Sort Sam file by chromosome and position in python
Hi, I'm trying to read a sam file and write another sam file sorted by chromosome and position.
The problem is that there are some sam files that have no alignment like
seq1 16 cr1 100 ....
seq1 16 cr2 100 ....
seq2 4 * 0 ....
So when I try to sort with this
df = pd.read_csv('file.sam', sep="\t", header=None).to_numpy()
list1 = sorted(df, key=operator.itemgetter(1, 2))
Returns this
seq2 4 * 0 ....
seq1 16 cr1 100 ....
seq1 16 cr2 100 ....
• 1,485 views
•
link
written
by
hectorbaigessanchez •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Loading the ID mapping file from Uniprot
written by MB •
-
samtools, convert BAM to CRAM
written by nrk_02 •
-
ValueError: Invalid file path or buffer object type: <class 'snakemake.io.Namedlist'>
written by Kaya_Lena •
-
Looping over a section of data and suming in python
written by elhamidihay •
-
how to fix the error - Too many open files - by changing code in python3.7
written by zhangdengwei
-
Faster processing of paired end FASTQ files
written by volatic •
-
Parsing df with pandas and some conditions
written by benjamin •
-
Mapping shorts reads using Bowtie
written by bioinfo
-
Comparing Alignments In An Iterative Process With Perl
written by loicatraile •
-
Protein Count Matrix In Perl
written by loicatraile •
Check
pysamrather than coming up with costom solutions, it is the swiss-army knife for sequencing data manipulation in python.So how would you sort the sam file by chromosome and position using pysam?
https://pysam.readthedocs.io/en/latest/api.html