Mercurial > repos > yufei-luo > s_mart
comparison commons/core/seq/test/Test_FastaUtils.py @ 18:94ab73e8a190
Uploaded
| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:20:15 -0400 |
| parents | 769e306b7933 |
| children |
comparison
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deleted
inserted
replaced
| 17:b0e8584489e6 | 18:94ab73e8a190 |
|---|---|
| 1500 | 1500 |
| 1501 os.remove(inFileName) | 1501 os.remove(inFileName) |
| 1502 os.remove(fileObs) | 1502 os.remove(fileObs) |
| 1503 os.remove(fileExp) | 1503 os.remove(fileExp) |
| 1504 | 1504 |
| 1505 def test_getNstreches_2(self): | |
| 1506 fileName = "dummy.fa" | |
| 1507 with open(fileName, "w") as f: | |
| 1508 f.write(">seq2\n") | |
| 1509 f.write("NNNNxxNNnNTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1510 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1511 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1512 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1513 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1514 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1515 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTTAGGGTTAGGGTTAGGGTTAGGGT\n") | |
| 1516 f.write("TAGGGCTAGGGTTAGGGGTTAGGGTTAGGGTTAGGCTTAGGGTTAGGGTTAGGGTTAGGG\n") | |
| 1517 f.write("\n") | |
| 1518 f.write("TTAGGGTTAGGGTTAGGGTTAGGAGTTAGGGTGTAGGGTTAGGGTTAGGGTTAGGGTTAG\n") | |
| 1519 f.write("GGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG\n") | |
| 1520 f.write("GGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGCTAGGGTTAGGGTTAG\n") | |
| 1521 f.write("GGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG\n") | |
| 1522 f.write("\n") | |
| 1523 f.write(">seq1\n") | |
| 1524 f.write("AAGTTGGACATTGAGGGCTTTCTTCGCCGTGTTTCGTTCTTTTCGACAAACAGCAGTGCT\n") | |
| 1525 f.write("TTGCGGATCATxxxxxxxxxxxxxxxTTTGTTTGAACAACCGACAATGCGACCAATTTCA\n") | |
| 1526 f.write("GCGTAGGTTTTACCTTCAGAGATCACGTTTTTAATCAAATTTCTTTTTTCGACGGTACAA\n") | |
| 1527 f.write("TGCTTTCCGCGACCCATGACTAGAGAATTTTTGGTCTTCGTTTGGAAAAAATTCAATTAA\n") | |
| 1528 f.write("AACCTTTAATACAACTCCTTNNTTTTCAAAATTTTTCGAAAAAAACCCAAAGCAATCACT\n") | |
| 1529 f.write("CCTATTAATTTTATTCAGCAAATACGTGTTCAGTGCTATTTTTGTNTACCGCCTCATTTC\n") | |
| 1530 f.write("\n") | |
| 1531 f.write("GCGCACTTTTGCAGCAAGTGCCCAAAAACAAAAAGAACCGTTACATTGAGAGACTAAAAA\n") | |
| 1532 f.write("TTTCTTGCTCAGAGAGCCAACATATGGTACTTATTATTCATGCAATCTGACTTAAAAAAA\n") | |
| 1533 f.write("TATAAACATTTAATAATTTTTTTTAGGAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n") | |
| 1534 f.write("NNATCAACTTTCCACCTGCAGTAGTGCTATTATTTTAACCGCAGCTGTATAxx\n") | |
| 1535 f.write("\n") | |
| 1536 f.write("") | |
| 1537 | |
| 1538 FastaUtils.writeNstreches(fileName, 2) | |
| 1539 obsFileName = "%s_Nstretches.map" % os.path.splitext(os.path.split(fileName)[1])[0] | |
| 1540 | |
| 1541 expFileName = "expNstretches.map" | |
| 1542 with open(expFileName, "w") as f: | |
| 1543 f.write("N_stretch\tseq1\t72\t86\n") | |
| 1544 f.write("N_stretch\tseq1\t261\t262\n") | |
| 1545 f.write("N_stretch\tseq1\t510\t542\n") | |
| 1546 f.write("N_stretch\tseq1\t592\t593\n") | |
| 1547 f.write("N_stretch\tseq2\t1\t10\n") | |
| 1548 | |
| 1549 self.assertTrue(FileUtils.are2FilesIdentical(obsFileName, expFileName)) | |
| 1550 | |
| 1551 os.remove(obsFileName) | |
| 1552 os.remove(expFileName) | |
| 1553 os.remove(fileName) | |
| 1554 | |
| 1555 def test_getNstreches_1(self): | |
| 1556 fileName = "dummy.fa" | |
| 1557 with open(fileName, "w") as f: | |
| 1558 f.write(">seq2\n") | |
| 1559 f.write("NNNNNNNNNNTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1560 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1561 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1562 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1563 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1564 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1565 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTTAGGGTTAGGGTTAGGGTTAGGGT\n") | |
| 1566 f.write("TAGGGCTAGGGTTAGGGGTTAGGGTTAGGGTTAGGCTTAGGGTTAGGGTTAGGGTTAGGG\n") | |
| 1567 f.write("TTAGGGTTAGGGTTAGGGTTAGGAGTTAGGGTGTAGGGTTAGGGTTAGGGTTAGGGTTAG\n") | |
| 1568 f.write("GGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG\n") | |
| 1569 f.write("GGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGCTAGGGTTAGGGTTAG\n") | |
| 1570 f.write("GGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG\n") | |
| 1571 f.write(">seq1\n") | |
| 1572 f.write("AAGTTGGACATTGAGGGCTTTCTTCGCCGTGTTTCGTTCTTTTCGACAAACAGCAGTGCT\n") | |
| 1573 f.write("TTGCGGATCATNNNNNNNNNNNNNNNTTTGTTTGAACAACCGACAATGCGACCAATTTCA\n") | |
| 1574 f.write("GCGTAGGTTTTACCTTCAGAGATCACGTTTTTAATCAAATTTCTTTTTTCGACGGTACAA\n") | |
| 1575 f.write("TGCTTTCCGCGACCCATGACTAGAGAATTTTTGGTCTTCGTTTGGAAAAAATTCAATTAA\n") | |
| 1576 f.write("AACCTTTAATACAACTCCTTNNTTTTCAAAATTTTTCGAAAAAAACCCAAAGCAATCACT\n") | |
| 1577 f.write("CCTATTAATTTTATTCAGCAAATACGTGTTCAGTGCTATTTTTGTNTACCGCCTCATTTC\n") | |
| 1578 f.write("GCGCACTTTTGCAGCAAGTGCCCAAAAACAAAAAGAACCGTTACATTGAGAGACTAAAAA\n") | |
| 1579 f.write("TTTCTTGCTCAGAGAGCCAACATATGGTACTTATTATTCATGCAATCTGACTTAAAAAAA\n") | |
| 1580 f.write("TATAAACATTTAATAATTTTTTTTAGGAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n") | |
| 1581 f.write("NNATCAACTTTCCACCTGCAGTAGTGCTATTATTTTAACCGCAGCTGTATAx\n") | |
| 1582 | |
| 1583 FastaUtils.writeNstreches(fileName, 1) | |
| 1584 obsFileName = "%s_Nstretches.map" % os.path.splitext(os.path.split(fileName)[1])[0] | |
| 1585 | |
| 1586 expFileName = "expNstretches.map" | |
| 1587 with open(expFileName, "w") as f: | |
| 1588 f.write("N_stretch\tseq1\t72\t86\n") | |
| 1589 f.write("N_stretch\tseq1\t261\t262\n") | |
| 1590 f.write("N_stretch\tseq1\t346\t346\n") | |
| 1591 f.write("N_stretch\tseq1\t510\t542\n") | |
| 1592 f.write("N_stretch\tseq1\t592\t592\n") | |
| 1593 f.write("N_stretch\tseq2\t1\t10\n") | |
| 1594 | |
| 1595 self.assertTrue(FileUtils.are2FilesIdentical(obsFileName, expFileName)) | |
| 1596 | |
| 1597 os.remove(obsFileName) | |
| 1598 os.remove(expFileName) | |
| 1599 os.remove(fileName) | |
| 1600 | |
| 1601 def test_getNstreches_0(self): | |
| 1602 fileName = "dummy.fa" | |
| 1603 with open(fileName, "w") as f: | |
| 1604 f.write(">seq2\n") | |
| 1605 f.write("NNNNNNNNNNTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1606 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1607 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1608 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1609 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1610 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1611 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTTAGGGTTAGGGTTAGGGTTAGGGT\n") | |
| 1612 f.write("TAGGGCTAGGGTTAGGGGTTAGGGTTAGGGTTAGGCTTAGGGTTAGGGTTAGGGTTAGGG\n") | |
| 1613 f.write("TTAGGGTTAGGGTTAGGGTTAGGAGTTAGGGTGTAGGGTTAGGGTTAGGGTTAGGGTTAG\n") | |
| 1614 f.write("GGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG\n") | |
| 1615 f.write("GGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGCTAGGGTTAGGGTTAG\n") | |
| 1616 f.write("GGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG\n") | |
| 1617 f.write(">seq1\n") | |
| 1618 f.write("AAGTTGGACATTGAGGGCTTTCTTCGCCGTGTTTCGTTCTTTTCGACAAACAGCAGTGCT\n") | |
| 1619 f.write("TTGCGGATCATNNNNNNNNNNNNNNNTTTGTTTGAACAACCGACAATGCGACCAATTTCA\n") | |
| 1620 f.write("GCGTAGGTTTTACCTTCAGAGATCACGTTTTTAATCAAATTTCTTTTTTCGACGGTACAA\n") | |
| 1621 f.write("TGCTTTCCGCGACCCATGACTAGAGAATTTTTGGTCTTCGTTTGGAAAAAATTCAATTAA\n") | |
| 1622 f.write("AACCTTTAATACAACTCCTTNNTTTTCAAAATTTTTCGAAAAAAACCCAAAGCAATCACT\n") | |
| 1623 f.write("CCTATTAATTTTATTCAGCAAATACGTGTTCAGTGCTATTTTTGTNTACCGCCTCATTTC\n") | |
| 1624 f.write("GCGCACTTTTGCAGCAAGTGCCCAAAAACAAAAAGAACCGTTACATTGAGAGACTAAAAA\n") | |
| 1625 f.write("TTTCTTGCTCAGAGAGCCAACATATGGTACTTATTATTCATGCAATCTGACTTAAAAAAA\n") | |
| 1626 f.write("TATAAACATTTAATAATTTTTTTTAGGAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n") | |
| 1627 f.write("NNATCAACTTTCCACCTGCAGTAGTGCTATTATTTTAACCGCAGCTGTATANN\n") | |
| 1628 | |
| 1629 FastaUtils.writeNstreches(fileName, 0) | |
| 1630 obsFileName = "%s_Nstretches.map" % os.path.splitext(os.path.split(fileName)[1])[0] | |
| 1631 | |
| 1632 expFileName = "expNstretches.map" | |
| 1633 with open(expFileName, "w") as f: | |
| 1634 pass | |
| 1635 | |
| 1636 self.assertTrue(FileUtils.are2FilesIdentical(obsFileName, expFileName)) | |
| 1637 | |
| 1638 os.remove(obsFileName) | |
| 1639 os.remove(expFileName) | |
| 1640 os.remove(fileName) | |
| 1641 | |
| 1642 def test_getNstreches_2_GFF(self): | |
| 1643 fileName = "dummy.fa" | |
| 1644 with open(fileName, "w") as f: | |
| 1645 f.write(">seq2\n") | |
| 1646 f.write("NNNNxxNNnNTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1647 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1648 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1649 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1650 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1651 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT\n") | |
| 1652 f.write("AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTTAGGGTTAGGGTTAGGGTTAGGGT\n") | |
| 1653 f.write("TAGGGCTAGGGTTAGGGGTTAGGGTTAGGGTTAGGCTTAGGGTTAGGGTTAGGGTTAGGG\n") | |
| 1654 f.write("\n") | |
| 1655 f.write("TTAGGGTTAGGGTTAGGGTTAGGAGTTAGGGTGTAGGGTTAGGGTTAGGGTTAGGGTTAG\n") | |
| 1656 f.write("GGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG\n") | |
| 1657 f.write("GGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGCTAGGGTTAGGGTTAG\n") | |
| 1658 f.write("GGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG\n") | |
| 1659 f.write("\n") | |
| 1660 f.write(">seq1\n") | |
| 1661 f.write("AAGTTGGACATTGAGGGCTTTCTTCGCCGTGTTTCGTTCTTTTCGACAAACAGCAGTGCT\n") | |
| 1662 f.write("TTGCGGATCATxxxxxxxxxxxxxxxTTTGTTTGAACAACCGACAATGCGACCAATTTCA\n") | |
| 1663 f.write("GCGTAGGTTTTACCTTCAGAGATCACGTTTTTAATCAAATTTCTTTTTTCGACGGTACAA\n") | |
| 1664 f.write("TGCTTTCCGCGACCCATGACTAGAGAATTTTTGGTCTTCGTTTGGAAAAAATTCAATTAA\n") | |
| 1665 f.write("AACCTTTAATACAACTCCTTNNTTTTCAAAATTTTTCGAAAAAAACCCAAAGCAATCACT\n") | |
| 1666 f.write("CCTATTAATTTTATTCAGCAAATACGTGTTCAGTGCTATTTTTGTNTACCGCCTCATTTC\n") | |
| 1667 f.write("\n") | |
| 1668 f.write("GCGCACTTTTGCAGCAAGTGCCCAAAAACAAAAAGAACCGTTACATTGAGAGACTAAAAA\n") | |
| 1669 f.write("TTTCTTGCTCAGAGAGCCAACATATGGTACTTATTATTCATGCAATCTGACTTAAAAAAA\n") | |
| 1670 f.write("TATAAACATTTAATAATTTTTTTTAGGAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n") | |
| 1671 f.write("NNATCAACTTTCCACCTGCAGTAGTGCTATTATTTTAACCGCAGCTGTATAxx\n") | |
| 1672 f.write("\n") | |
| 1673 f.write("") | |
| 1674 | |
| 1675 FastaUtils.writeNstreches(fileName, 2, outFormat = "gff") | |
| 1676 obsFileName = "%s_Nstretches.gff3" % os.path.splitext(os.path.split(fileName)[1])[0] | |
| 1677 | |
| 1678 expFileName = "expNstretches.gff3" | |
| 1679 with open(expFileName, "w") as f: | |
| 1680 f.write("##gff-version 3\n") | |
| 1681 f.write("seq1\tFastaUtils\tN_stretch\t72\t86\t.\t.\t.\tName=N_stretch_72-86\n") | |
| 1682 f.write("seq1\tFastaUtils\tN_stretch\t261\t262\t.\t.\t.\tName=N_stretch_261-262\n") | |
| 1683 f.write("seq1\tFastaUtils\tN_stretch\t510\t542\t.\t.\t.\tName=N_stretch_510-542\n") | |
| 1684 f.write("seq1\tFastaUtils\tN_stretch\t592\t593\t.\t.\t.\tName=N_stretch_592-593\n") | |
| 1685 f.write("seq2\tFastaUtils\tN_stretch\t1\t10\t.\t.\t.\tName=N_stretch_1-10\n") | |
| 1686 | |
| 1687 self.assertTrue(FileUtils.are2FilesIdentical(obsFileName, expFileName)) | |
| 1688 | |
| 1689 os.remove(obsFileName) | |
| 1690 os.remove(expFileName) | |
| 1691 os.remove(fileName) | |
| 1692 | |
| 1505 if __name__ == "__main__": | 1693 if __name__ == "__main__": |
| 1506 unittest.main() | 1694 unittest.main() |