splitmasked
splitmasked splits sequence records in FAST(A/Q) files based on their masking
status. What constitutes masking can be defined with the --maskchar option
(eg. N or lowercase). Both masked and unmasked parts can be retained and
written to separate output files.
Installation
pip install splitmaskedUsage
splitmasked \
--maskchar lowercase \
--minlength_masked 100 \
--minlength_unmasked 20 \
--outfile_masked /dev/null \
--outfile_unmasked unmasked.fastq \
input.fastqExamples
Input
@Seq1 comment1
aaaaaTTTTTTAAgatgatgatgAATGAA
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@Seq2 comment2
ATGATAGAgagagtTTTATA
+
HHHHHHHHHHHHHHHHHHHH
Output
With --maskchar lowercase:
unmasked.fastq
@Seq1_part2 comment1
TTTTTTAA
+
AAAAAAAA
@Seq1_part4 comment1
AATGAA
+
AAAAAA
@Seq2_part1 comment2
ATGATAGA
+
HHHHHHHH
@Seq2_part3 comment2
TTTATA
+
HHHHHH
masked.fastq
@Seq1_part1 comment1
aaaaa
+
AAAAA
@Seq1_part3 comment1
gatgatgatg
+
AAAAAAAAAA
@Seq2_part2 comment2
gagagt
+
HHHHHH
