Skip to content

Instantly share code, notes, and snippets.

Srividya Ramakrishnan srividya22

Block or report user

Report or block srividya22

Hide content and notifications from this user.

Learn more about blocking users

Contact Support about this user’s behavior.

Learn more about reporting abuse

Report abuse
View GitHub Profile
View Find_one_liners.txt
Identify a directory which does not contain a particular file
find base_dir -mindepth 2 -maxdepth 2 -type d '!' -exec test -e "{}/cover.jpg" ';' -print
@srividya22
srividya22 / README.md
Created May 29, 2018 — forked from jdblischak/README.md
snakemake_vmem_usage
View README.md

Testing Snakemake virtual memory usage

John Blischak 2014-05-14

Multiple users have observed that submitting jobs via Snakemake requires much more memory than is necessary to run the command (e.g. mailing list post, [Bitbucket issue][issue]).

@srividya22
srividya22 / README.md
Created May 29, 2018 — forked from jdblischak/README.md
snakemake_vmem_usage
View README.md

Testing Snakemake virtual memory usage

John Blischak 2014-05-14

Multiple users have observed that submitting jobs via Snakemake requires much more memory than is necessary to run the command (e.g. mailing list post, [Bitbucket issue][issue]).

View Advanced bedtools usage
Links:
http://quinlanlab.org/tutorials/bedtools/bedtools.html
Use Case 1: Given a.bam and b.regions.bed. how to get the parts of b.regions.bed that are not covered by a.bam?
Answer:
bedtools genomecov -ibam aln.bam -bga \
| awk '$4==0' |
| bedtools intersect -a regions -b - > foo
Option -bga Report depth in BedGraph format, as above (i.e., -bg). However with this option, regions with zero coverage are also reported. This allows one to quickly extract all regions of a genome with 0 coverage by applying: “grep -w 0$” to the output.
@srividya22
srividya22 / get_gap_postions.py
Last active Jan 25, 2018
Get gap positions in a fasta file
View get_gap_postions.py
#!/usr/bin/env python
# Script to identify gaps regions in an assembly
# input : fasta
# output : bed
# usage : get_gap_postions.py fasta bed
# Import necessary packages
import argparse
import re
from Bio import SeqIO
@srividya22
srividya22 / xargs.sh
Created Jan 5, 2018
xargs cheatsheet
View xargs.sh
# turn a find or cut (cut delimiter, get first column) output into a list
/etc find . -name "*bash*" | xargs
cut -d, -f1 file.csv | xargs
# find a file and grep for a word in the file
find . -name "*.java" | xargs grep "Stock"
# handeling filenames which have WHITESPACE
ls *txt | xargs -d '\n' grep "cost"
@srividya22
srividya22 / xargs.sh
Created Jan 5, 2018
xargs cheatsheet
View xargs.sh
# turn a find or cut (cut delimiter, get first column) output into a list
/etc find . -name "*bash*" | xargs
cut -d, -f1 file.csv | xargs
# find a file and grep for a word in the file
find . -name "*.java" | xargs grep "Stock"
# handeling filenames which have WHITESPACE
ls *txt | xargs -d '\n' grep "cost"
@srividya22
srividya22 / maker_genome_annotation.md
Created Sep 8, 2017 — forked from darencard/maker_genome_annotation.md
In-depth description of running MAKER for genome annotation.
View maker_genome_annotation.md

Genome Annotation using MAKER

MAKER is a great tool for annotating a reference genome using empirical and ab initio gene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.

Software & Data

Software prerequisites:

  1. RepeatModeler and RepeatMasker with all dependencies (I used NCBI BLAST) and RepBase (version used was 20150807).
  2. MAKER MPI version 2.31.8 (though any other version 2 releases should be okay).
  3. [Augustus](http://bio
@srividya22
srividya22 / maker_genome_annotation.md
Created Sep 8, 2017 — forked from darencard/maker_genome_annotation.md
In-depth description of running MAKER for genome annotation.
View maker_genome_annotation.md

Genome Annotation using MAKER

MAKER is a great tool for annotating a reference genome using empirical and ab initio gene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.

Software & Data

Software prerequisites:

  1. RepeatModeler and RepeatMasker with all dependencies (I used NCBI BLAST) and RepBase (version used was 20150807).
  2. MAKER MPI version 2.31.8 (though any other version 2 releases should be okay).
  3. [Augustus](http://bio
@srividya22
srividya22 / rename_genes_in_maker_gff.pl
Created Aug 24, 2017 — forked from avrilcoghlan/rename_genes_in_maker_gff.pl
Perl script that renames genes in the maker gff files so that they have unique names.
View rename_genes_in_maker_gff.pl
#!/usr/bin/env perl
=head1 NAME
rename_genes_in_maker_gff.pl
=head1 SYNOPSIS
rename_genes_in_maker_gff.pl input_gff output_gff outputdir species
where input_gff is the input gff file,
You can’t perform that action at this time.