAGAAGCTATAGAAATCATTTACATTTGCAAAAATAGTAATTCAATAC
+CATCTGTCAAGCAACATATTTGCCCATACCGGGGTGTGATTTAGGGTTAGGTTAAATAAA
+CCTTTACACCTAATCCACCATGTCCCATGAACTATTGTTAATATGTCATATTCTGCAACT
+ATTTATATACTCATGCAATTCAAATCATCCTTTCGG