In [1]:
import pysam
In [2]:
sequence = (
"AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC"
"TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA"
"TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC"
"ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG"
"CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA"
"GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC"
"AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG"
"AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT"
"GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT"
"GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC"
)
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len(sequence)
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def reverse_compliment(seq):
matches = {"A": "T", "T": "A", "G": "C", "C": "G"}
return "".join(matches[i] for i in reversed(seq))
In [5]:
with open("test_SE_plus.fastq", "w") as outfile:
for i in range(10):
outfile.write("@TEST_%d\n" % i)
outfile.write(sequence[i + 20:i + 55] + "\n")
outfile.write("+\n")
outfile.write("~" * 35 + "\n")
In [6]:
with open("test_SE_minus.fastq", "w") as outfile:
rev = reverse_compliment(sequence)
for i in range(10):
outfile.write("@TEST_%d\n" % i)
outfile.write(rev[i + 20:i + 55] + "\n")
outfile.write("+\n")
outfile.write("~" * 35 + "\n")
In [7]:
!bowtie2 "/home/pphaneuf/sequencing/NC_000913_2/NC_000913_2" test_SE_plus.fastq -S test_SE_plus.sam
!bowtie2 "/home/pphaneuf/sequencing/NC_000913_2/NC_000913_2" test_SE_minus.fastq -S test_SE_minus.sam
!bowtie2 -X 1000 "/home/pphaneuf/sequencing/NC_000913_2/NC_000913_2" -1 test_SE_plus.fastq -2 test_SE_minus.fastq -S test_PE.sam
!bowtie2 -X 1000 "/home/pphaneuf/sequencing/NC_000913_2/NC_000913_2" -2 test_SE_plus.fastq -1 test_SE_minus.fastq -S test_PE_rev.sam
In [12]:
from sequtil import makegff
In [9]:
makegff.write_samfile_to_gff("test_SE_plus.sam", "test_SE_plus.gff")
makegff.write_samfile_to_gff("test_SE_plus.sam", "test_SE_plus_5.gff", five_prime=True)
makegff.write_samfile_to_gff("test_SE_minus.sam", "test_SE_minus.gff")
makegff.write_samfile_to_gff("test_SE_minus.sam", "test_SE_minus_5.gff", five_prime=True)
makegff.write_samfile_to_gff("test_PE.sam", "test_PE.gff")
makegff.write_samfile_to_gff("test_PE.sam", "test_PE_5.gff", five_prime=True)
makegff.write_samfile_to_gff("test_PE_rev.sam", "test_PE_rev.gff")
makegff.write_samfile_to_gff("test_PE_rev.sam", "test_PE_rev_5.gff", five_prime=True)
In [10]:
!cat test_SE_plus.gff
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!cat test_SE_minus.gff
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!cat test_PE.gff
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!cat test_PE_rev.gff
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!cat test_PE_5.gff
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